Another Explanation for Multicellular Life

DrJay writes "Hot on the heels of Slashdot's coverage of a controversial model for a viral origin of the multi-cellular branch of life, Nature has published an alternative model that has nothing to do with viruses. Ars Technica's science journal has the rundown on the differences between these proposals." From the Ars article: "It's funny that this proposal for the origin of Eukaryotes should hit the popular press at a time where Nature has just published a hypothesis regarding the formation of the nucleus that has nothing to do with viruses, but everything to do with parasites. The parasites in this case are molecular: Type-II introns. These DNA sequences exist in both eukaryotes and bacteria, where they can insert in the middle of genes without causing harm because they can undergo chemical reactions by which they remove themselves from the RNA messages the genes make."

Comments

Uh

[Proc6]

Well, there's someone that obviously doesn't know it's Friday afternoon.

Re:Uh

[vertinox]

Well, there's someone that obviously doesn't know it's Friday afternoon.

What? This is slashdot. Do you really think we'd actually go out on a Friday night?

Laymans terms

[Lord_Dweomer]

I am fascinated by all this stuff, but I am not a biologist, so I don't understand most of these terms and names for things...can anybody here possibly supply an analogy or put things in laymans terms? Or possibly link to some good "beginners" material on this subject?

Re:Laymans terms

[theredmenace]

Depending on how much you know, skip ahead: There are two kinds of cells. Prokaryotes (bacteria) and Eukaryotes ("higher" organisms... plants, animals, fungi, etc). Viruses are officially not considered to be alive, because as part of the cell theory, cells must be capable of replication, which they are not, they need other cells (hosts), just like prions (proteins that act in a viruslike fashion). The debate about the "life" of viruses rages on. This giant uber virus shows a lot of sofistication, perhaps suggesting that viruses had some other role to play. The original article suggests that viruses like the giant one in question could be the reason for the nucleus. The current belief is that certain organelles, specialized structures in the eukaryotic cell, arose from a more primitive cell injesting another cell, but instead of digesting it, forming a relationship with it. This is where chloroplasts and mitochondria come from (both of which are used to "power" cells). The first article suggests that the nucleus arose in a similar way, only what was enveloped was a virus. Additionally, that article says viruses have evolved the opposite way the rest of live has, by shedding excess DNA instead of adding to it. This other article says that the nucleus developed as a way to protect the DNA from "introns" that floated off of these newly aquired mitochrondria. Most of DNA, especially higher DNA, codes nothing. It is just there to "pad" the good stuff. When a protein is going to be coded for, the DNA unwinds, and the section is copied. The copy is made of RNA, a single strand (not a double helix), which is then translated into the protein. Before the translation though, the extra stuff has to be cut out, and it is. The extra stuff has markers to tell the cell where to cut it and where to stop and how to patch it all together. The stuff that is cut out is called INTRONS. The good stuff is called exons. The exons tell the protein what to be. Think of it as trimming the fat. Just like you can tell the difference between the good and the bad, and trim accordingly, so can the cell. From what I understand, the introns from the mitochondria had the ability to insert themselves in the DNA. This causes what is known as a phase shift. Basically, you have all these lines of code, and inserting a bunch of extra code somewhere in the middle screws up the ability to either find the gene, or if it actually gets translated anyway, the protein is non functional. The nucleus is a defence, it keeps the introns out by barriering itself in. Transcription of DNA (copying to RNA) occurs in the nucleus, and translation (RNA -> protein) occurs in the cytoplasm outside the nucleus. The two conflict with one another, but could in theory be integrated, but it's not too likely. I personally doubt the nucleus is a virus, the nuclear membrane isn't really the right material. The question is whether these scientists have actually FOUND these introns floating around attacking DNA or not. I can't access the full article.

Re:Laymans terms

[jd0g85]

"I am fascinated by all this stuff, but I am not a biologist, so I don't understand most of these terms and names for things...can anybody here possibly supply an analogy or put things in laymans terms? Or possibly link to some good "beginners" material on this subject?" I don't know about the layman, but here's a nerd explaination: OK, lets say you've got your source code. In your source code you've got comments. Comments contribute no information to the parser and are effectively wasted space (ok, it's an analogy, it's not perfect). Now lets say that your language parser is fast but isn't very good and comments tend to screw it up. Assume you had another program in your toolkit that could preparse the source code removing all of the comments. That would fix your troubles right? Yes, but this preparser is very slow. In order for the whole thing to work reliably, your comment remover needs to have a chance to finish before your language parser gets started. You need something thing in place to prevent your language parser for starting to early. Solution: files that need preparsing should reside in a different folder from the files that have been preparsed. Because this is a biological system, your parser and preparser both run constantly as cron jobs. This physical division between the two types of files prevents the parser starting to soon. What these researchers are suggesting is that it was the rapid increase in the number of introns (comments) by the mitochondria (let's just say a new manager was added to your project!) that made nucleus-cytosol compartmentalization (the folder system) necessary. Before there were so many introns, the mRNA splicing (preparsing) just happened to work well enough. As the number of introns increased, the compartmentalization became advantagous it prevented the translation (lanuguage parsing) from occuring on unfinished files. Try reading the abstract again: "The origin of the eukaryotic nucleus marked a seminal evolutionary transition. We propose that the nuclear envelope's incipient function was to allow mRNA splicing, which is slow, to go to completion so that translation, which is fast, would occur only on mRNA with intact reading frames. The rapid, fortuitous spread of introns following the origin of mitochondria is adduced as the selective pressure that forged nucleus-cytosol compartmentalization." Hope this helps!

