Ferns have it made in the shade

Here's a great bit of research just reported by my colleague Emily over at the No seeds, no fruits, no flowers: no problem blog.  Everyone knows that ferns grow well in the deep forest shade, but this is no easy trick because that leaf canopy overhead captures most of the sunlight, especially at the blue end of the spectrum. Ferns have a neochrome pigment that allows them to use both red and blue light more efficiently.  This isn't news in and of itself, but the real news is that the gene for this pigment comes from a hornwort (image by Jason Hollinger, Wikimedia Creative Commons), a little bryophyte that may represent the basal lineage of living land

plants. Ferns are not a direct ancestor of hornworts, and the two lineages would have diverged over 400 million years ago, and the molecular clock would put the date at which ferns acquired these genes at less than 200 million years ago.  How did they do that?  The unsatisfying answer is that we don't know. This transfer of whole genes seems to happen way more commonly than biologists thought and the hypothesized mechanism is called horizontal gene transfer, basically nature's own GMOs.  But no one knows how it happens!  Maybe a virus does it?  This genetic event really allowed ferns to adapt to the understory of gymnosperms and then angiosperms, so it's a big event in fern evolutionary history.  Here's a nice news account of this research from the Economist (link also provided by Emily)((TPP only gets the Economist to read after his wife is done with it at her office, so he's behind.)).  Go ahead compare this science article to whatever news periodical you read.   

Need help understanding photosynthesis? This may help.

Here's some help understanding photosynthesis in the form of a graphic comic book starring a super hero scientist.  TPP will have to get a copy and see how it does, but it wouldn't have to be too good to be better than most pre-college biology books.  College biology books suffer from another problem, too much information and detail obscures a more general understanding.  If someone has read this, let us know how it is.

Death by crazy and willful ignorance

There's crazy, and then there's stupid crazy, and the latter can result in your death.  Now you can be crazy and put a gun to your head, or you can be like this lady and kill yourself ever so slowly.  A crazy lady named Navenna Shine, or Moonbean Butterfly, or Feelgood Featherweight, or something similar has this idea that she can live on just water, light, and air.  Wow!  Nuclear grade stupidity on display right there!  Guess what city she's from?  If you don't get Seattle in three guesses then you don't know much about where goofy new age thinking is concentrated.  Read a basic biology book, lady, concentrate on the differences between autotrophs and heterotrophs, producers and consumers.  Lady, autotrophy requires some metabolic machinery you ain't got, not to mention the pigmentation.  So here's the results of your "experiment" accurately predicted: you'll starve to death; you aren't living on air, water, and light, you're just dying very slowly.  With enough will power and stubbornness you will die, and probably get a listing in the Darwin awards except you look to be beyond your reproductive prime so you may have passed the genes for your particular intellectual gifts on to offspring already.  OK this "news" was in the HuffPo, but the news article fails to deliver this message as if there were some small chance she might just pull it off.  In all probabilty the communications major that wrote the article didn't understand that part of Bio 101. Why is this much crazy stupidity news at all?  Is it mildly amusing that this lady has decided to ignore everything known about biology and thus endangers herself?  Sometime a very long time ago, a cyanobacterium destined to become food for what was probably a amoeboid organism survived, entered into a symbiotic relationship with its consumer converting a heterotroph into an autotroph.  Humans last had a common ancestry with this lineage a couple to 3 billion years ago.  Here's the only truth there is.  Us heterotrophs need premade organic molecules for raw materials and energy, and their only source is from other organisms.  Get real, lady, or get help.  You crazy! 

