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Back To The Eocene?

eocene_rainforest2

From Anthropocene To Eocene II?

A mountainside near where I live gave way in January 2009 (as a result of torrential rains) resulting in Racehorse Creek rock slide.

This landslide revealed a treasure-trove of fossils, mainly 55-million-year old fossils of plants that were alive during the Eocene. Most interestingly, perhaps, this time corresponds to to a period called the Paleocene–Eocene Thermal Maximum (PETM), which is characterized by a rapid (about 20,000 years) increase in atmospheric CO2 (primarily of volcanic origin) and global warming.

On a recent trip to the Racehorse fossil field, I couldn’t help thinking that not only was I revisiting the Eocene but also maybe getting a glimpse of what the predominant plant life may look like here in the Pacific northwest in a few thousands of years.

Do these Eocene plant fossils provide clues to the ultimate botanical outcomes of the Anthropocene?

Related Links:

  • The BBC view of the Eocene
  • Could human CO2 emissions cause another PETM?
  • The Emerald Planet
  • HowPlantsWork © 2008-2014 All Rights Reserved.

    By 2050, What Will Be The Greatest Human Impact on Plants?

    I first encountered the term “anthropocene” back in 2007 when I was writing a manuscript regarding some of our research in Yellowstone National Park (see Ref. 1 below).

    A more detailed view regarding the nature and implications of the anthropocene is presented on YouTube here. Yet another YouTube video that’s a bit more technical can be viewed here. (And if you’re really pressed for time, then check out this 2-min YouTube video.)

    If you’ve watched any of these videos, then you probably have a pretty good basic understanding of the anthropocene. If you didn’t, then the anthropocene can be briefly defined as the current geologic age in which “…human impacts such as land use and industrial pollution have grown to become significant geological forces, frequently overwhelming natural processes.” (from Ref. 1 below)

    There are several major impacts on plants as result of the anthropocene.

  • Increase in Atmospheric Carbon Dioxide (CO2) Some of the impacts on plants are a direct result of the burning of fossil fuels. One major impact is the increase in atmospheric CO2 (please see previous post). Other effects include elevated ground-level ozone and “acid” rain, both of which can negatively impact plants.
  • “Global Weirding” The increased greenhouse gases carbon dioxide and methane resulting from the combustion of fossil fuels have significant indirect effects on plants primarily by causing significant global climate changes (e.g., drought, heat), otherwise known as “global weirding”.
  • Loss/Degradation of Native Plant Habitats Agriculture, logging and land “development” also contribute to the anthropocene not only because of increasing atmospheric CO2 but also because of causing loss of natural habitats, thus decreasing plant biodiversity, including plant extinctions. (Agriculture is also the main contributor to nitrate pollution, another attribute of the anthropocene that can decrease biodiversity.)
  • Genome Engineering Technologies And, finally, let’s not forget plant genetic engineering, which already has major impacts on agriculture and will likely have ever-increasing impacts on plants, not only within the realm of agriculture but also, perhaps, even in natural ecosystem management.

    OK, but let’s get back to the question I’m posing here: Which of the above will probably have the greatest overall impact on plants within the next 35 years?

    I’m Placing My Bet On CO2

    First off, let’s acknowledge that atmospheric CO2 levels will likely continue to increase within the next 35 years, and probably well beyond that, primarily from human activities (please see here, for example). At the current rate of increase (please see here for the data), atmospheric CO2 will likely reach 500 to 600 ppmv by 2050. (It was about 310 ppmv in 1950 and is currently at about 400 ppmv.)

    Although this may not seem like a big increase, it will likely have profound effects on plants, for several reasons.

    As mentioned in the previous post, most green plants will likely benefit photosynthetically from this increase in CO2.

    Why?

    Mainly because the enzyme in plants that captures CO2 from the atmosphere for photosynthesis is currently working at a sub-optimal rate. This is because the current level of atmospheric CO2 is so low (relative to when green plants colonized the land, for example) that it may actually limit the activity of this key enzyme, known as RuBisCo.

    Tumblr lr3navql0Q1qh1rkuLet me put it this way: Imagine that RuBisCo is like a high-performance car that can go 100 mph when you give it high-octane gasoline (petrol). But now, only low-octane gas is available, so the car can only go 50 mph max.

    By steadily increasing the CO2 available to green plants, we are enabling RuBisCo to “fix” CO2 into sugars at a faster and faster rate, resulting in improved photosynthetic productivity of the plants.

    This is great, right? More productive plants means higher crop yields, bigger vegetables, more fruit….without having to add any more fertilizer or water.

    WOOHOO!

    But wait. This isn’t the whole story…

    Other Effects of Elevated CO2 on Plants

    Increasing the rate of photosynthesis by accelerating RuBisCo is not the only effect that elevated levels of CO2 have on most green plants.