Re:Laymans terms

[frenchs]

Keep in mind that in biology always has exceptions, so while the following will give you a basic background, it's NOT a textbook. See the links for some reasonable pictures to describe what I'm talkin' bout.

Central Dogma

• DNA is used to create RNA, which is used to create a amino acid chain, which folds into a Protein.
  
  
• Protiens are different from each other by their structure, which is detirmined by the sequence of amino acids which were assembled from the RNA sequence.
  
  
• RNA sequences are different based on the DNA sequence that was used to make them, and therefore encode different protiens based on the DNA sequence that we used to make them.
  
  
• (this is the important one) Structure = Function. The way that a protein is shaped directly influences what it does.
  

So if you follow back up the chain, DNA is responsible for creating protiens which perform biological and chemical functions. DNA->RNA->AminoAcidChain->Protein

http://www.accessexcellence.org/RC/VL/GG/central.h tml

Prokaryote/Eukaryote

Life is classified into two major groups, prokaryotes and eukaryotes. They fall into these two groups based on what kind of cells they have inside them.

Prokaryotic cells are simple, not a lot of really complex organization inside of them. Bacteria like E.coli fall into this group. Prokaryotes can do some cool things with the incorpration of foreign DNA (other cells, viruses, etc.) into their own DNA.

Eukaryotic cells are more complex, they have more "organized" inside them. The biologists call it "membrane bound organelles". Humans have eukaryotic cells.

http://en.wikipedia.org/wiki/Prokaryote
http://en.wikipedia.org/wiki/Eukaryote

Introns/Exons

Introns are what you hear referred to as "Junk DNA". However it's becoming apparent that this is the worst naming possible, as there are theories about it's presence being an activator for other processes which take place during DNA replication.

Exons are the sections of the DNA that are directly tranlated into the coresponding mRNA

Here is a DNA strand, the "E" are exons, and the "o" are introns.
EEEEEEEEEEEEooooooooooooooEEEEEEEEEEEEEEEEoooooooo ooooEEEEEEEEEE

Now here is the coresponding RNA, the ^ denotes a splice point where introns were removed. (This is what's used to create a given protein)
EEEEEEEEEEEE^EEEEEEEEEEEEEEEE^EEEEEEEEEE

http://en.wikipedia.org/wiki/Intron
http://en.wikipedia.org/wiki/Exon

Summary

So basically this article is saying that there are parasitic sequences of non-coding DNA which survive simply because they are in the DNA of a sequence which survived replication. But in eukaryotes, these "non coding" secions starting causing havoc in the cell and cause altered function.

Here is a analogy, albeit a tasteless one:

Imagine a room full of mimes (yes, mimes). Normally, they would sit there, pretending to be a box and not saying a word. Now imagine there is one mime that snuck a baseball bat into the room and started clubbing all of the other mimes in the knees. What do you think is gonna happen? Yep, they are no longer mimes.. they are now just angry dudes with white face paint on screaming at the top of their lungs.

Cells with DNA in them = Room of mimes
Parasite = baseball bat equiped mime
Havoc = clubbing knees
Altered Function = screaming instead of being mime-like

http://en.wikipedia.org/wiki/Mime_artist

Biologists, feel free to correct any gross errors here. However, I stand by my analogy.

