Weekend follies, RNA-seq, Photosystem I, or the fate of ill-founded optimism at the hands of natural selection.

Please vote for one of the four topics listed in the title, the winner being our subject for the moment.  Well, we’re waiting…

Ok, the tally please… Oh my – this is special.  It seems we have a four-way tie.  Fine then, I will endeavor to weave a piece incorporating all four subjects.

Last week Chris Smaje (Small Farm Future http://smallfarmfuture.org.uk/?p=762   ) put up a fairly succinct review of several philosophical viewpoints he cares about.  In it he makes a statement without attribution or offer of evidence (which is not usual for Chris).   The remark caught me as potentially quite significant if true, so I quote:  “In most species, natural selection soon culls ill-founded optimism.”

Any ill-founded behavior is a likely target for natural selection’s ability to cull.  This might qualify as ipso-facto.  By this reasoning then, ill-founded pessimism should be similarly culled.  Ill-founded joyfulness, depression, mirth, misery, and a whole host of other outlooks or behaviors, if wrongly established, should quickly disappear.  But I’m not persuaded they’ve yet gone missing.  Perhaps ‘soon’ is the issue.  These ill-founded behaviors have not been exposed to selection’s culling power for a sufficient time.  Or, might ‘most’ be our crippling metric?  Certainly some species have culled ill-founded ways.  There are so many species one might borrow from the logic of the Drake Equation (  http://en.wikipedia.org/wiki/Drake_equation ) to argue that some species have likely succeeded.  But most?

I wanted to make this case in a comment on Chris’ blog, but in my haste I committed some unforgivable blogging faux paux and the comment vanished to some byte bucket.  I was hurrying as a weekend get-away lie ahead.  Philosophical disagreements still rank behind the opportunity to spend time with distant family.  Yes, ‘weekend follies’ refers to the trip.  The hills of East Tennessee and the hearth of a daughter, son-in-law, and their wee family beckoned.  Brian Miller was bailing hay, so I took my boots… but Knoxville didn’t seem to mind my presence.  I didn’t make it to Philadelphia (TN) – sorry Delores, maybe another time.

On Saturday morning we made it to the Knoxville Farmer’s Market.  Easily the nicest Farmer’s Market I’ve ever witnessed.  And this time we had clear skies… a beautiful day.  Joyfulness and mirth – springing from a proper foundation.  All culling avoided.

By now the scorekeepers among us are rightfully wondering where RNA-seq and Photosystem I fit in this tale.  And it’s not so complicated as their names might suggest.  Knoxville is a five hour drive from here.  I took the June issue of The Scientist and in particular the article by Kate Yandell comparing microarrays and RNA-seq.  I need more background on the strengths and weaknesses of these techniques and the article promised to assist.  It did help some.

RNA-seq is shorthand for RNA sequencing.  RNA is the molecular template from which proteins are manufactured in cells.  DNA might be the genetic code – but RNA is the messenger.  And we take it as a given you don’t shoot the messenger.  You do, however, sequence it.  Fascinatingly, one DNA sequence can give rise to different messenger RNA molecules.  Gene regulation also allows differing amounts of messenger to be made.  Gene regulation (of messengers) varies among different tissues and in response to varying environmental stimuli.  So merely decoding the DNA sequence doesn’t get you all the information about protein synthesis you might be looking for.  RNA-seq is another tool to help get closer to what is going on in the cell.

Photosystem I is part of photosynthesis – plants making food from sunlight, carbon dioxide, and water.  There is also a photosystem II.  These two photosystems comprise the light harvesting and water oxidation aspects of photosynthesis… the ‘photo’ part.   http://en.wikipedia.org/wiki/Photosynthesis

On the chance the article on RNA-seq wasn’t going to work for me I tossed the 29 May issue of Science in my bag as well.  The cover of this issue of Science has a computer generated image of what scientists now imagine photosystem I looks like.  When I was in graduate school, the existence of the two photosystems was still being worked out.  The biochemistry of the dark reactions (the Calvin Cycle) was fairly well understood.  The physics of light harvesting, at least as plants do it, is still being worked out thirty years later… though it appears we’re getting pretty close.  ‘We’ in this case are those scientists who do this kind of work.  I basically take their word for it.  I find it fascinating, and like to delude myself that I almost know what they’re up to.  Rocket science has nothing on this.

Later this year the temperatures will moderate and the hills of East Tennessee will begin to change hue from their current greens to a full pallet of reds, oranges, and yellows.  This transition will require changes in gene regulation modulated by RNA… something we now have tools to measure thanks to RNA-seq technology.  And those colors – the fall colors – will predominate because of the breakdown of chlorophylls in the two photosystems.  Thus leaving the carotenoids to show their true colors.

All the summer’s photosynthesis will have produced grains and grasses, vegetables, timber and old used up leaves.  Brian Miller’s hay will keep his livestock over the coming winter.  Knoxville’s farmer’s market will showcase pumpkins, winter squash, and seasonal trimmings.  I hope to make another visit, and if my optimism is just shy of ‘ill-founded’ I hope to be spared natural selection’s cruel culling.  At least for now.

Tags: Brian Miller, carotenoids, chorophyll, Chris Smaje, Photosynthesis, RNA, Weather