    And some of these other effects may actually negatively impact crop plants.

    Homer simpson doh

  • Decrease in Heat Resistance?
  • Elevated CO2 levels have at least two effects on leaf stomata:
    1. High CO2 tends to close stomata.
    2. High CO2 may lead to fewer stomata per leaf during plant development.

    Perhaps above all else, land plants try to minimize water loss via transpiration, which occurs mainly through the stomata. Thus, it makes sense that, if there is a relative abundance of CO2 for doing photosynthesis, plants would tend to close stomata, make fewer of them, or both.

    But isn’t this another good thing? On the one hand, yes. But on the other hand, keep in mind that leaves cool themselves via leaf transpiration through stomata. So less transpiration may mean that the plants become more susceptible to heat stress, which many believe is on the increase do to global warming. And plant heat stress typically inhibits photosynthesis. (For example, please see Ref. 4 below.)

  • Less Nutritious Crop Plants?
  • A recently published report (see Ref. 5 below) provides evidence that high-CO2 crop plants may have less protein, zinc and iron (see news report about this paper here).

    Scientists are uncertain why elevated levels of CO2 cause a decrease in zinc and iron in plants, though variation among different species indicates that it’s likely a complex mechanism. “Of all the elements, changes in nitrogen content at elevated [CO2] have been the most studied, and inhibition of photorespiration and malate production, carbohydrate dilution, slower uptake of nitrogen in roots and decreased transpiration-driven mass flow of nitrogen may all be significant.” (from Ref. 5 below)

  • Loss of Plant Biodiversity?
  • In a previous post we explored the origin of C4 plants in a past, relatively low-CO2 world and their fate in a future high-CO2 world. Though C4 plants likely arose as a result of decreased levels of atmospheric CO2, their fate is very uncertain in the face of the increasing levels of CO2 that will likely occur in the centuries to come. (If some C4 plant species are displaced by C3 species, primarily as a result of elevated levels of atmospheric CO2, then this may contribute to a loss in plant biodiversity.)

    Though it seems reasonable that many C4 plant species might lose their CO2-concentrating edge over C3 plants in relatively higher CO2 environments and be displaced, there is little evidence for this to date. Admittedly, this hypothesis is very difficult test, and, indeed, there is evidence to the contrary (e.g., see Ref. 6 below).

    Bottom Line: In 2011, I posted on how increased CO2 will affect plants. It was clear then that, because plants’ responses to elevated levels of CO2 were so significant and complex, it was difficult to make reliable predictions. Three years later, though we know more about how some crop plants will likely respond to a high-CO2 world, it’s still hard to make general predictions with high confidence. What I think is clear, however, is that, considering all the major impacts of the anthropocene, increased atmospheric CO2 will probably have the greatest overall effect on plants.

    “Prediction is very difficult, especially if it’s about the future.” – Nils Bohr, Nobel laureate in Physics

    “I never think of the future, it comes soon enough.” – Albert Einstein

    References

    1. Tercek, M. T., T. S. Al-Niemi and R. G. Stout (2008) “Plants exposed to high levels of carbon dioxide in Yellowstone National Park: A glimpse into the future?” Yellowstone Science, Vol. 16, pp. 12-19. (PDF)

    2. Terashima,I., S. Yanagisawa and H. Sakakibara (2014) “Plant responses to CO2: Background and Perspectives.” Plant & Cell Physiology, Vol. 55, pp. 237-240. (Full Text)

    3. Leakey, A. D. B., et al. (2009) “Elevated CO2 effects on plant carbon, nitrogen, and water relations: six important lessons from FACE.” Journal of Experimental Botany, Vol. 60, pp. 2859-2876. (Full Text)

    4. Ruiz-Vera, U. M., et al. (2013) “Global warming can negate the expected CO2 stimulation in photosynthesis and productivity for soybean grown in the midwestern United States.” Plant Physiology, Vol. 162, pp. 410-423 (Full Text)

    5. Myers, S. S., et al. (2014) “Increasing CO2 threatens human nutrition.” Nature, Vol. 155, pp. 139-142. (Abstract)

    6. Morgan, J. A., et al. (2011) “C4 grasses prosper as carbon dioxide eliminates desiccation in warmed semi-arid grassland.” Nature, Vol. 476, pp. 202–205. (Abstract)

    Acknowledgment

    Thanks to Prof. Lisa Ainsworth (USDA/ARS & University of Illinois) for generous input regarding the potential displacement of C4 plants by C3 plants in a high-CO2 world.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    It’s All About The CO2

    Sell all your bicycles. Forget about buying a Prius®. Drive the biggest gas-guzzler you can find. Crank up that home and work air conditioning, especially if you get your electricity from coal-fired power plants.