-s

Re:Laymans terms

[Henge]

Actually, it's a misrepresentation to assume introns are 'parasitic.' There's a good amount of speculation these days that introns actually confer an enormous selective advantage on their bearers, because they could facilitate 'swapping' of exons between genes during replication in a way that permits new genes to arise. Imagine this scenario: Consider two hypothetical genes with exons "A,B" and "C,D" interspersed by introns "o" with some degree of sequence similarity. AAAAAAAAoooooooooBBBBBB and CCCCCCCCoooooooooDDDDDD during cell division, the genes are duplicated and some "crossing over" (that is, homologous recombination) occurs between strands in a way that is facilitated by similar sequence. As a result, one copy each of genes "A,B" and "C,D" swap exons and become "A,D" and "C,B" AAAAAAAAoooooooooBBBBBB X crossing over of homologous strands CCCCCCCCoooooooooDDDDDD Voila! You now have two new genes. Considering the fact that exons are often generalized as acting as discrete, independent units once they are translated into two proteins, you've created two new proteins with a potentially meaningful switcheroo in function. In this way, new proteins can evolve by swapping independent modules. So don't knock the introns.

Re:Laymans terms

[ScentCone]

Actually, that really did help. Now, see if you can do a NASCAR analogy, or a perhaps a WoW analogy. We've got to cover all our bases, here.

Re:Laymans terms

[rootEToTheIPi]

Mimes. Fucking brilliant.

Re:Laymans terms

[bigsmoke]

Is that you, Lord Havelock Vetinari, Patrician of Ankh-Morpork?

Re:Laymans terms

[Anonymous Coward]

If mitochrondria is "powerhouse" of the eukaryot cell, how did some alleged proto-eukaryot cell function BEFORE acquiring it? I mean, who is the subject in that relation, who got who?

Could it be that eukaryot cell is actually a tightly coupled colony of symbiotic "organisms" (in this case, organelas)? Perhaps, some prokaryots had weird asymetric binary fission that left small "daughter" cells inside the big "mother" cell (after DNA duplication, when denting of the cell membrane begins, if the direction of the movement of the "daughter" is for some reason reversed, she ends having double cell membrane around herself, inside her "mother") and gradually, over time, a specialisation of this little "daughters" gave meaning to this quirk.

So, my guess is, if this is how it happened, then it should be possible to be happening all the time, and there could be some "defective" prokaryot strain out in the wild that suffers from carrying around (a) "swallowed daughter(s)" with itself.

OTOH, eukaryot cell has at least two "tenants", of which one, mitochrondria, has its own "personality" (own genome). That is certainly an argument against above little theory, but it could be countered that from initial split selective pressure somehow favorised least interfering between the two, virtually keeping mitohondria shielded from much of the change that occured in "outer" cell.

Re:Dupe!

[Tackhead]

> Another 'origins of life' story... Dupe

If you've got proof it's a dupe, the folks at SETI would like to hear from you.

History, not science

[Expert Determination]

In a sense what's going on here is history, not science. We're not looking at generalisations, like physical laws, that can be repeated in a lab, but an event that happened once in our ancient history. It seems to me that it's a little futile to speculate on how cellular and multicellular life first appeared because the evidence was lost long ago.

Towards the end of the 19th century the main French and British linguistic societies banned any further papers on the origins of langiage because unprovable speculation was so rife. I can't help feeling we need the same thing here.

Re:History, not science

[hunterx11]

While we may never know, I do think this is a different situation. We can't really recreate the conditions under which language initially developed, but no doubt we will eventually be able to synthesize multicellular life.

Re:History, not science

[meringuoid]

We can't really recreate the conditions under which language initially developed, but no doubt we will eventually be able to synthesize multicellular life.

But that would only tell us one way that life might form: in a test tube in some nanotech-era laboratory. That's probably not how it actually got started on Earth (although YMMV, especially if you're from Kansas.)

However, I don't think it's a lost cause. The fossil record won't tell us anything here, but evidence may well come from the details of the cell's structure and genetics. A bit like how you can see marks on an old arch bridge showing where there was scaffolding used to build it - so you might find genetic traces indicating how eukaryote life, and then multicellular life, got their starts.

Re:History, not science

[hunterx11]

But that would only tell us one way that life might form: in a test tube in some nanotech-era laboratory

Still, it could be something like an incredibly precisely-controlled Miller-Urey experiment, rather than an direct fabrication of life (though that could very well be harder to do).

Re:History, not science

[jotok]

Sure, but even Miller-Urey could only give us a plausible explanation for how life could have formed. Experiments such as these really can't tell us the explanation, can they?

Re:History, not science

[Anonymous Coward]

It seems to me that it's a little futile to speculate on how cellular and multicellular life first appeared because the evidence was lost long ago.

Wrong. The evidence is all around is in the branches of life existing today. The challenge to us is how to best interpret it the evidence of our biological past.

It' wrong to say that science cannot make claims about past events. We can not only say definitely, for instance, that speciation occurs and that different species have common ancestors. Nowadays we can even place all of these species into their proper place in phylogentic trees, and estimate the time of their divergence, witha high degree of confidence. We can do this through comparative genomics, using the genomes of different species (i.e. evidence existing today), together with empirically observable rates of genetic drift.

