Wednesday, July 28, 2021

Answer: How are these connected? (Islands, vertebrae, flowers)

 It's true... 

... I really was looking at a sunflower when I had this insight--the deep connections between the sunflower, the skeleton of a snake, and the Hawaiian archipelago.  

My initial thought process was roughly this:  "I wonder how the seeds in a sunflower form... what's the process that leads a single flower to grow from a single cell into a whole pile of seeds in the flower's disk?" 

I realized that I didn't know.  Naively, I just sort of assumed that they all grew in parallel, all at the same moment.  

When I did my search for the actual mechanism and found out, that's when I realized the invisible story that links island formation to the development of snake vertebrae and links that to the growth of a sunflower.  

Reminder: Challenge from last week: 

What's connects the archipelago of Hawai'i with the vertebrae of a snake?  What then connects that to the flowers in a sunflower?  Can you think of what these three very different things might share in common?  (And no, it's not "they're made of atoms..." or something similar. It's actually an interesting commonality.)  

If you're impatient, the common element between them is this:  

All three (Hawaiian island, snake vertebrae, sunflower seeds) are all created by a single point source that generates one thing (island, bone, seed) and then moves a bit to make another.. and another... and another... repeating the generation + move cycle.  It's a spatial-temporal process that creates such structures in the world.  

Now, how could you find this commonality?  

In the original post I gave a big hint.  To wit, "think about the processes involved in how they came to be."  That is, what's the origin story for each of these things?  

So I'd start with the simple case: How did Hawaii come to be? 

     [ Hawaii come to be ] 

You'll quickly discover that a “hot spot” in the Pacific plate is responsible for creating the islands.  How?  The Pacific plate moves over a stationary hot spot (a thin spot in the Earth's mantle where magma can emerge to the surface).  As the plate moves, it keeps creates the islands; that's why there's a long chain of Hawaiian islands, with the oldest (and most eroded) islands in the northwest.  See the long line in this map? 

P/C National Park Service. Oceanic Hotspots

You might notice Loihi--that's not an island you know about.  It's the newest island and is still being formed underwater.  It will probably emerge above the water in 10-100K years.  

It's worth noting that there are other hotspots--the most obvious one is the Samoa hotspot that created those islands.  

P/C NOAA. What is a volcanic hotspot?

Now we can do the same query, except with snake vertebrae:  

     [ how did snake backbones come to be ]  

This leads to several articles including this one about How snakes evolved.  From that article, I learned that HOX genes regulate backbone creation.  This query also got me to an article about how snake vertebrae are created embryologically (that is, when the snake is still in the egg).  In How the Snake Got Its Vertebrae, I learned that HOX genes switch on/off the creation of each vertebrae.  (Really? That sounds a bit like the volcanic island creation.) 

From that article:  

During development, vertebrate embryos grow from head to tail. As the body elongates, vertebral precursors known as somites, or segments, emerge from a group of immature cells called the presomitic mesoderm (PSM). These segments develop at regular intervals, much as a plant's stem forms branches at regular intervals as it grows.

“The way the body of a human or mouse or any vertebrate forms is from a growth zone - like the tip of a shoot - which is called the tail bud. First you produce the head, then the neck, then the thorax, and so on, until the tail,” said Pourquié. The long chain of vertebrae that defines a snake's body takes shape in about 23 days.

The regular emergence of segments from the PSM is driven by a cell signaling system known as a “clock and wavefront.” The clock is a simple set of signaling molecules that accumulate and disappear in rhythmic oscillations. Each time the clock molecules peak, a new vertebral segment is created.

Left to their own devices, the oscillating proteins would stay in one place, and create vertebrae one on top of another. But in developing embryos, the clock is whisked along the extending tail by another set of signaling molecules called the wavefront. 

In other words, vertebrae are made one after another by the PSM, which spits out a new proto-bone, grows a bit, and then creates another, making back bones that line up like pearls on a string. That's how volcanic island chains are formed, except with lava instead of bone. 

You can read about it in the original paper:  From Lizard to Snake; Behind the Evolution of an Extreme Body Plan, which comes from the journal Current Genomics.  

