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Field of Science
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RFK Jr. is not a serious person. Don't take him seriously.2 months ago in Genomics, Medicine, and Pseudoscience
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The Site is Dead, Long Live the Site2 years ago in Catalogue of Organisms
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The Site is Dead, Long Live the Site2 years ago in Variety of Life
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What I read 20194 years ago in Angry by Choice
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Histological Evidence of Trauma in Dicynodont Tusks6 years ago in Chinleana
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Posted: July 21, 2018 at 03:03PM6 years ago in Field Notes
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Why doesn't all the GTA get taken up?6 years ago in RRResearch
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Harnessing innate immunity to cure HIV8 years ago in Rule of 6ix
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post doc job opportunity on ribosome biochemistry!9 years ago in Protein Evolution and Other Musings
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Blogging Microbes- Communicating Microbiology to Netizens10 years ago in Memoirs of a Defective Brain
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Re-Blog: June Was 6th Warmest Globally10 years ago in The View from a Microbiologist
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The Lure of the Obscure? Guest Post by Frank Stahl12 years ago in Sex, Genes & Evolution
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Lab Rat Moving House13 years ago in Life of a Lab Rat
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Goodbye FoS, thanks for all the laughs13 years ago in Disease Prone
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Slideshow of NASA's Stardust-NExT Mission Comet Tempel 1 Flyby13 years ago in The Large Picture Blog
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in The Biology Files
A plant pundit comments on plants, the foibles and fun of academic life, and other things of interest.
Berry-Go-Round #34
OK the Phactor doesn't like to complain, but the month of December is not here yet and already the November Berry-Go-Round #34 is up over northern Utah at Watching the World Wake Up. It was especially nice to be included in the round up of plant blogs because while field tripping in the rainforest the end of the month snuck up and nothing got submitted. This is pretty timely because the field trip is wrapping up and all that remains is the travel misery of going home. Remember when traveling, especially air travel, was fun? Many younger people might not believe that at one time airlines vied for your business by being good; now they rely on being a necessity. But the trip home begins tomorrow at 6 AM, yes, with or without college students who do not know what those single digit numbers are used for in mornings.
Rainforest Field Trip - Lianas
Another feature of rainforest communities are life forms uncommon in the temperate zone. Here in the rainforest epiphytes and lianas, woody vines, festoon the forest in great profusion. Some of these lianas reach considerable size and their load can sometimes overwhelm the tree breaking their support. Further lianas commonly survive the fall of their support tree and start over again climbing another tree. Often only fallen fruits, seeds, and flowers are the only clue to vines far above in the canopy. Virtually every woody stem that can be seen in this image are lianas. Lastly lianas are a life form not a taxonomic group, and many different organisms in many different plant families grow as lianas. In fact one of the lianas in this view is the broad-leafed gymnosperm Gnetum.
Rainforest Field Trip - Unrelenting Green
Rainforest Field Trip - Canopy Trees & Digital Photography

