Friday, March 21, 2025

A note about Heterophylly in the real world

Our Challenge about leaf variation on an individual plant made me more observant in the real world... 

Holly leaf variation on the same plant. Taken in Zürich by Dan.  The left image is from 3 meters above the ground in an unpruned part of the plant. The right image, from a well-pruned part of the bush, is about 1 meter off the ground.  

... I hope that being a Regular Reader of SRS does the same for you as well. 


I was out walking last week, not long after having written about Mimicry in Plants (March 14, 2025), when I happened to cross paths with a beautiful holly bush.  Like most holly bushes, it had the usual assortment of glossy green prickly leaves--it was lovely, but not the kind of bush you'd reach out and touch.  

But having just read/written about heterophylly, I took a closer look--sure enough, just as it says in the books, there was a distinct variation between the lower branches (which had been pruned extensively) and the upper branches (which had never been pruned).  Even better--the right side of the bush had a slight overhang into a neighbor's yard.  They clearly had been pruning there--on the right was an armada of sharp-tipped leaves. 

However, on the upper branches, especially on the left (and unpruned) side, smooth edge leaves abounded.  

As I wrote last week, the mechanism of holly heterophylly is pretty well understood.  The prickly/smooth variations are a result of damage to the leaves.  When the leaves are damaged (say, by a passing hungry deer or by a neighbor’s pruning shears), methylation of the DNA in the leaves happens as a result of tissue damage.  (Side note: methylation is the process of adding methyl groups onto pieces of large molecules, like DNA, to modify their behavior. This is the way much of epigenetics works. When an animal chomps on a leaf, methylation happens.)

By comparing the DNA of prickly leaves vs. smooth leaves, it turns out the prickly ones were significantly less methylated than prickless leaves, suggesting that methylation changes are ultimately responsible for leaf shape changes.  More methylation = more prickly leaves.  What's more, the methylation has an effect on nearby leaves.  Other holly leaves nearby will also develop the prickles, with the effect diminishing with distance.


I was delighted to see heterophylly in action while just strolling down the street.


Keep looking... and searching.





Wednesday, March 19, 2025

SearchResearch Challenge (3/25/25): To search, or to AI? That is the question...

Looking for an answer? 


Online search can often get to an accurate, trustworthy answer quickly.  But as you know, it really helps if you know a bit about what works.  

One of the major tools has been Search-by-Image, through either Google, Bing, Tineye, or Yandex.  

But now multimodal AI systems can analyze an image and tell you the story... or can they? 

As a skilled and literate searcher, you should understand the differences.  So let's give this Challenge a try to see what works, what doesn't work, and how you can tell the difference.  

I was looking for a couple things the other day while traveling through Switzerland.  When you try to find out the story of these images, where you able to use "regular" Search-by-Image, or did you use AI image descriptions?  If so, what prompt did you use, and how well did it work for you? 

1. While traveling in northwest Switzerland, I saw this emblem all over the city I was visiting.  Can you tell me what city I was in?  Just as importantly, what IS this thing? 

On a box of chocolates... 

Carved into a stone wall


Seen on a parade float

2. In open green spaces all over Zürich I keep seeing this flower popping up--they're growing everywhere in vast numbers.  What is it?  Again, how do you know?  What search method did you use? 

A few flowers carpeting the lawn. What are they?


The point of this week's Challenge is that I've had mixed results with both kinds of image searches.  When you do searches like this, what works for you?  Can you tell us HOW you got to the correct answer? 

Lots more data next week.  In the meantime... 

Keep searching! 



Saturday, March 15, 2025

The road to 5 million blog views on SearchResearch!

 Without much notice... 

SearchResearch Overview, as imagined by Gemini

... SearchResearch just passed a major milestone.  We are now officially well over 5 million blog views!  (The actual number today is 5.4 million--I somehow missed the last 400,000 views by not paying attention.)

If you remember, back in mid-December 2015, we crossed over 2 million views.  