Here's the key passage in fairly dense technical language:  

“The somitogenesis clock comprises genes from the Notch, Wnt and FGF pathways, which are expressed in a rhythmic fashion in the PSM. Because cells are out of phase depending on their time of creation in the tail bud, the expression of the clock genes appears to occur as a wave, sweeping through the PSM, inducing the formation of a somite each time a ‘wave’ passes the determination front. The rhythm of this oscillator thus determines the periodicity with which somites are produced.” 

That is, the somites (the early-stage vertebrae) are created by the "hot spot" of the embryo, and then expand out into full-fledged bone as the snake matures.  

Okay, what about sunflowers?  I tried the same query pattern for this:  

     [ how do flowers on a sunflower come to be ] 

…and ... I had lots of failures… couldn't find anything too useful. 

But I DID learn something interesting about how the arrangement of seeds in a sunflower is a result of how they were formed.  So I changed my strategy a bit.  Following up on that clue, I searched for:  

     [ pattern of seeds in sunflower ]  

which took me to and article about the Fibonacci series in the sunflower.  "Oh no!" I thought. 

I'd read such things before.  They're cute and mathematically fun, but what do they have to do with my question?  

But this time I noticed that each seed of a sunflower comes from one flower. Not a surprise. But each FLOWER is made at a single point of origin.  I found that a flower germ is created, then the primal flower head turns 137.5 degrees and creates another one. Repeat.  

THIS sounds a lot like volcanos, or the backbone development… or flowers. 

This page also tells me about phyllotaxis--that is, how plants move.  (Which we've talked about before in SRS: What do you call a rotating flower?)  

This led me to the key insight:  The disk of a sunflower is made by a moving flower head that emits flowers every so often.  

This same query also gets me to another sunflower page: Nature, the Golden Ratio and Fibonacci too  which tells me that the spiral arrangement of flowers happens because each new baby flower is formed, then the flower bud makes a 137.5 degree turn, and makes another flower.  The flower disk grows slowly outward as new flowers are created (and then rotated) from the center.  (Check out the animation on this page.  It's really good at explaining the idea.)  That magic number: 137.5 degrees, happens to be the Golden Angle (yes, related to the Golden Ratio), which is what gives rise to the Fibonacci numbers in numbers of sunflower seeds in a spiral of the flower.  

One can go into infinite regress on this topic.  (For the math-curious, check out Fibonacci Numbers and Nature.) In this article, they point out how this “point source + moving part creates distribution of objects in space over time.”  

BUT ... That's IT!  

In each of our examples, islands, backbones, sunflower seeds--they're all created by a point-source that's attached to a moving part.  

This same generative process also brings about the shape of a nautilus and many other naturally occuring spirals.  

For SRS purposes (and to find even better sources), I then searched for this technical term (phyllotaxis) with my target (flower development):  

     [ phyllotaxis flower development ] 

This leads to wealth of fascinating papers, all fairly technical, e.g., Computational models of Auxin-driven patterning in shoots,  or the completely absorbing:  Phylloatactic patterning of gerbera flower heads, which taught me about primorida--the cells that originate body parts, like flowers or vertebrae.  If a primordia is on a rotating (phyllotactic) stem, then spirals emerge.  The rate of spin and the rate of growth determine what kind of spiral will be made.  

And this finding answered an earlier question:  What's that "hot spot" thing called in biology?  Answer: It's a primordia.  That's what makes the proto-flower, and the proto-vertebrae.  Same idea. 

And, while doing all this search, I found a RadioLab episode that tells this story (about HOX genes and vertebrae development) in a story about genes and body shapes.  (Check it out: RadioLab Dispatch 6: Strange Times -- the discussion is right about 30:05 into the program.)  

SearchResearch Lessons

As I said last week:  Why is this an interesting SearchResearch Challenge?  Because people are ALWAYS noticing connections between things.  Sometimes they're deep and interesting, sometimes they're spurious--we have to know how to tell the difference.  This is a Challenge about how to seek out and validate a suspected connection.

1. Use a pattern to find similar answers to a common question.  

In this case, we looked for similar features between each of the three very different things (islands, bones, flowers) by starting off with searches for their origins.  I just used a search like: 

     [ how did X come to be ] 

I figured that people would have written out the origin stories for each of these things.  And, sure enough, they do.  