    Yes, your houseplants – all green (photosynthetic) plants, for that matter (with, perhaps, a few exceptions) – want you to increase your carbon footprint. That is, burn as much fossil fuel as humanly possible, so that you maximize your CO2 output. This is because most green plants currently need and want more CO2.

    Why?

    Well, at the present time, most plants are “gasping” for CO2, somewhat like you would probably be “gasping” for O2 if you were hiking around Machu Picchu, at nearly 8,000 feet (2,430 meters) in elevation.

    Allow me to explain.

    When plants were colonizing the land – roughly, 400 to 500 million years ago (MYA) – Earth’s atmosphere may have had over 20 times the current level of CO2. (Please see here for atmospheric carbon dioxide through geologic time.)

    By the way, do you know what the amount of CO2 is in our atmosphere?

    In general, Earth’s atmosphere currently contains about 0.04% CO2 by volume (often expressed at 400 parts per million or ppm). Sometimes people have a hard time getting their heads around proportions expressed in this way. Most, however, can understand relative amounts of money. So let’s say that all the gases in the Earth’s atmosphere add up to $100 (analogous to 100%). If so, then carbon dioxide’s share would only amount to about four pennies. In contrast, oxygen’s share would be about $21 (or 21%).

    The early photosynthetic land plants (400 to 500 MYA) were probably luxuriating in nearly 1% atmospheric CO2, compared to today’s paltry 0.04% CO2. It’s no wonder that plants are “cheering us on” as we continue to burn fossil fuels, releasing more and more CO2 into the air.

    So, can we expect ever-increasing plant growth leading to improved crop yields as we continue to pump more CO2 into the atmosphere?

    Unfortunately, probably not.

    Why?

    Well, partly because of CO2‘s “greenhouse effect” on climate (which, I presume, you’re already familiar with) that is causing “global weirding”.

    But also, it turns out that increased atmospheric CO2 has profound short-term (minutes) and long-term (days to years) effects on plant physiology and plant development, such as a decrease in leaf stomata.

    More on this to come…

    HowPlantsWork © 2008-2014 All Rights Reserved.

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    FCWhat’s That Plant? What’s That Mushroom? And More…

    On this brief tour of botanical apps, we previously had a look at Garden Compass. This plant identification app is for IOS devices, such as iPhones and iPads.

    But what about all those millions of people who use Android-based smartphones and tablets? Is there something equivalent to Garden Compass for them?

    I’m pleased to say that the answer is yes. And, somewhat surprisingly, this Android app may actually be better than Garden Compass, which I think is quite an impressive app.

    So, why may this Android app be better than Garden Compass?

    Well, for one thing, this Android app maybe useful for identifying not only garden plants, but also wild plants, and even mushrooms, mosses, and lichens.

    And, also, I prefer the way they have “monetized” this app compared to the Garden Compass model. To wit:

    Bucks For Botanists

    With Garden Compass, plant identifications are “free” (limited to 20 per month, however), but you must provide them your location and device identification information (so that they can attempt to sell you other stuff).

    Wouldn’t it be better to simply pay (say, for example, a dollar) for each plant ID?

    This is the primary monetization model used by the Android app I’ve been talking about, which is:

  • FlowerChecker

    FlowerChecker is a free (to install) plant identification app for Android devices (not yet available for iPhones and iPads, but they are working on it – from an email I received from a member of the FlowerChecker development team on 6/20/2014: “The development of iOS app starts next week so that the betaversion is expected to be released in August or September. We have a waiting list for those who want to try a betaversion — http://www.flowerchecker.com/waiting-ios (we’ll send them e-mail when it is finished)“.

  • According to the FlowerChecker website:
    This app provides plant identification service. You simply take a picture of an unknown plant (or moss, lichen and even fungi) and get it identified by international team of experts.
    The identification process is not computer-based, it requires human involvement. Therefore each identification is paid using Google’s in-app purchase. One plant identification costs 1 USD / 0.7 EUR. If we can’t identify your plant, you don’t pay anything.
    Everybody gets one identification for free as a trial.
    Our team will respond as soon as possible, but the identification usually takes minutes or hours. So far, we have been able to identify 90% plants in average.

    Please Note: Before installing the FlowerChecker app on your Android device, you should be aware that, like Garden Compass, this app can access personal information on your device, including location. (Of course, you should always carefully read the capabilities of any app before you install it on your device.)

    Anyway, I was OK with all this, and I installed the free FlowerChecker app on a Nexus 7 (2013 version), got my free identification, and prepaid for five more (prepaid, it’s $1 for one, $4.50 for five, and $15 for twenty identifications). By the way, according to an email I received from FlowerChecker, “the income is half-half divided between botanists and developers“.