I started the blog on January 30th, 2010 (the very first post) and we quickly became a community of interested searchers sharing tips about the obvious and the (incredibly) obscure.  (In the Obscure Hall of Fame: How flowers rotate--March 25, 2010; Zouave uniforms in the Civil War--October 27, 2011; too many others to list here.)  

And, as I'd hoped, I rewrote several of my favorite posts into a book, The Joy of Search (now available in paperback).  It was a real joy to see my book in airports: 

At San Francisco airport

It was also wonderful to be able to visit bookstores and find it on the shelves: 

Found in Kramer's book shop in Washington DC

Or even MORE fun, to visit bookstores and libraries (including the Library of Congress) to speak about The Joy of Search.  Every time I spoke I mentioned our SRS blog community and how incredibly wonderful the experience has been.  

The announcement for my book talk at Books Inc. Thanks, folks!  


In a very real sense, congratulations to you all.  Without your devoted readership, 5.4 million views would not have been possible. 

As you know, I'm working on a new book (working title: "Unanticipated Consequences").  If you want to follow along in that work, subscribe to my Unanticipated Consequences substack.  Maybe I'll get the book out this year.  When I do, you'll be the first to hear about it right here in SearchResearch.  

Forward, to 10 million views!   



Hasta Luego from the SearchResearch Rancho where I'm taking the weekend off to celebrate.  (And work on my book...)  

Keep searching.  

Another view of the SRS Rancho as envisioned by Gemini. Imagine I'm relaxing here.




Friday, March 14, 2025

Answer: Mimicry in plants?

It's a simple question... 


The question this week was pretty straightforward:  


And you probably also know about some insects that mimic plants: 

 

Leaf insect. P/C Wikipedia.


Mimicry is a fairly common trick in the world of living things--mussels mimic fish, flies mimic spiders, fish mimic their environment... it continues: walking stick insects mimic sticks, mussels can mimic small fish, and Viceroy butterflies mimic Monarch butterflies. This is all well known. But..


1. Can a plant mimic another plant?  Can you find an example of one plant that does this? 


Somewhat unexpectedly, the simple query: 

     [ plant that mimics another plant ] 

teaches us that Boquila trifoliolata, a shrub common in the rain forests of Chile (and much of South America) can somehow mimic the leaves of the plant that it grows on.   It's also called the pilpil, producing edible fruit and stems that can be used for making rope.  

P/C Wikimedia image of B. trifolioata vine mimicking the leaves of the host plant



But knowing THAT leads immediately to a much harder question:  

2. How does the mimicking plant come to be a mimic?  What’s the mechanism by which Plant A comes to look like Plant B?  


This is a bit of a mystery. The pilpil is the only plant species reported to engage not JUST in mimickery, by also in in mimetic polymorphism. That is, the ability to mimic multiple host species simultaneously. This obviously doesn't happen in animals--each animal mimics only one other animal at a time. But somehow, the pilpil manages to mimic multiple species at once.


As Wikipedia tells us, this is a form of Batesian mimicry, when a harmless species mimics a harmful one to ward off predators.


But how does it do the mimicking?


There are a lot of hypotheses about the mechanism include (e.g., microbially mediated horizontal gene transfer, volatile organic compound sensing, and the use of eye-like structures), but nothing seems to have panned out.


On the other hand, looking for:


[ leaf variation on single plant ]


leads us to learn about two concepts new to me: heteroblasty and heterophylly.


Heteroblasty is a significant and abrupt change in form and function, that occurs over the lifespan of certain plants. Like the pilpil changing leaf shape to match the host plant.


Heterophylly is when a plant has multiple leaf shapes on a single plant due to its environment.


As an example, Sassafras (Sassafras albidum) is well-known for having three distinct leaf shapes on the same plant - oval (unlobed), mitten-shaped (two-lobed), and three-lobed all on the same plant. It's the best known example of heterophylly.

