BS: DNA Knowledge Advance

Subject: BS: DNA Knowledge Advance
From: JohnInKansas
Date: 15 Nov 08 - 07:50 PM

Elusive microbe fertilizes oceans

[quote]

The single-celled critter has a very telling and surprising genome
By Larry O'Hanlon,
Discovery Channel
updated 11:03 a.m. CT, Fri., Nov. 14, 2008

After a long search researchers think they have found a cryptic microbe that helps fertilize ocean waters worldwide. Or at least they have found the single-celled critter's very telling and surprising genome.

The actual microbe — a type of bacteria known as cyanobacteria — has so far eluded direct observation

[end quote - check the link for the details]

The gist of this article is that scientists have been unable to actually find this little critter, so they gave up on looking for it and just mapped its DNA instead.

1. They think it exists (but aren't too sure?)

2. Nobody has ever seen it.

3. They think it's very important, and that life as we know it couldn't possibly exist without it.

4. And they now know a whole lot about it.

5. Except the still haven't actually found it.

Is it ? ... ? ... ***?

[The FSM isn't this mysterious.]

John

Subject: RE: BS: DNA Knowledge Advance
From: Ebbie
Date: 15 Nov 08 - 10:46 PM

Sounds like spirit!

Subject: RE: BS: DNA Knowledge Advance
From: Alice
Date: 15 Nov 08 - 10:52 PM

And the earth was waste and void; and darkness was upon the face of the deep: and the Spirit of God moved upon the face of the waters...

Subject: RE: BS: DNA Knowledge Advance
From: Amos
Date: 15 Nov 08 - 11:17 PM

Two things may both be mysterious without being equally real.



A

Subject: RE: BS: DNA Knowledge Advance
From: Desert Dancer
Date: 15 Nov 08 - 11:20 PM

The frontiers of microbiology have opened onto an unforseen universe through the use of pcr (the polymerase chain reaction - a surprisingly simple process that allows minute amounts of DNA to be replicated in the "test tube" so that it can be studied) and DNA sequencing.

Previously we could only study the bacteria that we could see and/or could grow in artificial conditions. By being able to scan for DNA, now we can see that there's much, much more out there... cyanobacteria ain't the half of it.

And, for MUSIC content: The PCR Song.

(For more info, see links here: links.)

~ Becky in L.A.
(but who works in Tucson in a microbial genomics lab -- my training is in vertebrate behavior; it's a whole different world...)

Subject: RE: BS: DNA Knowledge Advance
From: Uncle_DaveO
Date: 16 Nov 08 - 10:09 AM

Forgive my ignorance, but can someone explain to me how they can "map the DNA" for an organism that they can't find? And, I might suggest, which may not even exist, but, if there is an organism that fills that ecological place, may accomplish it in a different way than their hypothetical DNA sequence would dictate?

Dave Oesterreich

Subject: RE: BS: DNA Knowledge Advance
From: JohnInKansas
Date: 16 Nov 08 - 02:26 PM

DaveO -

Starting with a glop of sea water, a normal procedure would be to add a culture medium so that the critter you're looking for grows and multiplies, preferably faster than the other critters in your sample. Once you have enough of them to see them and play around with them, you add something to the soup to kill of "everything else."

The cyanobacteria, unfortunately, has been impossible to "culture" in this way.

On the assumption that it exists, and is in the sample, with the new DNA replication process(es), you can make selected DNA bits replicate to get larger samples of just the DNA "pieces."

The article doesn't give details, but it might be expected that the researchers have then "subtracted out" (probably via computer analysis) the DNA bits known to be parts of the "genetics" for any other organisms they found in the sample.

What's left over must have come from the cyanobactera.

(A problem not mentioned is how they decided what to do for the bits that may be in both the cyanobacteria and in other "organisms" that might have been in the sample; but other research has suggested quantative methods for estimating the probabilities - if they had a big enough computer.)

The value of what's (maybe) been done is that it revealed that the cyanobacteria (probably) lacks any photosynthesis mechanism, so light exposure (possibly) should be omitted from new attempts to culture it directly. It also (maybe) is adversely affected by oxygen, so an anearobic condition (perhaps) is needed. The results cited (appear to) confirm that genetic mechanisms exist (probably) in this critter for benefiting from lots of nitrogen.

The results, if confirmed, may suggest ways to actually "grow" the bacterium in question so that sufficient (and sufficiently pure) samples can be cultured. If that can be done, eventually someone may be actually able to "see" this particular varmint and learn what it can do.

Similar(?) nitrogen fixing organisms are found in soils, and my impression is that a little more is known about them. If enough can be learned about these sea-faring organisms, the vast areas of the sea suggest that we may learn ways to make them "healthier" so that more available nitrogen can stimulate the phytoplanktons that may help with CO₂ sequestering.

Present knowledge doesn't tell us how we can stimulate this critter, and of course the next (eventual) question will be whether we should try to help it along.

John

Subject: RE: BS: DNA Knowledge Advance
From: Bill D
Date: 16 Nov 08 - 03:27 PM

I expect they will soon discover that it comes in up, down, strange, charm, top & bottom.... and is made up entirely of Higgs Bosons.

Subject: RE: BS: DNA Knowledge Advance
From: JohnInKansas
Date: 16 Nov 08 - 04:06 PM

Nah Bill.