    Thus, I sent FlowerChecker six different photos to test their identification skills – 3 garden plants, 2 wild plants & 1 mushroom.

    Untitled How did they do? All of the identifications were spot on.

    Briefly, here’s how FlowerChecker works:

    1. After installing and launching the app for the first time, you have one free identification credit to use.
    2. Select “New Request” and you’re then presented with a fresh screen allowing you (a) to ask a question, most commonly, “What is this plant?”, (b) to select a category, such as “garden plant”, “wild plant”, “mushroom”, etc., and (c) finally, to take a photo or to select one or more photos from your “Gallery”. (Please see here for a series of screen shots.)
    3. After you submit your request, the FlowerChecker team will process it within 24 hours.
    4. Nice Feature: Unlike Garden Compass, all of this occurs within the FlowerChecker app rather than via email.
    5. After a few hours, check back with your FlowerChecker app, and the team most likely will have processed your request and identified your plant. You don’t pay unless you accept, and, if so, then your request is marked “Resolved”.

    Two Thumbs Up (Way Up!) For FlowerChecker

    If you are looking for a plant identification app for your Android device, I highly recommend
    FlowerChecker.

    I found that their identifications were both accurate and delivered within the time they promised.

    However, as I didn’t have them try to identify any lichens or mosses, and only one mushroom, I can’t vouch for their competence in identifying these categories of “plants”.

    But, based on the positive feedback for this app posted on the Google Play store, I’m confident that the FlowerChecker team can do about as well as one could expect.

    Please keep in mind that even the best botanists can only go so far in identifying plants from merely pictures. Frankly, I’m amazed how well the FlowerChecker team did in my cases, considering that all they had to go on were my crappy photos.

    It’s said that “actions speak louder than words”. So, perhaps my most sincere endorsement is that, after using the FlowerChecker app for this blog post, I purchased 20 more identifications for $15.

    Personally, I prefer paying developers and botanists directly for their services, rather than indirectly, via advertising.

    Finally, as previously mentioned, can providing employment for botanists (and developers) be a bad thing? I think not!

    Disclaimer: I receive no financial remuneration or any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    IMG 0097What’s That Plant?

    Though I’m very interested in plants, I’m terrible at identifying plant species and remembering plant names. (That’s probably why I’m a plant physiologist.) I’m pretty sure there are other folks reading this blog that also have this “problem”.

    For people like us, wouldn’t it be great if we could take photos of plants with our smartphones or tablets and have an online botanist or horticulturist identify the plant for us? (Dream on, right?)

    But it’s not a just a dream, it’s now a reality. There are at least a couple of remarkable apps available that may help you to determine a plant from your photos.

    First up:

  • Garden Compass

    One app that I’ve recently used is Garden Compass (Compatible with iPhone, iPad, and iPod touch and requires iOS 6.0 or later. This app is optimized for iPhone 5.)

    To visit the Garden Compass website, click here, and to watch a 90-second video about this app, please click here.

  • Here’s the way it works:
    (1) After installing the app, you can take a photo inside the app or select a photo from your camera role. (Note: The first time you use the plant identification function, the app asks your permission to access your camera role. The app may also ask you to turn on location services under the “Privacy” settings on your device – this turns on the GPS.)
    (2) Once you snap a photo or select a picture from your camera roll, a text box appears below the photo to allow you to add comments about the plant.
    (3) When you touch the “send e-mail” button, the app will likely ask you for permission to use your location. (This, I presume, is mainly to help them ID the plant. But I notice that after you send e-mail, the app asks you if you want to see closest garden retailers in your area. So this is likely part of how they make money. More about this below.)
    (4) If you are okay with the app using your location, then you are redirected to your e-mail app where you can see/edit your draft e-mail message before you send it to Garden Compass. (I noticed that not only is your geolocation included in the e-mail but also your device ID.) If you’re cool with this (I didn’t mind), then touch “Send” and your e-mail message blasts off into the “cloud”.
    (5) If Garden Compass has received your e-mail message, you will receive e-mail confirmation within a few minutes. They also tell you what position you are in their queue. (The times I used Garden Compass, I ended up with 500 to 600 people ahead of me.)
    (6) Despite the long line ahead of me, I received e-mail messages from Garden Compass with my plant identifications in under 5 hours. Each was spot on.

    Two thumbs up for Garden Compass

    I must say I was pretty impressed with the Garden Compass app, and I didn’t even use all of its features. In addition to garden plant ID, they also provide a “Problem ID” service. This is to help you identify plant diseases or plant insect pests. Since I didn’t use this feature I can’t comment on its accuracy.

    I also can’t comment on how well this app works on the identification of wild plants. I presume their aim is mostly restricted to domesticated plants.