More relevant to our discussion, holly leaves (Ilex aquifolium) can also make different types of leaves at the same time, even on the same branch--some with prickles, others without.


P/C after Herrera 

But the mechanism of holly heterophylly is pretty well understood. The prickly variations are a result of deer eating the leaves of the plant. When the leaves are damaged (say, by a passing hungry deer), methylation of the DNA in the leaves happens as a result of tissue damage. (Side note: methylation is the process of adding methyl groups onto pieces of large molecules, like DNA, to modify their behavior. This is the way much of epigenetics works. When an animal chomps on a leaf, methylation happens.)


By comparing the DNA of prickly leaves vs. smooth leaves, it turns out the prickly ones were significantly less methylated than prickless leaves, suggesting that methylation changes are ultimately responsible for leaf shape changes. More methylation = more prickly leaves. What's more, the methylation has an effect on nearby leaves. Other holly leaves nearby will also develop the prickles, with the effect diminishing with distance.


While the variation in leaf shape has been known for a while, it’s now clear that changes in leaf type are associated with differences in DNA methylation patterns, that is, epigenetic changes do not depend on changes in the sequence of DNA, but result from trauma to the plant.


What does this mean for our friend the shape-shifting pilpil? It demonstrates that changes to leaf shape can be epigenetic (that is, the plant doesn't have to modify its DNA, but just tack on a few extra methyl groups here and there).


That doesn't fully explain the way that pilpil leaves can mimic the host plant, but it does suggest a mechanism for changing the leaf structure.


Another intriguing hypothesis is that there is some kind of "visual sensing" that's going on with the vine. What makes this idea particularly interesting is that Boquila can mimic different hosts on the same vine without direct contact with the model leaves, suggesting some form of distance sensing. If the vine is truly using visual cues, it would be amazing--and completely novel. The big problem here is that nobody seems to be able to (pardon the pun) see any such organs!


A more probable hypothesis is that there is some kind of individual plant recognition, perhaps by sensing the release of nearby volatile organic compounds from recognized plants.


Kudu grazing on an acacia tree, causing the tree to put out a cloud of ethylene, telling other
nearby acacias that the browsers are here--increase your tannin load.  

Acacia trees, for instance, can detect ethylene emissions from neighboring damaged trees, triggering increased tannin production in the leaves of the acacia tree as defense against grazing kudu. [Heil, 2010] Other plants do similar things: Arabidopsis thaliana (a small plant in the mustard family) can also detect volatile compounds like methyl jasmonate from neighboring plants that are injured, which triggers its own defensive responses.


So it's not much of a leap to imagine that as a Boquila trifoliolata vine grows from tree to tree, each part of the plant might sense a different host that it's growing on, and invoke different responses--on each different part of the vine--depending on what chemical signals that part of the vine senses. It's also true that mimetic changes appear to be very localized, primarily affecting the leaves within 60 centimeters of the host plant. That's perfect chemical sensing range.


This effect would be mimetic polymorphism at a very fine level of detail.


To broaden my search I asked Claude for:


[ any plant that grows differentially depending on the chemical signals it senses]


I learned about the Centaurea maculosa (spotted knapweed) that detects specific root compounds from competing plants, responding by increasing production of allelopathic compounds (deadly poisons for the competition), essentially tailoring its chemical warfare based on which neighbor it detects.


Obviously, I did a Google Scholar search to verify that claim, and found a wonderfully detailed paper [Kong, et al, 2024] that goes into great detail about how the spotted knapweed senses the competition and then emits specific poisons to kill off the competition!


Just as obviously, I don't know if this hypothesis is correct--we need a good field botanist to do some studies, but it's not crazy.  All of the mechanisms are there and could be the product of evolution.  (And is very similar to the mechanism proposed by [Gianoli, 2014].)  


It's remarkable what you can learn (and hypothesize about) with some desk research!   