Re:History, not science

[Anonymous Coward]

I think you are missing the point.

Yes, we can't demonstrate in some perfect sense that it must have happened a particular way, historically. But we can test hypotheses about how it could have happened, and potentially eliminate them, and that's all that is needed for it to be a scientific process.

For example, we can't duplicate the historical possibility that a huge asteroid impact caused the extinction of the dinosaurs and other creatures, and, if we were capable of repeating that event, we probably wouldn't *want* to anyway.

So, does that mean the question isn't open to scientific investigation? No. The physics of large impacts are reasonably well-known, can be modelled in fair detail, and we have smaller and more recent impacts and explosions with which to compare the products. The predictions are pretty clear, if such an event ever happened.

There are all sorts of ways to test the hypothesis: We can look for the crater, we can look for the impact melt (rock melted by the force of the impact), we an look for tektites (melt splashed out of the crater) deposited in a layer at the the time of the extinction, we can look for soot produced by the wildfires that would start as blobs of melted rock rained out of the sky and ignited the vegetation, we can look for megatsunami deposits (if it landed in the ocean), we can look for a spike in iridium abundance (iridium is much more abundant in asteroidal rock than terrestrial rock), we can look for the laminations in quartz grains that are associated with intense shock (from explosions or impacts), et cetera.

With these kinds of predictions, we can go out and look for evidence in the Earth's geology that will test the hypothesis that a large impact occured at the same time as the dinosaur extinction (or, for that matter, at other points in Earth history). Testing whether such an impact actually caused the extinction is a tougher question, and one that is still debated, but whether or not there was a large impact at that time is not really debated anymore -- the evidence is quite strong that a big one happened at that time (everything I've mentioned has been found).

The remoteness in time does make it more challenging to test things, but to insist that the event itself must be repeatable is an unreasonable requirement. There are all sorts of events that are not repeatable for practical reasons -- even very recent events. But scientists can independently repeat the *tests* and *observations* many times to verify them. That is what counts, not the event itself. Whether something happened in the lab last Thursday or back in the Jurassic doesn't really matter, except in terms of the practicalities. They are both "history".

If your versus of "history, not science" were accepted, the results would be perverse. Large swaths of what is conventionally regarded as science would be eliminated. I also hesitate to imagine what would happen to court cases without a personal witness to an event, but where the physical evidence consistent with its occurrence was extremely compelling. I think you misunderstand what aspect of "repeatability" actually matters to science.

Re:History, not science

[Moofie]

When was the last time a ban solved a problem?

Re:History, not science

[Expert Determination]

It' wrong to say that science cannot make claims about past events

I never said any such thing. But I don't think we can make accurate claims about a specific event that happened a few billion years ago - even with the wealth of genetic evidence we have today. The genomes we see today are like a palimpsest - they're been edited again and again through evolution. There's no reason to believe that there is any readable sign of the first cellular or multicellular organisms. Of course we can accurately order today's species into phyla using a variety of methods. But that's not what I'm talking about. I'm talking about an event in our deep past that will probably always be beyond reach.

Re:History, not science

[jafiwam]

No, they probably won't find the way.

However, they can no doubt rule out a lot of ways that might help get closer to the truth of what actually happened.

Re:History, not science

[Expert Determination]

Well it allowed linguists in France and Britain, at the end of the 19th century, to get more linguistics done, wasting less time on idle speculation.

Re:History, not science

[AJWM]

It seems to me that it's a little futile to speculate on how cellular and multicellular life first appeared because the evidence was lost long ago.

No, speculation -- coupled with observation and experiment -- is always useful. Even if we'll never know (without a time machine) how life did arise on Earth, knowing possible mechanisms helps both our understanding of biology as a whole as well as provides insights when looking for life elsewhere in the Universe.

Indeed, it's possible that life arose several times in Earth's history because the planet underwent some pretty severe planet-sterilizing (or perhaps just nearly so) events early in its history.

As for evidence being lost -- most of it has, yes, but there are still a few fossils around from as much as about 3.45 billion years ago, and there's some progression in complexity moving forward in time. Part of the problem was and is knowing what to look for and how to look for it.

Re:History, not science

[Jarn_Firebrand]

Yes, I mean, who cares if people want to think? If it's controvertial, get rid of it! And next, we can start burning the books!

Re:History, not science

[jc42]

I don't think we can make accurate claims about a specific event that happened a few billion years ago - even with the wealth of genetic evidence we have today. ... I'm talking about an event in our deep past that will probably always be beyond reach.

Well, maybe, maybe not.

But one thing is certain: If you refuse to speculate, hypothesize, or test ideas, then it will certainly always be beyond your reach.

And if it turns out not beyond our reach, someone other than you will solve the puzzle.