    Since this app is free, you may be wondering how they monetize it. Well, along with providing you plant information, they also facilitate you buying stuff, mainly from them. This app is part of a larger venture called Garden Compass that you can read about here.

    Perhaps the Garden Compass app is a marketing strategy for the Garden Compass online store. If so, it may be a brilliant one. My hat’s off to them, because, in my experience, this app delivers accurate garden plant IDs within several hours…for “free”. (Yes, you do provide them your information, however, and photo submissions are limited to 20 per month.)

    But can providing employment for botanists and horticulturists be bad? I think not.

    Next Time: Another plant identification app…for Android devices.

    Disclaimer: I receive no financial remuneration or any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    There’s An App For That?

    I can’t believe it’s only been seven years since the iPhone was first introduced by Steve Jobs in 2007 and only four years since Jobs introduced the iPad.

    Since then, hundreds of millions of iPhones and iPads have been sold, and dozens of other types mobile-computing devices with cameras have been developed and sold in the millions.

    And as you can see if you cruise through the iTunes App store or through Google Play app store, software developers have been busy filling virtually every imaginable niche with computer applications for your smartphone or tablet.

    Among these hundreds of thousands of different apps are some that are botany related. What I’d like to do is offer you a sampling of some of my favorite plant-related apps.

    (Please Note: This is NOT a comprehensive list of plant-related apps. And most of such apps I’ve used are for North America (particularly the U.S.) because that’s where I live. There are lots of other botany-related apps out there, which you can find by searching online, including the various app stores.)

    OK. Here we go……

  • leafsnap
  • Way back in 2011, I scribbled a post about one of the earliest botany-related iPhone apps leafsnap.

    Well, leafsnap is still available (requires iOS 4.2 or later. Compatible with iPhone, iPad, and iPod touch), and it’s only gotten better.

    (And now there’s even a version for our friends in the UK, named, appropriately, leafsnap UK.)

    Simply put, leafsnap helps you identify trees from snaps (photos) of leaves that you take with your smartphone or tablet.

    Leafsnap works by using technology similar to facial-recognition software, by matching a simple photograph of a leaf against a database of tree species.

    Perhaps the best place to go in order to understand and to use leafsnap is Leafsnap: An Electronic Field Guide.

    According to the leafsnap website and iTunes app store: “Leafsnap currently includes the trees of the Northeast and will soon grow to include the trees of the entire continental United States.

    Did I mention that leafsnap is a FREE app?

  • HighCountry Apps

    Slide 1If you live in the Western United States or plan to visit there this summer, and you’re interested in electronic field guides of the wildflower kind for your smartphone or tablet, you should probably check out HighCountry Apps.

    These folks provide wildflower field guide apps not only for the major national parks such as Yellowstone, Glacier and Yosemite, but also for the states of Idaho, Colorado and Washington.

    Newly added for 2014 are apps for the wildflowers of Oregon state and also for the grasses of Montana. (I suspect my former colleague Prof. Matt Lavin may have had something to do with the Montana grass guide.)

    I’ve used their Washington state wildflower guide app, and I think it’s great. (But don’t take my word for it. Check out the many positive reviews on their website and the various app stores.)

    Most of the Highcountry apps cost $7.99. All of them work on iPhone, iPad, and Android devices, and many of them also work on the Kindle Fire.

    Quoting from their website: “High Country Apps is dedicated to developing applications that deliver high quality natural history information with an intuitive, easy-to-use interface. Our goal is to enable discovery! We present information in simple, non-technical language that will delight and empower the rank amateur who loves the outdoors and wants to learn more. Yet we are also meticulous about creating scientifically accurate apps, thus making them excellent tools for serious biologists.”

    Disclaimer: I receive no financial remuneration nor any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

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  • Plant “Extremophiles”?

    Recently, I was reading about a new species of metal-eating plant discovered in the Philippines, and I discovered a new word (to me, at least).

    This new word is “extremophyte“.

    Simply put, most extremophytes are plants evolutionarily adapted to thrive in highly stressful environments. Physically stressful, that is, such as extremely high or low pH soils, very high or very low temperatures, highly saline soils, or geochemically toxic soils (think heavy metal… no, not Metallica…. heavy metals such as lead or mercury). I think these plants are more commonly referred to as “plant extremophiles”.

    Extremophiles = living organisms that “love” extreme environments.

    Perhaps a more precise definition of “extremophiles” would be: organisms, primarily microorganisms, that have evolutionarily adapted to extreme physical conditions, such as extremely acidic or alkaline pH, boiling hot temperatures, subfreezing cold, high concentrations of toxic compounds (think arsenic), etc.

    In other words, these organisms survive, even thrive, under physical conditions that would be lethal to most other living organisms on Earth.