SearchResearch Lessons 


1. As with most complex searches, you have to learn as you go.  Note the new terms we had to learn to answer this question (mimetic polymorphism , methylation, heteroblasty, heterophylly).  Learn as you go in order to get more deeply into the topic.  


2. Interleaving "regular search" with LLMs (e.g., Claude, Perplexity, ChatGPT, etc.) can be really useful.  I was able to learn new terms and concepts by working with the AIs.  As always, be sure to CHECK their work. It's like reading an unreliable narrator in a novel--they're useful, but can't be trusted.  


 


Keep searching!



----

Citations:


Gianoli, E., & Carrasco-Urra, F. (2014). Leaf mimicry in a climbing plant protects against herbivory. Curr Biol, 24(9), 984-987.


Heil, Martin, and Richard Karban. "Explaining evolution of plant communication by airborne signals." Trends in ecology & evolution 25.3 (2010): 137-144.


Herrera, C. M., & Bazaga, P. (2013). Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllous Ilex aquifolium (Aquifoliaceae) trees. Botanical Journal of the Linnean Society, 171(3), 441-452.


Kong, C. H., Li, Z., Li, F. L., Xia, X. X., & Wang, P. (2024). Chemically mediated plant–plant interactions: Allelopathy and allelobiosis. Plants, 13(5), 626.



Thursday, March 6, 2025

SearchResearch Challenge (3/6/25): Mimicry in plants?

 We’ll return to Deep Research next time... 


But for this week, we’ll do a “traditional” SRS Challenge–one that asks a question about the world, leading to a surprising result.


If you’ve been reading SearchResearch for a while you know I’ve got several topics that seem to recur–Egypt is one, fish is another… but another repeating topic is mimicry.  


As you know, mimicry is the ability of a plant or animal to disguise itself as another plant or animal.  Sometimes you see plants looking like insects as we see in the above images.  Here, a Bee orchid (Ophrys apifera) looks enough like a female bumblebee that males get confused.  They try to mate with the floral fake (so-called pseudo-copulation) and get pollen all over their nether regions.  An enthusiastic bumblebee then distributes pollen widely in the area.  


And you probably also know about some insects that mimic plants: 

 

Leaf insect. P/C Wikipedia.


In these virtual pages we’ve talked about mussels mimicking fish, flies mimicking spiders, and fish mimicking their environment. The list goes on and on.


But I wonder… can a plant mimic another plant?  That seems unlikely… how would it manage such a trick? 


1. Can a plan mimic another plant?  Can you find an example of one plant that does this? 


2. How does the mimicking plant come to be a mimic?  What’s the mechanism by which Plant A comes to look like Plant B?  


As always, let us know HOW you found the answers by leaving a comment in the blog.  


Keep searching!     



Thursday, February 27, 2025

Answer: Asking questions of images with AI?

 Image searches are great... 


...  until they don't work. Since skilled researchers use Search-by-Image a fair bit (at least *I* do), it's always useful to understand just how well it works.  And since the LLMs have introduced multimodal capabilities, it's just as important to see how well the new search tools are working.  
 

Last week I gave you 4 full-resolution images that you can download to your heart's delight (with links so you can get the originals, if you really want them).  Here, taken on a recent trip, are 1. my hand; 2. a bottle of wine; 3. a piece of pastry; and 4. a beautiful flower.  So... what ARE these things?  

Our Challenges for this week is are: 

1. How good, really, are the different AI systems at telling you what each of these images are?  

2. What kinds of questions can the AI systems answer reliably? What kinds of questions CAN you ask?  (And how do you know that the answers you find are correct?)  

I did several AI-tool "searches" with each of these images.  For my testing, I used ChatGPT, Gemini 2.0 Flash, Meta's Llama, and Anthropic's Claude (3.7 Sonnet).  I'm not using anything other than what comes up as the default when accessed over the web.  (I didn't any additional money to get special super-service.)  