2. Keep searching... the pattern will emerge.  

That search took a few extra steps in the case of the sunflower seeds, but at each step I was able to learn enough to do the next search, which ended up leading me to the answer.  It's all about time and space... and the willingness to keep searching for a deep connection, even when it's not obvious.  

Hope you enjoyed this as much as I did.  


Search on!  

Wednesday, July 21, 2021

SearchResearch Challenge (7/21/21): How are these connected? (Islands, vertebrae, flowers)


While looking at a sunflower the other day... 

... I had an insight... and thought I'd share this with you. 

I realized that there is a deep, underlying, common property that connects the sunflower to the skeleton of a snake to the Hawaiian archipelago. In other words, there's a fascinating connection that I hadn't thought about before. 

This is a lovely observation, and it seems to be a great SearchResearch Challenge for us.  Can you figure this out? 


What's connects the archipelago of Hawai'i with the vertebrae of a snake?  What then connects that to the flowers in a sunflower?  Can you think of what these three very different things might share in common?  (And no, it's not "they're made of atoms..." or something similar. It's actually an interesting commonality.)  

Every day I'll post a hint in the comment thread of this post, giving small nudges as needed.  

I know this is fairly abstract, but I'll shed a bit more light each day until you make the connection that I made last week.  

Step back for a second and think to yourself, what's shared among these three things?  Don't worry too much about trivial connections--think about the processes involved in how they came to be.  What might that be?  

Once you have an insight about what they could possibly have in common, then you'll need to figure out how to search for confirmation.  

(Metacomment:  Why is this an interesting SearchResearch Challenge?  Because people are ALWAYS noticing connections between things.  Sometimes they're deep and interesting, sometimes they're spurious--we have to know how to tell the difference.  This is a Challenge about how to seek out and validate a suspected connection.)  

Ready?  Go.  

Search on!  

Saturday, July 17, 2021

Answer: All about Bonaire?

Trying to find answers is easy... 

... sometimes.  This week's Challenge is a great mix of straightforward and complex.  Let's dive right in. 

The Challenges were: 

1. "Slagbaai" is the name of a large park on Bonaire.  What does the name Slagbaai" mean? 

As most everyone figured out, 

     [ Slagbaai ] 

gives a pretty good answer.  In particular, the second result, is the "official" national park web page.  You can read the page to learn that "STINAPA N.A." is a Dutch acronym, Stichting Nationale Parken Nederlandse Antillen, which is the national park system of the country.  Check out the lovely overview video (with killer drone shots) on that page (at the very top).  

On that page, you'll get a short history of Slagbaai, but not a definition of what the word means.  You have to click around a bit (or search for [what does Slagbaai mean ] and click on the STINAPA page that answers the question.  To quote from their page

The name ‘Slagbaai’ is often said to derive from the Dutch word ‘Slachtbaai’, meaning slaughter bay. Historians, however, say the name more likely originates from salt harvesting activities since the times of the original Indian population. In the past the bay was called ‘Sla baai’. ‘Sla’ comes from the Papiamentu word ‘salu’, meaning salt.

I'm going to accept their story (stories!) as the best authority for this Challenge.  They're locals.  They also know the local language, Papiamentu. And it could well be that both stories are correct.  Etymology is complicated, especially in places where creolization happens.  

2. Bonaire is now a desert island, but it used to be covered in a forest that was dominated by a particular kind of tree. What kind of tree was so dominant? Why was it heavily logged?  

I searched for: 

     [ history of trees on Bonaire ] 

This finds a variety of sources. A good one is the Blue Oceans page.  Here we find that there are 5 major kinds of trees on Bonaire.  

Tabebuia Billbergi  (Kibrahacha tree): blooms rarely; very hard wood; grows everywhere.  

Bourreria succulenta (Watakeli) grows to about 7-8 meters; 

Caesalpinia coriaria (Divi-divi tree) grows pods which contain large amounts of tannin, useful for tanning hides--and an export product for a short time.  

Guaiacum officinale (roughbark lignum-vitae, guaiacwood or gaïacwood) is a species of tree in the caltrop family, Zygophyllaceae, native to the Caribbean and the northern coast of South America. Used primarily for medicinal purposes and incredibly tough wood (which would be used for ship pulley-blocks).  