Rainforest Field Trip - Death March 2010
A front moved in last night bringing steady rain with it. While frequent rain is expected it can make doing field research challenging to nigh on impossible, and of course that is what the students are expected to be doing, field research. As the end of this field trip nears they should be putting the finishing touches on their projects, getting more data, trying new manipulations to figure out even more, or just trying to get something to work, pleeease! But the rain is interfering with many projects, so what to do? Why, Death March 2010, of course! The field station is a pretty big place and relatively few people ever hike all the way to the "back", and the reasons are simple, it's quite a ways, the trails get progressively more primitive as you go further, and the relief gets greater, more ups and downs. So my esteemed colleague, a younger and foolishly energetic fellow takes our students on his death march hike to see these more remote areas. In all the hike will cover about some 16-18 km, 10-12 mi over tropical hill and dale, stream and swamp. Not really so far a distance, but has anyone ever explained about tropical clay? Something about the aluminum silicates and micell structure (little flat crystal-like plates) makes them slide about at a microscopic level very easily, and the practical take home message is that tropical clays like these are extremely slippery. So now combine the rubber boots, the primitive up-and-down trails, and the tropical clays well lubricated by a night of rain and you have a perfect formula for a thrilling hike. So what is the Phactor doing you may ask? Why someone must survive to chronicle these adventures; someone must hose them down enough to recognize the individual bodies. Someone smart enough to know about tropical clays and the trails back there. Someone who thinks these distant realms have probably not changed very much since his last visit about a decade and a half ago. My colleague does have an ulterior motive; this will be a pretty quiet Saturday night!
Rainforest Field Trip - Luscious Lips
Rainforest Field Trip - Friday Fabulous Flower - Angelic Orchid
Rainforest Field Trip - Thanksgiving in the Tropics
Thanksgiving is of course only a holiday in the USA. Here in Costa Rica at the field station they have begun putting up Christmas decorations and shops have decorations and gifts prominently displayed, so the Christmas calendar creep is not just a North American thing. Some of our students have never been away from home on a major holiday before, and the field station in deference to all the gringos makes us a pretty fancy Thanksgiving dinner. It was a hot sunny day this morning, now cooled off by some afternoon downpours; at home a wintery mix is falling, and nothing can explain this to our tropical hosts. How could it actually be that cold? The Phactor, thinking well ahead, brought cranberry jelly/sauce, a true North American contribution to the traditional Thanksgiving dinner. Amusingly, the Costa Ricans are as suspicious of the cranberry sauce as our students are of new Costa Rican foods. Unfortunately some things just don't translate very well; some how salsa de pavo just doesn't seem the same as gravy, but what else are you going to call it? And what will the Phactor miss the most? Well, that's so easy it isn't even a contest; Mrs. Phactor is a world class pie maker and the most difficult choice you will ever have is pumpkin, apple, or pecan? Readers, care to chime in?
Rainforest Field Trip - Hats off to Cyclanths
Rainforest Field Trip - The Understory
Rainforest Field Trip - Picky Eaters
This post could go several different ways and maybe you're expecting specialist herbivores or specialist carnivores, but actually it's about a much more mundane group of picky eaters that in particular are found in the great 'Merican midwest, our students. One thing about field trips is that you spend a lot more time with your students than usual, and on most levels this is a good thing. Students find out we are more or less normal, approachable people, and not quite as intimidating as they thought. On the other hand we often find out more about students than we would like. So here is an observation and a big of advice that arises from our 3-meals a day experiences at a tropical field station, which by all reasonable accounts does a very good job of providing decent interesting food, and besides for a few days you can stand to eat more rice and beans than you would like.
Mothers don’t let your children grow up to be picky eaters. To some extent that's tolerable, but the fact that they are not just choosy mind you, but down right crazy, loony, nothing new or different will cross these lips picky, is your fault as a parent. Who was in charge when your child was young? You don’t let a fox watch the hen house and you don’t let 5-year olds dictate the menu. You are not doing them any favors especially if they ever plan to venture beyond the great Midwest, and oh,they have, so put quite simply being irrationally picky is not a characteristic that one associates with being smart, educated, sophisticated, professional, or accomplished. Now certainly the human brain is quite capable of maintaining a considerable disconnect between its rational thought on some issues and its irrational leanings about others, but it’s a sign of growing up when you put the rational part of your brain in charge and put the childish irrational brain to bed for good. With few exceptions food is not going to kill you, so when someone simply refuses to try a new food, for ridiculous reasons, what other people observe is an indulged little kid who is still engaging in very childish behavior. Granted in my tropical wanderings there have been a few times when something new was really was not very good, something that did not at all appeal to me, but nothing so terrible, ugly, or foul it could not be tried and survived. So do your kid a favor, do yourself a favor, feed them adult food, teach them about food as an adventure, and do not cave in to their childish likes and dislikes, and if they are this way because you are this way, well, what can be said because this message will only elicit indignant responses, and anyways by the age of 20-something, it’s too late for most of them now anyways, so the Phactor hopes the world is kind enough to let them live comfortably in some little Midwestern town. Is the Phactor being too harsh?
Mothers don’t let your children grow up to be picky eaters. To some extent that's tolerable, but the fact that they are not just choosy mind you, but down right crazy, loony, nothing new or different will cross these lips picky, is your fault as a parent. Who was in charge when your child was young? You don’t let a fox watch the hen house and you don’t let 5-year olds dictate the menu. You are not doing them any favors especially if they ever plan to venture beyond the great Midwest, and oh,they have, so put quite simply being irrationally picky is not a characteristic that one associates with being smart, educated, sophisticated, professional, or accomplished. Now certainly the human brain is quite capable of maintaining a considerable disconnect between its rational thought on some issues and its irrational leanings about others, but it’s a sign of growing up when you put the rational part of your brain in charge and put the childish irrational brain to bed for good. With few exceptions food is not going to kill you, so when someone simply refuses to try a new food, for ridiculous reasons, what other people observe is an indulged little kid who is still engaging in very childish behavior. Granted in my tropical wanderings there have been a few times when something new was really was not very good, something that did not at all appeal to me, but nothing so terrible, ugly, or foul it could not be tried and survived. So do your kid a favor, do yourself a favor, feed them adult food, teach them about food as an adventure, and do not cave in to their childish likes and dislikes, and if they are this way because you are this way, well, what can be said because this message will only elicit indignant responses, and anyways by the age of 20-something, it’s too late for most of them now anyways, so the Phactor hopes the world is kind enough to let them live comfortably in some little Midwestern town. Is the Phactor being too harsh?
Rainforest Field Trip - Forest Decor
Rainforest Field Trip - It's not nice to fool mother nature.
Rainforest Field Trip - When is a flower open?