I started with a simple [ please describe what you see in this image ] , running this query for each image on each of the four LLMs.  Here's the first row of the resulting spreadsheet looks like (and here's a link so you can see the full details):  

Click to expand to readable size or click the link above to see the entire sheet.

Overall, the LLMs did better than I expected, but there are clear differences between them.  

ChatGPT gave decent answers, getting the name of the pastry correct (including the spelling!), and getting much of the wine info correct. The flower's genus was given, but not the species.  

Gemini gave the most details of all, often 3 or 4X the length of other AIs. The hand was described in excruciating detail ("no immediately obvious signs of deformity"), and Gemini also got the name of the pastry correct (although misspelled: it's Kremšnita, not Kremsnita).  Again, immense amounts of detail in the description of the pastry, and definitely a ton of information about the wine photo.  Oddly, while Gemini describes the flower, it does NOT identify it.  

Llama doest okay, but doesn't identify the pastry or the flower.  The wine image just extracts text, but has little other description.  

Claude is fairly similar to ChatGPTs performance, though with a bit longer description.  It also doesn't identify the pastry or the flower.  


You can see the differences in style between the systems by looking at this side-by-side of their answers.  Gemini tends to go on-and-on-and-on... 

Click to see at full-size. This is at the bottom of the sheet.

It's pretty clear that Gemini tries hard to be all-inclusive--a one-query stop for all your information needs.  

Interestingly, if you ask follow-up questions about the flower, all of the systems will make a good effort at identifying it--they all agree it's a Hellborus, but disagree on the species (is it Orientalis or Niger?).  

By contrast, regular Search-by-image does a good job with the flower (saying it's Helleborus niger), an okay job with the wine bottle, a good job with the pastry (identifying it as a "Bled cream cake," which is acceptable), and a miserable job with the hand. 

On the other hand...asking an LLM to describe an image is a very different thing than doing Search-by-Image.  

Asking for an image-description in an LLM is like asking different people on the street to describe a random image that you pop in front of them--you get very different answers depending on the person and what they think is a good answer.  

Gemini does a good job on the wine image, telling us details about the wine labels and listing the prices shown on the list.  By contrast, Claude gives much the same information, but somehow thinks the prices are in British pounds, quoting prices such as "prices ranging from approximately £12.50 to £36.00."  (I assure you, the prices were in Swiss Francs, not pounds Sterling!)  So that bit seems to be hallucinated.  

I included the hand image to see what the systems would do with a very vanilla, ordinary image... and to their credit, they said just plain, vanilla ordinary things without hallucinating much.  (Although Claude did say "...The fingernails appear to have a purple or bluish tint, which could be nail polish or possibly a sign of cyanosis..." I assure you, I'm just fine and not growing cyanotic nor consorting with fingernail polish!  It didn't seem to consider that the lighting might have had something to do with its perception.

And, oddly enough, as Regular Reader Arthur Weiss pointed out, the AIs don't seem to know how to extract the EXIF metadata with GPS lat/long from the image.  If you download the image, you can get that data yourself and find out that the pic of the pastry was in fact taken near Lake Bled in Slovenia.  This isn't just a random cubical cake, but it is a Kremšnita!  

Here's what GPS info I see when I download the photo and open it in Apple's Preview app, then ask for "More info."  


Not so far from Lake Bled itself.  


SearchResearch Lessons 

1. No surprise--but keep checking the details--they might be right, but maybe not. I was impressed with the overall accuracy, but errors do creep in.  (The prices are nowhere noted in British pounds.)  

2. If you're looking for something specific, you'll have to ask for it.  The prompt I gave ("describe the image...") was intentionally generic, just to see what the top-level description would be. Overall I was impressed with the AI's ability to answer follow-up questions.  I asked [what was the price of Riveria 2017] and got correct answers from all of them.  That's a nice capability.    

Overall, we now have another way to figure out what's in those photos beyond just Search-by-image.  Try it out and let us know how well it works for you. 


Keep searching!