Haematoxylon brasiletto (Brazil tree, aka Palu di brasil, Brazil, Brazia, Stokvishout, Dyewood, Verfhout, dyewood). The dyewood has a distinctive, twisted shape and a deeply grooved trunk.  The oldest known map of the Caribbean (from 1513) labels the island as "Ysla do Brasil" ("Island of the Brazil tree").  The Dutch seized Bonaire from the Spanish in 1636 in part to gain access to this commercially profitable product. In former centuries the wood was used to prepare a red dye. The wood was shipped to Holland where it was shredded in a “rasp house” to extract the dye which was then used to color cloth, hence the name Dyewood.

In the process of doing this research, I happened to run across this early map showing Bonaire:  

Excerpt of the 1513 map of the world, highlighting Bonaire ("Ysla de Brazill"). See arrow and filled-in island boundary.  

After getting this basic information, I then searched in Books and found several books that mention trees and forests on Bonaire, the most intriguing one is "A Short History of Bonaire, which includes a couple of intriguing comments.  The Dye-wood tree was apparently all over the island AND all over Klein Bonaire (the circular, nearly perfectly flat island nestled in the bight of western Bonaire).  "In 1623 a Dutch vessel cast anchor off Bonaire, and the sailors were at once struck by the fact that there was such an abundance of dye-wood standing about the island which, mor over, grew conveniently close to the shore." (p. 15)

Later we find that "In the 17th century this little island was covered with it.  Here too, ruthless cutting destroyed the trees."  (p 32) 

Alas, we also read the "the guaiac or wayacá trees suffered the most destruction.... it was a great piece of good fortune for the island that, owing to a lack of shipping facilities, this unwise wasteful felling of trees was checked somewhat."  

So, both kinds of trees were heavily logged, but the Brazil tree / dyewood seems to have had the largest range, and therefore the most damage.  

Brazilwood tree (in Brazil)

3. Can you find an early / historic period image of Bonaire?  (The earliest image wins!) 

This was a pretty ambiguous question on my part.  Sorry about that.  When I read Jon's comment ".. just what DR means by historic period?" I realized that I'd left the question pretty open-ended.  

This question COULD MEAN "an image of Bonaire made within the historic period" OR "an image on Bonaire that was made in prehistoric times.  

In searching for the answer to the previous Challenge, I found that 1513 map.  Finding that map was intriguing, so I kept looking for more early maps.  I found that by searching for: 

     [ map Bonaire 16th century ] 

I could find another map from 1522.  (I kept looking but these were the earliest maps I could find.)  

Subsection of 1522 map of the coast of Venezuela (Getty Images).  Here, north is to the bottom, and an inaccurately drawn Bonaire is on the far lower left of the map, with Curaçao and Aruba to the right.

But I really was looking for earlier For the "within the historic period" version, I naturally looked at Bonairean history books--again looking on Google Books for

     [ History of Bonaire ] 

We know that in 1499, Alonso de Ojeda arrived in Curaçao and visited a neighboring island that was almost certainly Bonaire.  

So, in a way, the earliest European image of Bonaire is that 1513 map from above.  

BUT if you want something more like a "traditional" image, a quick scan through a few history books shows things like this: 

Photo of Fort Orange, Bonaire. 1896

Krajlidihk, 1913.  (From Wikimedia)

In both cases, I found the images in history texts, and did Search by image to find other sources.  I found a nice quality image in Wikimedia of the "
Gezicht op Kralendijk."  For older images, you can almost always do this and work around copyright issues.  (That is, find it in an open-source collection.)  

To find prehistoric images on Bonaire, I did a search for: 

     [ prehistoric artwork on Bonaire ] 

which took me to a bunch of resources, although perhaps the most interesting was a research paper "Distinguishing authentic prehistoric from historical replication rock painting features at prehistoric sites on Bonaire" published in the proceedings of the 21st International Association for Caribbean Archeology.   

The paper is about the problem of accurately identifying prehistoric rock art from fake prehistoric paintings (and the modern "updates/improvements" to the underlying rock art).  

In that paper, the following image is presented as original rock art from the Ceramic Period (450 - 1500 CE).  