The history of science is full of example of things that were far beyond the reach of one generation, but a later generation was able to get the evidence. We've had several such "impossible" successes in the last couple of decades.

Re:History, not science

[bigpicture]

Ah, Ah, Ah, science can from the available physical evidence imply theories about the "process", the "how it happened", but they are still largely in the dark about the "cause", the "why it happened". Why do these micro organisms behave this way?

But if you look at insects that have been trapped in amber, that some say are 100 million years old. These don't look very much different from today's variety of the very same species. Is that not a strike against this "empirically observable rates of genetic drift."

Maybe they should compare the DNA and genomes of these 100 million year old life forms, to see if there is any drift at all.

Re:History, not science

[Profane MuthaFucka]

Science and history aren't exclusive. You can approach historical questions from a scientific perspective.

Re:History, not science

[MrFebtober]

That would be awesome, if DNA lasted that long. They're just now finding proteins that have lasted 67 million years, but DNA itself is a whole different matter, not to mention a complete strand. It's very likely that it doesn't really exist past 30 million years, if that. Besides, a lot of the critters in question aren't actually body fossils (except those in amber, like you said) - they're imprints in sediment or carbon films left over from a decaying body. Incredible detail, sure, but no actual tissue in which to even look for DNA. And it's amazing that we're finding such similar bugs in amber, but genetic drift occurs in different species at different rates, and sometimes may not occur at all.

Re:History, not science

[ScentCone]

Experiments such as these really can't tell us the explanation, can they?

True, but what they can do is illustrate to those that think there is only one (magic, devine) just-add-water explanation that they're simply, demostrably incorrect.

Re:History, not science

[Moofie]

Free expression is more important that the convenience of some academics.

If they couldn't separate idle speculation from well founded hypotheses, they weren't very good academics.

Re:History, not science

[ultranova]

While we may never know, I do think this is a different situation. We can't really recreate the conditions under which language initially developed,

Sure we can. We just need to bring up a bunch of people without ever talking to them, and watch them growl to each other. Of course it takes a pretty monstrous mindset to conduct this kind of experiment, but since the world seems headed towards another era of fascism, it is just a matter of time.

no doubt we will eventually be able to synthesize multicellular life.

I sincerely doubt that. The effort needed to develop this process is tremendous, due to the complexity of living organisms and the tendency of organic structures to degrade with the absence of life support systems of living cells. It may be doable in theory, but in practice it will always be easier to just take some already-existing lifeform and modify it to whatever you want, therefore making it very unlikely that any life-creation experiment would ever get the funding needed.

And in any case, even if you did manage to synthesize life, what would that really prove ? It just proves that life can begin in a certain way, not that it did began that way originally.

Re:History, not science

[ultranova]

True, but what they can do is illustrate to those that think there is only one (magic, devine) just-add-water explanation that they're simply, demostrably incorrect.

Um, if someone believes that life needs an intelligent designer to start, and you intelligently design a device which creates conditions where life can start and then turn it on and watch lifeforms come to be, how have you disproven the belief ?-)

Re:History, not science

[Anonymous Coward]

History IS some kind of science

Re:History, not science

[Ginger Unicorn]

the use of intelligence would be in figuring out what naturally occuring circumstances could generate this event.

you wouldnt be intelligently designing multicellular life. you would putting some single celled organisms in a particular environment and waiting for spontaneous evolution to multicelled organisms.

if that environment was one that can be shown to have occured naturally in the dim and distant past, you have demonstrated a convincing mechanism whereby single cells could have evolved into multi cellular organisms.

naturally, you wouldnt have proved that it DID happen, just that it isn't impossible, thus advancing the theory of evolution and eliminating the creationists' argument that its statistically impossible to have happened.

Re:History, not science

[Anonymous Coward]

That mind experiment with mimes looks like a good start in "origin of language" exploration...

The Red Queen.

[TrevorB]

The vector is different, but the mechanism is the same. Multicellular life fighting an endless arms race against parasites.

Anyone remotely interested in this discussion who has not yet read Matt Ridley's The Red Queen should try to grab a copy from their library.

More info on the Red Queen Hypothesis at wikipedia.

What about Lawyers & PHBs?

[Anonymous Coward]

What about Lawyers & Pointy Headed Bosses?
I've heard that they are, in fact, aliens and unicellular

Re:Meanwhile...

[Anonymous Coward]

...the religious explanation has gone untestable for thousands of years: God did it. QED

Fixed that for you.

Nahh...

[inode_buddha]

It was a mistake to come down from the trees, and the girls *still* wanted to be just friends. Prolly shoulda just stayed single-celled, it was a lot less hassle. Besides, no brain equals no pain.

Re:Nahh...