I don't think it's all that exotic, although perhaps it may have been hiding in a black hole.

If progress is made in stimulating its nitrogen fixing efficiency, someone will file a suit in international court(s) asserting that it's likely to suck all of the nitrogen out of the atmosphere, leaving only pure oxygen; and will demand an immediate ban on hammers lest someone hit an anvil, strike a spark, and cause the entire earth to be consumed in fire.

A counter suit will claim that the earth being consumed by fire is "God's will" and will insist that the organism should be worshiped and cultured as quickly as possible to hasten the end.

As soon as the microbe is identified and photographed, someone will find a potato chip that looks "just like the photo," and will sell it on eBay for $9.74 (US), but the chip will be broken in shipment and a law suit will ensue.

All kinds of quite ordinary progress could come from this one very basic research report.

John

Subject: RE: BS: DNA Knowledge Advance
From: semi-submersible
Date: 16 Nov 08 - 05:52 PM

This DNA-finding technology is a powerful new way to look at what's around us. I heard recently that this technique has shown, for instance, DNA of the fungal kingdom being part of the community of life in sea floor sediments!

Since molds, yeasts, and other fungi normally grow either as solitary cells or in networks of fragile microscopic threads (some of which occasionally build themselves great skyscrapers called mushrooms to catch breezes or attract animals to help spread their spores) I don't see how we ever could have found delicate marine fungi by looking, even with electron microscopes.

Subject: RE: BS: DNA Knowledge Advance
From: Richard Bridge
Date: 16 Nov 08 - 06:06 PM

You omit to mention that Ciba Giegy (or someone similar) will seek patent or plant varietal rights in respect of the organism and in exercise of such (or plant breeders) rights seek a worldwide injunction on anyone eating anything derived from or at any time living in the or transported by sea without paying them royalties.

Subject: RE: BS: DNA Knowledge Advance
From: Desert Dancer
Date: 17 Nov 08 - 12:29 PM

There are two other important parts of the process that I didn't mention: sequencing and bioinformatics.

How sequencing machines work I have not had to figure out. You can undoubtedly Google for more info... ;-) But, once you get your little chunks of DNA replicated by PCR, you can submit them to a sequencing facility and get the actual DNA sequence. To figure out a whole genome sequence, you send off lots of little bits, and then you spend a lot of time on the computer sorting out how those bits must fit together.

Then, once you have a decent sized chunk, you compare it to the sequences in the GenBank database -- a publicly accessible database of DNA sequence information. You can find out if it's entirely new, or a variation on something else that's out there.

Then there are ways of mapping these comparisons to make phylogenetic trees to see where your bit of DNA fits in the family (or doesn't).

There's lots of computer work, and a surprising amount of eyeballing the data. The people who do it are puzzle experts.

My understanding of it all is relatively superficial, but I hope this helps.

~ Becky in L.A./Tucson

Subject: RE: BS: DNA Knowledge Advance
From: Rowan
Date: 17 Nov 08 - 11:10 PM

Similar(?) nitrogen fixing organisms are found in soils, and my impression is that a little more is known about them.

Interesting!
It's a while since I was formally into all this stuff but my recollection is that all nitrogen-fixing. whether in root nodules of legumes or by free living organisms, involves cyanobacterial activity at some point. Most of the free-living organisms are species of cyanobacteria ("blue-green algae" in the older texts) but it would be interesting to see whether the current DNA analysis is of something independent and completely new or freed fragments of something that previously had an integral (if unknown) existence but has subsequently become disintegrated. It is reasonable to infer from the article that the source of the DNA is "single-celled" but I'm not yet sure they've eliminated "all the usual suspects"; so little is known at this level.

Cheers, Rowan

Subject: RE: BS: DNA Knowledge Advance
From: Paul Burke
Date: 18 Nov 08 - 03:25 AM

all nitrogen-fixing...involves cyanobacterial activity

Don't forget electrical fixing, that would have been the main source before life got going.

They probably need to look somewhere with low oxygen content to find these elusive beasticles- either in the seabed, or inside another organism.

Subject: RE: BS: DNA Knowledge Advance
From: The Fooles Troupe
Date: 18 Nov 08 - 09:20 AM

"more available nitrogen can stimulate the phytoplanktons "

Too much fertiliser run off is destroying the marine environment, especially The Great Barrier Reef anyway, and now we want MORE of this stuff loose?

Subject: RE: BS: DNA Knowledge Advance
From: JohnInKansas
Date: 18 Nov 08 - 12:04 PM

[16 Nov 08 - 02:26 PM] Present knowledge doesn't tell us how we can stimulate this critter, and of course the next (eventual) question will be whether we should try to help it along.

Too much of anything in the wrong place nearly always leads to disaster. Unwanted concentration in one place doesn't mean that other places don't have a need for more, or that we don't need to understand how all the parts of the system work in order to try to get the right resources in the right places and in the right amounts to make things work better.

John

Subject: RE: BS: DNA Knowledge Advance
From: Rowan
Date: 18 Nov 08 - 04:46 PM

Don't forget electrical fixing

Good point, Paul. Perhaps I should have included "biological" in my comment; John's original post and the thread title had 'focussed' my thought processes.

Cheers, Rowan