    Anyway, back to the extremophytes….

    A New Name For Weird Plants?

    A search for the term “extremophyte” on Google Scholar revealed that it hasn’t been used in the scientific literature very much, and most instances of the word occurred after 2004.

    Google the word “extremophyte”, and some pretty interesting results pop up, especially Dr. Neal Stewart’s Weird Plant Genomics webite.

    Dr. Stewart is interested in two kinds of unusual plants, primarily from a genetic standpoint. According to his website, he is interested in (1): “plants that produce novel proteins and metabolites (but not drugs, which is another part of the project). The discovered genes can subsequently be used in genetic engineering and synthetic biology.” and (2) “plants with novel properties and behaviors. The genes novel to fascinating plants that do uncommon things will be excellent teachers…

    To see a partial list of Dr. Stewart’s unique plants, please click here (PDF).

    One of the most interesting plants on his list is Dictamnus alba, the so-called “gas plant” (see the YouTube video below)

    As exemplified by Dictamnus alba, some of Dr. Stewart’s “extremophytes” are not necessarily adapted to extreme environments, but are simply “plants that do uncommon things”. However, most research interest seems to be on the extremophytes adapted to stressful environments.

    Weird Plants = Weird Genes?

    The chief rationale for genetically sequencing “extremophytes” is to discover novel genes that may help genetically engineer crop plants to be more stress-tolerant.

    …extremophytes [may] have more activated forms of genes or gene products that function in tolerance;…” and “We will not be able to determine the genetic bases of those specialized mechanisms without effective extremophyte genetic models.” (from Ref. 1 below; see also Ref. 2)

    References

    1. Inan, G., et al. (2004) “Salt Cress. A Halophyte and Cryophyte Arabidopsis Relative Model System and Its Applicability to Molecular Genetic Analyses of Growth and Development of Extremophiles.” Plant Physiology, Vol. 135, pp. 1718-1737. (Full Text)

    2. Amtmann, A., H. J. Bohnert, and R. A. Bressan (2005) “Abiotic Stress and Plant Genome Evolution. Search for New Models.” Plant Physiology, Vol. vol. 138, pp. 127-130. (PDF)

    HowPlantsWork © 2008-2014 All Rights Reserved.

    Helix cloud contrail spotted near moscow russia december 24 2012 2A DNA Cloud?

    In the recent (and brilliant) Richard Powers novel Orfeo, composer Peter Els attempts to encode a digital rendition of one of his musical compositions into a strand of DNA, then splice it into the genome of a living cell. This, he hopes, will perpetuate his music for all eternity.

    Science fiction?

    Maybe not….

    In January, 2013, a multidisciplinary study in synthetic biology demonstrated a system for the DNA-based storage of digital information. (see Ref. 1 below)

    The project, led by Nick Goldman of the European Bioinformatics Institute (EBI) at Hinxton, UK, marks another step towards using nucleic acids as a practical way of storing information — one that is more compact and durable than current media such as hard disks or magnetic tape.” (From: Synthetic double-helix faithfully stores Shakespeare’s sonnets.)

    Researchers have already developed software that makes it “easy” to store digital data on DNA.

    DNAcloud: “A Potential Tool for storing Big Data on DNA.

    From the DNAcloud website:
    “…we have been able to develop a software called ‘DNA Cloud’ that can convert the data file to DNA and vice versa. You can send the output to any biotech company and they will send you the synthetic DNA that you can store in your refrigerator.
    The software ‘DNA Cloud’ will encode the data file in any format (.text, .pdf, .png, .mkv, .mp3 etc.) to DNA and also decode it back to retrieve original file. Enjoy the software by storing your Facebook data or your video in synthetic DNA.
    DNA Cloud has been developed for the sole-purpose of generating a user-friendly, interactive environment for users to envisage their DNA data storage.

    Goldman, et al. (Ref. 1 below) encoded 5.2 million bits of information (equivalent to 739 kilobytes of hard-disk storage) into DNA, which is not very much data compared to the gigabytes you likely have on your computer’s hard-drive. But, of course, these are “early days” in field of DNA data storage.

    Currently, a major obstacle to storing more data on DNA is the cost. “With negligible computational costs and optimized use of the technologies we employed, we estimate current costs to be $12,400/MB for information storage in DNA and $220/MB for information decoding.” (From: Ref. 1 below) It’s likely, however, that these costs will decrease by orders of magnitude within the next decade.

    Plant DNA as Self-Replicating Digital Hard-Drive?

    Goldman, et al. (Ref 1 below) envision the long-term (millennia) storage of “digitized” DNA will likely occur in the form of isolated, freeze-dried or “solid-state” DNA, stored in a “…a cold, dry and dark environment (such as the Global Crop Diversity Trust’s Svalbard Global Seed Vault….)”.