Exobotany, Astrobotany, Alien botany

A couple of weeks ago a discussion of alien biology asked if life was found on other planets would some of it be plants? A reasonable question, and there are reasons why biologists would expect photoautotrophs and why any such organisms of any size would have some similarities to plants, but the more intriguing question was would they be green?
Plants, or more correctly, photoautotrophs on other planets may well be green, but not necessarily. Different stars have different light quality just as incandescent and fluorescent bulbs each produce a different spectrum of light, and neither are the same as sunlight. Perhaps you’ve noticed that plant grow lights, light bulbs designed to produce a spectrum of light more like the sun, look sort of reddish to us. So the spectrum of light may be such that a non-green pigment would work fine. If there is life on a planet, it needs energy and the only three sources that make any sense are geothermal, geochemical, and light, and organisms using all three types of energy can be found on Earth. Geothermal and geochemical energy sources are quite site specific in comparison to light, and so photoautotrophs are common on the surface of our planet, although most of them are unicellular so not plant-like at all. The geochemical autotrophs are probably wide spread too deep within the Earth's crust (they're every where we look).
You probably realize that the “visible electromagnetic spectrum” is a very small portion, a narrow band of wavelengths, and perhaps you wonder why out of all those wavelengths plants just use the portion that we see. Is this some kind of cosmic coincidence or purposeful design? First, there isn’t just one visible spectrum; different organisms have sight adapted to seeing different wavelengths, e.g., bees and lots of other organisms see into the ultraviolet wavelengths and this is why flowers under UV light look different then when seen with just light visible to us. But in general no one would expect photoautotrophs to be using wavelengths of energy very much beyond the visible spectrum and the reasons are pretty simple. As you move up into the ultraviolet wavelengths they become energetic enough to damage many different organic molecules and lots of organisms have UV filters to prevent such damage. You wear sunblock to reduce damage from UV. At the other end of the spectrum infared wavelengths (heat) are beyond red, and except for those wavelengths closest to red, they are not energetic enough to be used by photoautotrophs although a geothermal autotroph is known to exist. Many organisms see this same range of wavelengths because these wavelengths are abundant enough and enegetic enough to be useful and not particularly harmful. So light sensing organs and photoautotrophy are adapted to using some of the same wavelengths, although not exactly the same. Any pigment that captures a useful amount of “light” energy could work, so photoautotrophs could be several colors: reddish-brown, blue-green, green, yellow-green, and that’s just here on Earth. An alien photoautotroph could be, but wouldn’t necessarily have to be, green. Green predominates because chlorophylls are more efficient than bacteriochlorophylls and work well under water, and since land plants have an aquatic ancestry, they acquired their green pigment from them.

Don't take air for granted

Whether you knew it or not, the oxygen in Earth’s atmosphere, which you probably think of as a life-giving gas, is actually the toxic metabolic byproduct of the particular type of photosynthesis found only in cyanobacteria (blue-green algae) and chloroplasts, which is actually one and the same place as any loyal reader of the Phactor knows.

All evidence tells us that life on Earth when Earth was young was a very different from what we think of today even if we try to avoid the bias inherent in having a big organisms perspective. Life on Earth is still mostly unicellular. All organisms were anaerobic meaning their metabolisms did not require free oxygen. Actually most “modern” metabolic machinery operates in the absence of oxygen too; what changed was the last step where oxygen became a handy place to stick a leftover hydrogen with the added benefit of changing toxic oxygen to harmless water.

New evidence has been reported that pushes the “origin of photosynthesis” back by some 750 million years to about 3.46 billion years ago. Hmm, ever the prescient biologist, the Phactor has been telling students for years that oxygen-generating photosynthesis began about 3.5 billion years ago, clearly on the basis of some pretty sketchy evidence, but clearly what those fossils implied was correct. And how long did it take to convert the Earth’s atmosphere? "Once cyanobacteria appeared in one area of the ocean, it probably took less than 10 million years to fully oxygenate the atmosphere and oceans." Translation: not very long at all.

Now I hate to niggle, but this is research does not provide evidence for the origin of photosynthesis, but only an earlier appearance of oxygen liberating photosynthesis. Both the green sulfur and green non-sulfur bacteria (chloroflexi bacteria) are also photosynthetic, but neither liberates oxygen. This requires a set of metabolic equipment only found in the cyanobacteria (and then, after some became intracellular slaves, in chloroplasts). Chloroflexi bacteria are arguably the most ancient lineage of living organisms, so there is good reason to think other forms of photosynthesis are older. Perhaps photosynthesis using chlorophyll was derived from bacteriochlorophyll, and some photosynthetic bacteria are capable of functioning in the “dark” by using infrared wavelengths.

Still we shouldn’t take oxygen for granted; you never can tell when some bacteria may go some bacteria may go bad. The picture at this link gives new meaning to “black smoker”.