Into each forest some rain must fall
Students in an intellectual sense know that rain forest means a forest community of high rainfall, but until they experience rain in the tropics they will not have an true understanding of what we speak. Following a mini-drought of six rainless days a system has moved in from the Caribbean, bumped into the central cordillera and the rain began to fall. It's a medium high overcast and it produces a very steady rain, about a 2.5 out of 10 on the tropical rainfall scale, but after a couple of hours out in the forest, you are quite wet, except for your head and shoulders tucked under you umbrella. This is also when students learn that a good pair of tall rubber boots are their best friends, and when a mud hole trys to steal one, you'd better help pull your friend free. Still is was a productive morning for my ducklings splashing along behind me. The Phactor managed to help them find several ant plants, plants that interact in a mutualistic manner with ants: balsawood and cercropia saplings, a piper, and a melastom. Found a place where fruit-eating fish could be fed fruit. This is an important part of doing field research: if you cannot find your research organism say in a week or two, some die-hards would give it a month, then you'd better find something else to study. The Phactor has always found his plants; they've just refused to cooperate by flowering whenever he was present, but the nice thing about the tropics is that some other interesting thing is just right over there. The low rumbling from the east would suggest that the Aztec weather gods do not think students have learned this lesson yet, and as this is being typed, the rain has gone up another notch to about a 3. Still there is little chance this will set any records for us; a field trip back in the 1990s recorded 474 mm in 8 days. That's why they call it rain forest.
Rainforest Field Trip - Corkscrew Flower
Rainforest Field Trip - BE CAREFUL OUT THERE PEOPLE!
Rainforest Field Trip - Oh, Toto, we aren't in Lincolnland anymore.
Two buses, two planes, and 16 hours - In the rain forest
It takes a bit of travel, more or less, 4 3-hour stints by coach and plane, to get to rain forest. As you might expect it's hot and humid, although a bit dry (no rain for 5 days). Right now the Phactor needs food and sleep for a complete recovery, and will stop before incomprehensible babbling takes over. Already saw a pair of green macaws, one of less that 100 pairs that exist in Costa Rica.
On the Road Again - Rain Forest Ecology Field Trip
How to write a science news article
Oh, this is so absolutely spot on it's hard to stand. The template provided is widely used. And of course because real news is "even-handed" you always have to find a science crank to offer a dataless alternate opinion so that politicians can then say the matter has yet to be decided. HT to Angelo.
Real Life Fruit Quiz
The decision was made to return them and the impertinent clerk, who had no idea who he was dealing with, wanted to know how anyone would know they weren't clementines? There are times one dusts off the PhD and pulls rank.
Symbioses and the Origin of Life on Land
Holiday Gift Idea for Botanists & Gardeners - Wear Your Produce

Holiday Gift Idea for Botanists & Gardeners - PlantCam
No question about it, The Phactor is a hard dude to buy presents for, especially according to Mrs. Phactor and the F1 (Hmm, actually no one else buys me presents.), but he appreciates their persistence. How anyone has managed to live this long without owning a time lapse PlantCam is beyond me! And it has other applications like finding out which of two totally innocent looking who me felines broke that lamp or chewed on that plant while you were out. If someone out there has used the PlantCam, let us know about how you liked it. In keeping with his independent approach to blogging, and the fact that no one has offered a kickback for my endorsements, no vendor is being provided, but if you shop it around the web, you should be able to find a PlantCam for under $80. This link goes to a U-tube video sales pitch. This would be so cool for student use on tropical field trips where we would find out if it's really water-proof or just sort of. Surely some generous donor wants to enhance the educational experience of a budding botany student.
Friday Fabulous Flower - Thanksgiving Cactus
Failed Experiment in Web Searches
Someone thought it would be a nifty idea to cram a bunch of "hot" keywords into a blog title (Naked truth about sex, gardening, religion, and politics in American government) and then poll people to see which word would be the hottest, get the most hits, and then compare that to the actual keyword data. Part of the rationale was to just try doing a poll. Well, like a number of the Phactor's research projects over the years, this one was an abject failure. In the opinion of 56% of the poll takers, "naked" would be the hottest keyword, but while that sounds impressive, only 9 people took the poll. But then the keyword data could not be recovered from any of the freebe stat counters in use, so the whole thing really was disappointing. Even the number of page views for the "Naked Truth" failed to deviate from the Phactor's average. But you do learn some things from even failed experiments, and some of them are pretty scary. Ever since its posting just over 2 years ago, a blog about whether an artichoke was a fruit or a vegetable has gotten on average the most page views, week after week, and keyword phrases including the term artichoke, even with misspellings, account for over 50% of the subject web searches that end up at on the Phytophactor's blog! That is pretty disturbing. Who knew so many people were so concerned, so curious, about a big old thistle? So do they want to know a cucumber is a fruit?
Fall Color - Bayberry