    Rather than plastic vials, could living seeds – even living plants – be used as the receptacles for this “digitized” DNA?

    Once cost is no longer an obstacle, then it may be possible to routinely insert “large chunks” of DNA (e.g., about a million base pairs) and even small chromosomes (see Ref. 2 below, for example) into plant cells.

    Genomes of some higher plants are huge–tens to hundreds of billions of bases. So why the heck does it take a genome thirty times the size of yours and mine to make a trumpet lily plant? Most people believe it’s simply because there’s a colossal amount of junk DNA in the plants (and amphibians) with these enormous genomes. If these organisms have no problem carrying around all that excess baggage in the nuclei of their every cell, there’s no reason we can’t add a little more of our own devising.” (From: Ref. 4 below)

    Maybe someday digital information will be stored in part of the DNA of genetically-modified Bristlecone pine trees, which could potentially live for over 5,000 years.

    To archive digital records of human activity in the genomes of plants that may propagate for thousands, even millions, of generations – perhaps long after humans are gone – certainly captures the imagination.

    Online Resource

  • Video – Information Storage in DNA (From: Wyss Institute, Harvard University; see also Ref. 3 below)

    References

    1. Goldman, N., et al. (2013) “Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.” Nature, Vol. 494, 77-80 doi:10.1038/nature11875. (PDF)

    2. Gaeta, R. T., R. E. Masonbrink, L. Krishnaswamy, C. Zhao, and J. A. Birchler (2012) “Synthetic chromosome platforms in plants.” Annual Review of Plant Biology, Vol. 63, pp. 307-330. (Abstract)

    3. Church, G. M., Y. Gao, and S. Kosuri (2012) “Next-Generation Digital Information Storage in DNA.” Science, Vol. 337, p. 1628. (Abstract)

    4. Walker, J. “Storing data in DNA.” (Full Text)

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  • Biocoder 2014spring 286x430DIY Plant Biotech

    It’s been over three years since I first explored the field of do-it-yourself plant biotechnology in a blog post entitled DIY Plant Genetic Engineering?

    Since then, interest and activity in DIY biotech has grown. For instance, please see a more recent blog post on the subject Bio-Hacking Plants?.

    You can also read about this subject in Chapter 8 of my e-book Plant Trek.

    And now, thanks to O’Reilly Media, there is even a quarterly newsletter on this interesting and timely subject.

    As described on their website, BioCoder is the newsletter of a “biological revolution“.

    “What revolution?”, you may ask.

    Well, according to O’Reilly: “We’re at the start of a revolution that will transform our lives as radically as the computer revolution of the 70s. The biological revolution will touch every aspect of our lives: food and health, certainly, but also art, recreation, law, business, and much more.”

    In the Winter 2014 online issue of BioCoder there are a couple of chapters regarding plant biotechnology. One is called “Molecular Tools for Synthetic Biology in Plants”, and the other has the fascinating title “How We Crowd-funded $484k to Make Glowing Plants”.

    If you’re curious about this subject, you surely should check out BioCoder.

    And one of the coolest things about this newsletter is that it’s FREE.

    Thanks O’Reilly!

    HowPlantsWork © 2008-2014 All Rights Reserved.

    Signature Scents of Death & Decay

    In a previous post, we explored the discovery that plants emit a wide array of volatile organic compounds (VOCs) and that, because of this, sometimes plants stink.

    But I think few would argue that the prize for the “stinkiest” plants would have to go to the “Voodoo Lilies” and “Corpse Flowers”.

    Indeed, if you wanted to create perfumes for zombies, you probably could not find better ingredients than extracts from “Voodoo Lilies” or “Corpse Flowers”.

    This is because these flowers produce what has been described as “the signature scents of death and decay”. Their odors are most often compared to the putrid smells of decaying flesh or rotting meat.

    My current favorite description of a Voodoo Lily smell is: “Dead mice. For a couple of days. In a plastic bag that you then open up and take a whiff.” (from livescience.com)

    (Of course, zombie perfumes already exist – see here and here, for example. The American Chemical Society even has a YouTube video on “Eau de Death”. Interestingly, its ingredients include chemicals called putrescine and cadaverine, both of which are polyamines that may have hormone-like biological activity in plants – more on this later.)

    A Voodoo Lily By Any Other Name Would Still Smell as Bad

    Although several plant species sometimes wear the moniker “voodoo lily”, they all have at least two things in common – (1) their flowers smell like rotting flesh or feces (2) they are all members of the plant family Araceae.