[Anonymous Coward]

Hey, thanks for giving me a good laugh at the end of a long week. Your post had me rofl. :)

Re:All we know is that we don't know.

[LordofEntropy]

Some terms and stuff for the laymen:

Eukaryotes are 1 of 3 domains of life in the current popular classification of life. The other 2 domains are Prokaryotes(single cell organisms) and Archaea(these tend to be the thermal vent/volcanic organisms, extremophiles.)

Eukaryotes are characterized by being mostly multicellular organisms(that is made up of more than 1 cell), and those cells have membrane bound organelles(think of little organs but for cells). Eukaryotic cells also have a nucleus which protects and regulates access to the DNA material. In the other domains the DNA is just floating around.

When the cell goes to make proteins, the blueprints are found in the DNA. When a template for a protein needs to be made, it is copied from the DNA, processed and then transported out of the nucleus to be further process into a protein, this template is called mRNA(messenger RNA).

In Eukaryotes you also find what is referred to as "junk DNA". Although this term isn't entirely accurate, this junk DNA is called such because no active proteins are made from the DNA sequences in this region. These non-coding regions are cut out from the template mRNA are called introns. The segements that are kept are called exons.

Basic rundown of some of the concepts the article refers to.

viral origin

[Anonymous Coward]

Did anyone else read this as "virgin oral"?

Well, we're here now so...

[Anonymous Coward]

... could somebody please just tell me which one we'll decide is the truth so I can begin beating it over the heads of the intelligent design crowd? Thanks.

Jargon explanation...

[Anonymous Coward]

The DNA in your genes isn't arranged in a static manner. It's constantly re-arranging itself- a fraction of it is used by the cell for turning genes on and off, and another fraction of it is caused by viruses and other invading entities. Not all the arrangements happen cleanly, sometimes chunks get left behind. Most of the genes in your cells are chock full of chunks like that, and are called introns. (Which can corrupt the reading of the information in the DNA)

Most of the DNA in the cell is wrapped in a fat and protein membrane. The whole bundle is called the nucleus. The idea mentioned in The Letter to Nature is that the nucleus protects the information carried by the DNA from getting corrupted. (and all the stuff that's stuck to it, like proteins and RNA).

I thought introns exist in Eukaryotes only..?

[Anonymous Coward]

Introns are noncoding regions of a gene, which occur only in Eukaryotes. Exons are coding regions. By the way, phylogenetic analysis done by people who sequenced Mimivirus genome (Science, 2004) placed Mimivirus in the Eukaryotic Domain, which questioned Mimiviruses ancient origin (although they mentioned this might not be 100% true...)

What the hell?

[autopr0n]

How is an interon a "parasite" They provide useful genetic services by providing alternative splice points in eukaryotes. Calling them 'parasites' is nothing more then bread-dead flabbergastating (which I am defining, here and today, to mean acting flabbergasted at things which are not at all flabbergasting)

Re:What the hell?

[Anonymous Coward]

But the alternative splicing effects likely developed after the introns were already there. So originally they could have been parasites and only later recruited for a 'useful' purpose.

Re:What the hell?

[espressojim]

I just saw a talk at MIT by a grad student who was looking at conserved sequences and repeat regions. Looks like he found a repeat region that actually provides regulation in the genome. That's sequence that was inserted by a 'genetic parasite' (repeats make copies of themselves in the genome), and wound up getting 'lucky' and taking on function. Once it took up useful function, it could be selected for, and the frequency of that repeat region could rise.

It blew my mind, because we always filter out things like repeat regions when we're doing analysis.

Oh, and if this makes it any more believable, I just had a paper published in nature genetics last month about Conserved Noncoding Regions under selective constraint...

huh?

[atheist666]

Does this article deal with the origins of eukaryotic cells? Or multicellular organisms? Because they are two different issues.

Re:huh?

[AJWM]

Offhand I can't think of a multicellular organism that doesn't comprise eukaryotic cells.

Sure, there are things that are colonies of prokaryotic cells, but those are recognized as organisms at the individual cell level, not the colony level. Do you have a counterexample?

Of course, there are plenty of single-celled eukaryotic organisms, and I think that's what the article is really talking about.

Re:All we know is that we don't know.

[KlomDark]

Please tell us more about BSD and Solaris. I didn't get enough in your other thread.

Reflections

[gidds]

they can insert in the middle of genes without causing harm because they can undergo chemical reactions by which they remove themselves from the RNA messages the genes make.

Am I too much of a geek, or did this remind anyone else of a rather similar situation with source code, Ken Thompson's fascinating 'Reflections on Trusting Trust'?

sorry--you're all wrong

[idlake]

We're not looking at generalisations, like physical laws, that can be repeated in a lab, but an event that happened once in our ancient history.