Garden Gift Ideas
Loopy Leaf Research

Indiana Jones of Ginger

Really really green animals
This demonstrates what happens when you try to catch up on your science reading; you discover all the neat things that scientists have figured out recently, and this is really the neatest thing about being part of science, there are always new things to learn, figure out, and understand. The previous blog mentioned green sea slugs, a organism introduced to me decades ago by a former colleague who went West. Sea slugs eat algae, harvest the chloroplasts and keep them in body cavities where they continue to photosynthesize providing food to the slug. Now it turns out this symbiosis has been going on so long the slug has acquired enough of the chloroplast genes that it can synthesize chlorophyll! Apparently this replenishes the chlorophyll in the captured chloroplasts so that they can function longer. While chloroplasts used to be independent organisms, they long ago lost some genes to the host cell nucleus that were necessary for synthesizing chlorophyll, which makes the symbiosis permanent, except for green sea slugs. Evolution is pretty nifty because biological weirdness makes no sense otherwise. The other thing to note is that green sea slugs actually look sort of leaf-like, now they almost are; they just need a bit of cellulose.
Really green animals
Generally organisms are green for one of two reasons: they use chlorophyll for photosynthesis, what the Phactor calls "really green", or they have a green-pigmented camouflage, which produces a pretty clear dichotomy between plants and animals. Down deep in the animal clade where you begin to get close to the never never land of unicellular organisms where distinctions like plant and animal do not work, you find some exceptions: green hydra, green clams, green sea slugs, green corals, and all of these harbor symbiotic algae in their bodies, but not in their cells. So of course once you get used to making such pronoucements, an exception pops up and forces you to go find the bloody thing in your book manuscript and add a dinged dang endnote! Algae are known to live within amphibian eggs in the "gell" surrounding the embryo, which might be considered intracellular, but maybe the Phactor misremembers something about amphibian eggs. The algal cells take up nitrogenous waste and get a nice wet habitat. But now the algal cells have been found inside a salamander embryo itself, the first truly cholophyll green vertebrate, although still lacking vertebrae at that stage of development. Does the embryo gain some benefit from the algal symbiont in addition to the removal of nitrogenous wastes? Does the algae share its photosyntetic products with the salamander? Maybe this will get those darned vertebrate physiologists to learn something about photosynthesis.
Fall Color - Winterberry
Friday Fabulous Flower - Japanese Anemone
Out of your gourd!

