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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."
Well, there's someone that obviously doesn't know it's Friday afternoon.
I'm Rick James with mod points biatch!
If you've got proof it's a dupe, the folks at SETI would like to hear from you.
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.
"The White House is not an intelligence-gathering agency," -- Scott McClellan, Whitehouse spokesman.
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.
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.
C|N>K
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.
Entropy just isn't what it used to be.
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.
"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!
There is no belief, however foolish, that will not gather its faithful adherents who will defend it to the death.-Asimov
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)
autopr0n is like, down and stuff.
Does this article deal with the origins of eukaryotic cells? Or multicellular organisms? Because they are two different issues.
Please tell us more about BSD and Solaris. I didn't get enough in your other thread.
Central Dogma
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.
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.
EEEEEEEEEEEEooooooooooooooEEEEEEEEEEEEEEEEooooooo
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
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'?
Ceterum censeo subscriptionem esse delendam.
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 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?
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.
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.
Dude, thanks. Seriously. Very handy to have a short explanation of background concepts like this.
Pessimism of the intellect, optimism of the will! - Antonio Gramsci.
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.
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.
-Tom
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.
Don't disappoint your bird dog. Go to the range.
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....
The Bigger The Headache The Bigger the Pill
Mimes. Fucking brilliant.
When it comes to pastry theft, I take the cake.
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.
Is that you, Lord Havelock Vetinari, Patrician of Ankh-Morpork?
Morality is usually taught by the immoral.
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.