How do you know it can't be repeated in a lab? In fact, there is increasing experimental evidence that the steps that lead to life are not a unique accident, but repeatable.

(Not that repatability in a lab is a necessary or sufficient condition for something to be scientific anyway.)

It seems to me that it's a little futile to speculate on how cellular and multicellular life first appeared because the evidence was lost long ago.

The evidence is preserved in the fossil record, and many of the steps can be repeated expreimentally.

Towards the end of the 19th century the main French and British linguistic societies banned any further papers on the origins of langiage because unprovable speculation was so rife. I can't help feeling we need the same thing here.

Well, fortunately, science has overcome that folly--research into the origins of language is a hot field.

I'm a noob. How do I read this article?

[AndyKron]

I sure wish I had $199/year for a subscription to Nature, but I just don't. I guess I will be one of the "have nots". An intellectually inferior burger flippin' weasle, UNLESS... I'm missing something all of you know. How can I read this?

Re:I'm a noob. How do I read this article?

[cheesygrapes]

There's a link to the abstract from slashdot and the abstract has a link that sayeth: "full text"

Re:I'm a noob. How do I read this article?

[AndyKron]

You're right. I don't know how to spell. Thank you Mr. Anonymous Coward for showing me how inferior I am. I don't deserve the information Nature magazine has to offer. I am truly a weasel.

Re:I'm a noob. How do I read this article?

[AndyKron]

Thanks cheesygrapes, but I think I'm missing something. Do you mean the link at the top that takes me to Nature? I clicked on "full text" at Nature, but then I was sent to a page that said I needed a subscription.

Re:I'm a noob. How do I read this article?

[Rutulian]

Just sneak into your local university library and get it off the computers there. Most universities have institutional subscriptions, so if you have a uni ip address you can access the article.

Re:I'm a noob. How do I read this article?

[rmayes100]

Science is a little cheaper but not much.

Re:I'm a noob. How do I read this article?

[Anonymous Coward]

The full text is available... only if you pay for it.

Things like this...

[thebudgie]

Subjects such as this make me wish I had chosen a rudimentary biology class in my first year of University so I could have a small idea of what exactly they are talking about in biological subjects.

Re:All we know is that we don't know.

[Nomad37]

Dude, thanks. Seriously. Very handy to have a short explanation of background concepts like this.

So much misinformation

[bllius69]

For some basic (and free info), try NCBI's bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=B ooks Molecular Biology of the Cell is nice, as is Biochemistry, or The Cell. (Note: Koonin works at NCBI).

Or search Wikipedia, google, etc.

1. "Most of the DNA in the cell is wrapped in a fat and protein membrane."

Most of the DNA in "all" three kingdoms are wrapped up in proteins. In eukaryotes there is a membrane that surrounds the entire set of chromosomes (except during cell division) called the nuclear membrane. Chloroplasts and mitochondria are also surrounded by membranes. All membranes have proteins in them. In Prokaryotes, the entire cell is surrounded by at least one membrane, and the DNA is inside of this in the cytoplasm. It does not float freely. In prokaryotes, most chromosomes are circular (but not always) and most organisms have one chromosomes (but not always). In eukaryotes, most organisms have multiple linear chromosomes.

NB: Membranes are comprised of lipids and proteins and in some cases other molecules like cholesterol. Lipids are also known as "fat" and there are many different types.

2. Central dogma/transcription/translation.

In prokaryotes, transcription (copying DNA to mRNA) and translation (translating the RNA to create polypeptide (protein) chains, done by the ribosome) are coupled. In eukaryotes it is uncoupled as the RNA has to be transported out of the nucleus through the nuclear pore, where the mRNA is then translated by ribosomes in the cytoplasm, or by ribosomes attached to the ER and exported.

3. Prokaryote/Eukaryote introns

Introns are not eukaryotic-specific. All three branches of life have introns, however, they are far rarer in the archaea and bacteria (especially rare). Some introns can self-splice (remove themselves), while others do not. Lots of different "types" of DNA can move themselves around, insertion sequences, transposons, phages, viruses, conjugative DNA, etc. This movement of DNA is a driving force in evolution itself, not merely in a host organism protecting itself from invasive DNA, but in the evolution of novel protein functions.

4. Single/multicellular

There are single-celled eukaryotes (yeast cells) and there are prokaryotes that form developmentally specialized conglomerations of cells (biofilms, cyanobacterial chains, mycelial hyphae) where some cells are specialized as compared to others. Many prokaryotes can signal to, as well as receive signals from, other cells.

5. Mimivrius

Mimivirus is interesting, but it is an extreme outlier. More work on the full range of virus forms and genome ranges will help in this arena. Some of the metagenomic projects will definitely help in this area. It's like attempting to hypothesize the evolution of mulicellular organisms based on the blue whale.