Plant Respiration Question
Dear Phytophactor,
My fiance and i have recently gotten into a debate about plant respiration.
She is worried about the amount of CO2 that plants may be giving off at night and prefers that we do not have them in the bedroom where we sleep.
I love plants....but i love her more.
So, the question is, what is the ratio of O2 to CO2 that plants give off? How much CO2 can a single medium size house plant give off in one night? How much CO2 is being produced if I have a bedroom full of plants? (five or six)?
I have searched the internet, and many sites agree that plants give off CO2 at night when they are in the process of respiration, but no one seems to provide any information about the exact amount of CO2 that plants actually produce.
Thank you!
Matthew
The Phytophactor responds:
Dear Matthew,
You make the Phactor feel like the Car Talk guys when you send me a question like this. The basic idea is correct; plants respire and give off CO2, all the time, and at night the respiration is not off set by photosynthesis, but here's the critical thing to understand. Plants respire at a much, much lower rate than a nice warm-blooded mammal. So if your fiance is worried about oxygen depletion and CO2 buildup at night, guess who ends up in another bedroom? Alternatively you could keep your bedroom really cool at night which will slow down plant respiration even more, while at the same time providing a good reason for keeping your warm carbon dioxide producing body around. Since your plants do grow, your plants are capturing more CO2 during the day than they release via respiration all day. The two cats sleeping on my bed respire a lot more than a whole roomful of plants. So plant respiration just isn't a problem, and here the Phactor stops short of saying a silly concern although it is, but I did hear this concern once with respect to giving plants to hospital patients. Even if plants gushed carbon dioxide at night hospital rooms and your bedroom are not sealed boxes, so gases can easily diffuse to equilibrate any tiny differences that might occur. So sleep well, the plants and their respiration aren't a problem; if they were we'd have be careful about entering my greenhouse or the rainforest at night, and both of them have far greater mass of plants respiring than your bedroom. Hope this helps you sleep in restful assurance, providing you do not handle being on the winning side of this debate with a certain air of superiority and condescension (And depending upon the particular nature of your fiance, please recall the scene in the 1st Star Wars movie where the R2D2 is beating Chewbacca at a chess-like game. Let the Wookie win may be very good pre-maritaladvice.).
My fiance and i have recently gotten into a debate about plant respiration.
She is worried about the amount of CO2 that plants may be giving off at night and prefers that we do not have them in the bedroom where we sleep.
I love plants....but i love her more.
So, the question is, what is the ratio of O2 to CO2 that plants give off? How much CO2 can a single medium size house plant give off in one night? How much CO2 is being produced if I have a bedroom full of plants? (five or six)?
I have searched the internet, and many sites agree that plants give off CO2 at night when they are in the process of respiration, but no one seems to provide any information about the exact amount of CO2 that plants actually produce.
Thank you!
Matthew
The Phytophactor responds:
Dear Matthew,
You make the Phactor feel like the Car Talk guys when you send me a question like this. The basic idea is correct; plants respire and give off CO2, all the time, and at night the respiration is not off set by photosynthesis, but here's the critical thing to understand. Plants respire at a much, much lower rate than a nice warm-blooded mammal. So if your fiance is worried about oxygen depletion and CO2 buildup at night, guess who ends up in another bedroom? Alternatively you could keep your bedroom really cool at night which will slow down plant respiration even more, while at the same time providing a good reason for keeping your warm carbon dioxide producing body around. Since your plants do grow, your plants are capturing more CO2 during the day than they release via respiration all day. The two cats sleeping on my bed respire a lot more than a whole roomful of plants. So plant respiration just isn't a problem, and here the Phactor stops short of saying a silly concern although it is, but I did hear this concern once with respect to giving plants to hospital patients. Even if plants gushed carbon dioxide at night hospital rooms and your bedroom are not sealed boxes, so gases can easily diffuse to equilibrate any tiny differences that might occur. So sleep well, the plants and their respiration aren't a problem; if they were we'd have be careful about entering my greenhouse or the rainforest at night, and both of them have far greater mass of plants respiring than your bedroom. Hope this helps you sleep in restful assurance, providing you do not handle being on the winning side of this debate with a certain air of superiority and condescension (And depending upon the particular nature of your fiance, please recall the scene in the 1st Star Wars movie where the R2D2 is beating Chewbacca at a chess-like game. Let the Wookie win may be very good pre-maritaladvice.).
A truffle trifle?

Herbal Remedies and Supplements – Do you get what you pay for?

But at a more basic level, when you buy some herbal health products, what are you getting? When you buy a bottle labeled GINKGO BILOBA, you have this crazy idea that ginkgo is what is inside, but maybe not. The Phactor has been asked to identify crumbled up, dried, green, plant material on more than one occasion, and quite frankly from an anatomical perspective, you cannot find out too much. New molecular methods can provide an alternative via DNA fingerprints that look at characteristic components of the genome as a means of determining if a particular plant is present or not. Unfortunately while such testing is positive when something is absent, you still may not have a positive identification unless the DNA fingerprint profile matches another plant you have a profile for.
So how’s it going out there in herbal health supplement land? Not well, if the DNA fingerprint testing conducted at the New York Botanical Garden is any indication of the quality of herbal health products. Many herbal teas are so diluted by a cheaper/tastier filler that an effective dosage seems unlikely, so you certainly are not getting very much of what you are paying for. Only one in 4 samples that were supposed to have ginkgo had the DNA fingerprint of ginkgo, and since ginkgo is an extremely common tree in cultivation and extremely easy to identify, even for amateurs, its absence from herbal supplements must be considered deliberate. Or maybe they just forgot. Although the testing is still dealing with smallish sample sizes, if the materials tested are representative at all, then the vast majority of the herbal supplement industry would seem to be a fraud on more than one level. Lastly the botanist in this interview, Dennis Stevenson, is one of my long-time professional friends.
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