    Both an online and a scholarly search revealed that several plant species are often referred to as “Voodoo Lily” (though none is classified by botanists as a true lily):

  • Sauromatum guttatum & Sauromatum venosum appear to be the most common examples in the scientific literature. (And are you ready for the taxonomic synonyms of these species? Here they are: Arisaema venosum, Arum venosum, Arum sessiliflorum, Desmesia venosum, and Typhonium venosum)
  • Dracunculus vulgaris has several common names, including “Voodoo Lily”.
  • Several species in the genus Amorphophallus have also been called “Voodoo Lily”.
  • Though many of the Voodoo Lily flowers may smell like a rotting corpse, the flowers of two other plant species Amorphophallus titanium and Rafflesia arnoldii appear (to me , at least) to most commonly share the title “Corpse Flower” (a.k.a., “Carrion Flower”).

    For neither “Voodoo Lily” nor “Corpse Flower” was I able to identify the originators of these common names. (Dear Reader – Please feel to jump in with a comment if you happen to know.)

    Why Do “Voodoo Lilies” and “Corpse Flowers” Smell So Bad?

    If you think that the main reason these flowers produce fragrances reminiscent of rotting meat or feces is to attract some insect pollinators, such as flies and scavenger beetles, you’d be correct.

    In a previous post entitled “Death and Pollination”, we saw how not only voodoo lilies but also other flowers, such as orchids, mimic the smell of carrion, which may attract a certain subset of potential pollinators. Such pollinators, especially flies, are also attracted to certain mushrooms, such as the Stinkhorn mushrooms (including the species Phallus impudicus), which also produces odors mimicking carrion or feces. (Since mushrooms are the sexual fruiting bodies of these fungi, the flies help disperse fungal spores.)

    An interesting evolutionary question is: Do diverse plant species, as well as some fungal species, use the same or similar scents of carrion or feces to attract the same type of pollinators/spore dispersers, namely, flies? And could this be an example of convergent evolution ?

    Some recent evidence seems to indicate that the answer is yes. For example: “We found that scents of both the fungus and angiosperms tended to contain compounds typical of carrion, such as oligosulphides, and of faeces, such as phenol, indole and p-cresol.” (From Ref. 1 below)

    Funghi (CC BY 2.0) by macinate

    A Stinkhorn Mushroom Funghi (CC BY 2.0) by macinate

    This was in general agreement with a previous study: “The odour released from the flower of the voodoo lily Sauromatum guttatum Araceae and the odour of the mushroom Phallus impudicus Phallaceae were analysed. The two species had the major constituents dimethyl disulphide and dimethyl trisulphide in common. Other major components of the S. guttatum excretion were β-caryophyllene, dimethyl sulphide, dimethyl tetrasulphide, indole and skatole. Linalool, trans-ocimene, and phenylacetaldehyde were released by P. impudicus.” (From: Ref. 2 below)

    So, the biochemical answer to the question: “Why do “Voodoo Lilies” and “Corpse Flowers” smell like rotting meat?” is mainly because they produce sulfur-containing organic compounds, in particular dimethyl disulphide and dimethyl trisulphide, as mentioned above. But these flowers also produce other volatile organic compounds that add to their appeal to certain flies and beetles.

    Though the precise nature of the chemicals responsible for the smell of “Voodoo Lilies” and “Corpse Flowers” is a complex subject, it has been nicely summarized as follows: “…there appear to be two major odour types among sapromyiophilous [pollinated by dung flies] Araceae: carrion smells (mainly oligosulphides) and dung-like odours (complex scent profiles with p-cresol, indole, 2-heptanone and others). Other aroids with distinct odours were generally dominated by one or two compounds, for example fish-scented species by trimethylamine and ‘cheesy’ pungent smelling species by isocaproic acid. (From Ref. 3 below)

    By the way, another reason that some “Voodoo Lilies” and Corpse Flowers” smell so intensely bad is that part of the flower may actually heat up in order to promote the volatilization of these foul-smelling organic compounds. (This subject was explored a bit in a previous post.)

    References

    1. Johnson, S. D. and A. Jürgens (2010) “Convergent evolution of carrion and faecal scent mimicry in fly-pollinated angiosperm flowers and a stinkhorn fungus.” South African Journal of Botany, Vol. 76, pp. 796–807. (Abstract)

    2. Borg-Karlson, A.-K., F. O. Englund, and C. R. Unelius (1994) “Dimethyl oligosulphides, major volatiles released from Sauromatum guttatum and Phallus impudicus.” Phytochemistry, Vol. 35, pp. 321–323. (Abstract)

    3. Jürgens, A., S. Dötterl and U. Meve (2006) “The chemical nature of fetid floral odours in stapeliads (Apocynaceae-Asclepiadoideae-Ceropegieae).” New Phytologist, vol. 172, pp. 452-468. (Full Text PDF)

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