That's a pretty broad range of time, but it's definitely before any European maps were made, so I'd have to give this image at the Onima Site award as the "earliest image" of Bonaire.    

4. I saw flamingos on Bonaire.  Growing up, I saw lots of National Geographic specials on TV that told me they lived in Africa!  Are flamingos native to the area, or were they imported?  Have they always been on Bonaire?  

Flamingos on the solar salt ponds on the south part of the island.

This wasn't hard, but it was a surprise--my intuitions about flamingos being only in Africa was dead wrong.  

A quick search for [ flamingos ] and a bit of reading in the results teaches us that flamingos ARE widely distributed.  The Wiki article says flamingos are in:

"the family Phoenicopteridae, the only bird family in the order Phoenicopteriformes. Four flamingo species are distributed throughout the Americas, including the Caribbean, and two species are native to Africa, Asia, and Europe."

(Of course, as always, I found other references that agreed with this description of flamingos and their global distribution.)  

However, I was surprised to learn that the American flamingo (Phoenicopterus ruber and the other variant species, including the Caribbean flamingo, P. ruber ruber) is found in Central and South America and throughout the Caribbean. It's occasionally seen in Florida and along the Gulf Coast as a vagrant. Oddly, the American flamingo doesn't breed in the United States. The American flamingo was once considered to be the same species as the greater flamingo (Phoenicopterus roseus) that is found in Africa, Asia and parts of southern Europe, but is is now considered a separate species. 

Finding this was pretty straightforward, but the results are fascinating!  

SearchResearch Lessons 

1. Some research Challenges are complicated.  Finding the original trees of Bonaire wasn't hard, but finding which was the dominant tree, and why it was so aggressively removed, took a bit of reading.  

2. You find things by reading widely.  In our case here, as I was reading about the trees, I found an early map.  That turned out to be handy when (later) I was searching for early images of/about/on Bonaire.  The earliest maps are pretty interesting "images" of Bonaire, suggesting that it was a real place, even if the map outline wasn't especially accurate.  

3. Research questions need careful descriptions to know what you're really searching for in your quest.  SRS Regular Reader comments made me realize that my Challenge was "open-ended."  That's what made me realize that a map would be an "early image of Bonaire" AND that prehistoric rock art would be an even EARLIER depiction of life on Bonaire.  I wrote the Challenge without providing enough details to tell when you'd found an answer.  (Teachers:  Pay attention!  Writing research questions is a tricky business.  Be sure that you know what kinds of results would be good answers.)  

Footnote:  Sorry about this Answer being so late this week.  It was a busy, busy, busy week.  I'm glad I got this post done today! I'll be back on Wednesday of next week to do the next one.  It will be a bit more complex... so look for it then. 

Search on! 

Wednesday, July 7, 2021

SearchResearch Challenge (7/7/21): All about Bonaire?

The Caribbean is a wonderful place... 

This is sunset from the tiny beach on the south side of Kralendijk (how to pronounce), the capital city of Bonaire.  Yes, the sunsets really do look like that.  

I've visited many times, and still find it fascinating.  It's a desert island that's managed to preserve its reefs in good shape--and the fact that it's a desert island means that the water around the island is supernaturally clear.  Because it's in the tropics, it's also warm and just about perfect.  

But for as many times as I've been there, I still have a few questions--I suppose I'll always have questions, but let's start with these.  Can you SearchResearch the answers?  

1. "Slagbaai" is the name of a large park on Bonaire.  What does the name Slagbaai" mean? 

2. Bonaire is now a desert island, but it used to be covered in a forest that was dominated by a particular kind of tree. What kind of tree was so dominant? Why was it heavily logged?  

3. Can you find an early / historic period image of Bonaire?  (The earliest image wins!) 

4. I saw flamingos on Bonaire.  Growing up, I saw lots of National Geographic specials on TV that told me they lived in Africa!  Are flamingos native to the area, or were they imported?  Have they always been on Bonaire?  

Flamingos on the solar salt ponds on the south part of the island.

Be sure to let us know, in the comments below, what you've found.  AND, of course, let us know how you did it. Anything you can teach us to improve our SearchResearch skills will be happily accepted!