6. Introns and domains.

Proteins fold into 3D structures to perform functions. The basic unit is a domain, which are units that can fold into a 3D structure themselves and perform some function (basically). Exons and domains are not a 1 to 1 relationship. IMO, intron evolution has a lot more to do with alternative splicing events and regulation in developmental pathways than it does in driving new functions for genes (you can duplicate genes and domains without introns/exons).

7. Membrane evolution.

Membrane compartmentalization is a key step in evolution. Interestingly the prokaryotes (archaea and bacteria) have two different types of lipids, suggesting that in the early stages of this evolutionary step that two pathways were chosen, and both have been maintained since that time. Again, another point in evolution is not that one system is always better than another, but that endpoints are achieved through multiple pathways.

8. Koonin et al., hypothesis.

Their hypothesis is interesting. I haven't read the paper, but I have seen Koonin's seminar from a few months ago. Unfortunately there is so much we don't know yet. His ideas may be skewed towards analyses based simply on comparative genomics and not enough on biochemistry.

slashdot coverage?

[caudron]

Hot on the heels of Slashdot's coverage of a controversial model [...]

Slashdot covers news like David Spade's jacket covers Chris Farley's back. ;-)

Re:slashdot coverage?

[rootEToTheIPi]

Dude, that's not funny. Farley's dead.

Re:slashdot coverage?

[Anonymous Coward]

> Dude, that's not funny. Farley's dead.

So are Slashdot's days as a 'news' site.

Virus's are hot

[threedognit3]

I love virus'. They're cool. They're something that brings forth new challenges. Must of all they'll kill you. God love virus' They're not wll known, understood and misconceived. They're losing now...they evolve. Long live virus'. Virus rule.

Re:Virus's are hot

[Anonymous Coward]

I see you love misusing the apostrophe too...

Welcome the inevitable

[threedognit3]

Virus's will kill you. Hell, they're going to kill all of us. Most of you loser f**ks are going to die. Virus' are just now coming on the scene. You can't image the havoc they'll rain. It's not about astroids, metorites or some earth borne disease springing forth. Virus' will win big time. No known cures. Simple, sweet. They're coming...in every way. God loves virus'. They are the creation of creator.

Re:Welcome the inevitable

[Anonymous Coward]

uh, medication might be needed here.

introns & junk DNA

[supertsaar]

Introns and Exons are found within a gene. They are important for such things as alternative splicing, which can be used to generate diversity 'on demand', for instance this plays a part in the immune response.
It seems that Introns are considered part of 'junk DNA', but given the fact that in some cases introns play an important part I think this is unfair to introns....

Re:introns & junk DNA

[espressojim]

Introns haven't been considered junk in quite a while. It's been know that there are some regulatory regions hiding out in introns.

For more interesting 'proof', see my paper in febuary nature genetics about conserved noncoding regions under selection - one of the strongest signals for selection was seen in intronic regions. We found parts of introns that were under as strong selection as coding regions.

It's nowhere NEAR junk DNA.

Re:introns & junk DNA

[supertsaar]

Yup, I have to agree with you: Introns are absolutely not junk DNA.
But the Wikipedia seems to think so, and some of he post I read also think Introns are ' just junk'. Off course it may turn out that there is no such thing as junk DNA and all this non coding stuff serves a purpose.

Re:introns & junk DNA

[espressojim]

Who do you believe more, peer reviewed abstracts, or wikipedia?

Re:introns & junk DNA

[supertsaar]

I believe _you_ :)

How life started (intelligent design)

[Mysund]

Here is one suggestion:

In some years experiments with timemachines will transport living cells back in time to before life was present here on earth.

So, we create life.
Thats intelligent design.

Re:All we know is that we don't know.

[Bastard of Subhumani]

So let me get this right. Eukaryotes are like a microkernel, and there seem to be a lot of comments in the code?

Re:All we know is that we don't know.

[Anonymous Coward]

more like: a lot of branches in program, seldom taken.

Random, Chance Processes Always Dilatorious

[artbulla]

The effect upon existing organisms by viruses is cancer. It would be easier for Niagara Falls to flow backwards than a human body, (not to mention the concurrent ecology) to arise out of chemicals such as methane, ammonia, etc. These naturalist philosophers have never studied mathematics to any serious degree, or they would not propound such absurdities. The amount of taxpayer money wasted upon these grant-funded pinhead projects in order to free the rebellious so that they can lift up their heads and roll sin upon their tongues is truly amazing. Nimrod and the Tower of Babel was a similarly government-sponsored project, engineered to reach heaven by some other means than repentance and entering in at the gate.