Complex Cells Likely Arose from Combination of Bacterial and Extreme-Microbe Genomes

National Science Foundation ^ | 08 September 2004 | Staff, Office of Legislative and Public Affairs

[PatrickHenry]

According to a new report, complex cells like those in the human body probably resulted from the fusion of genomes from an ancient bacterium and a simpler microbe, Archaea, best known for its ability to withstand extreme temperatures and hostile environments. The finding provides strong evidence that complex cells arose from combinations of simpler organisms in a symbiotic effort to survive.

Jim Lake and Maria Rivera, at the University of California-Los Angeles (UCLA), report their finding in the Sept. 9 issue of the journal Nature.

Scientists refer to both bacteria and Archaea as "prokaryotes" -- a cell type that has no distinct nucleus to contain the genetic material, DNA, and few other specialized components. More-complex cells, known as "eukaryotes," contain a well-defined nucleus as well as compartmentalized "organelles" that carry out metabolism and transport molecules throughout the cell. Yeast cells are some of the most-primitive eukaryotes, whereas the highly specialized cells of human beings and other mammals are among the most complex.

"A major unsolved question in biology has been where eukaryotes came from, where we came from," Lake said. "The answer is that we have two parents, and we now know who those parents were."

Further, he added, the results provide a new picture of evolutionary pathways. "At least 2 billion years ago, ancestors of these two diverse prokaryotic groups fused their genomes to form the first eukaryote, and in the processes two different branches of the tree of life were fused to form the ring of life," Lake said.

The work is part of an effort supported by the National Science Foundation—the federal agency that supports research and education across all disciplines of science and engineering—to re-examine historical schemes for classifying Earth's living creatures, a process that was once based on easily observable traits. Microbes, plants or animals were said to be related if they shared certain, mostly physical, characteristics. DNA technology now allows much closer scrutiny of hereditary molecules, which provides a more accurate and detailed picture of the genetic relationships between and among living things.

"New computational tools and comparative analyses will undoubtedly find instances in which the evolutionary record will need to be set straight," said James Rodman, a program officer in NSF directorate for biology, which funded the research. "This new fellowship among microbiologists, evolutionists, and computationalists will provide a much fuller picture of the relatedness of living things."

Lake and Rivera analyzed and compared the genomes of 30 microorganisms selected from the three categories (eukaryotes, bacteria and Archaea). All of the microbes contained about the same number of genes. The researchers then used the computer to produce genome combinations that reflected the most likely ancestors of modern eukaryotes. Their analysis, they say, showed that two ancient prokaryotes —- one most similar to a bacterium, and one an Archaea -— combined genomes out of a mutually advantageous need to survive.

That theory, known as endosymbiosis, has been a popular explanation of how eukaryotic cells acquired smaller components to carry out cellular processes. According to the report, modern eukaryotes obtained genes required to operate the cell from the bacterial side of the family, and the information-carrying genes from the Archaea side.

Further, the authors say, the work also sheds light on the “horizontal” transfer of genes—sideways from organism to organism, rather than from parent to offspring. The U.S Department of Energy, the National Institutes of Health, and NASA also supported this work.

[Alamo-Girl]

Thanks for the ping!

[ScuzzyTerminator]

Lake and Rivera analyzed and compared the genomes of 30 microorganisms selected from the three categories (eukaryotes, bacteria and Archaea). All of the microbes contained about the same number of genes. The researchers then used the computer to produce genome combinations that reflected the most likely ancestors of modern eukaryotes. Their analysis, they say, showed that two ancient prokaryotes —- one most similar to a bacterium, and one an Archaea -— combined genomes out of a mutually advantageous need to survive.

Nothing here proves endosymbiosis.  Lake and Rivera assume endosymbiosis and then show that a bacterium and an Archaea are the "most likely ancestors." That's like pulling thirty people off the street and, by examining their DNA, declaring two of them my "most likely ancestors."

[tallhappy]

The criticism referenced by VR in post #10 goes into some detail on this point

I am not interested in the cat fight about arguments etc...

What was the article about and what were the criticism -- I'm talking methods and data and analysis.

Forget the political stuff.

[Ichneumon]

In my mind he has a definite flaw in his reasoning. The early bacteria evolved (or were created) in METHANE atmosphere on Earth.

No... Nor does the author say that.

The pre-oxygen atmosphere of the Earth mostly consisted of nitrogen, ammonia, carbon dioxide, and water vapor.

Later after plants arose with photosynthesis, oxygen appeared in the atmosphere.

Yes, around one billion years ago -- which is around a billion years after the appearance of the first eukaryote. (Oxygen was being produced long before that, but it was rapidly reacting with various compounds, including iron, until finally enough was produced to remain free in the atmosphere in significant amounts.)

The author wants us to believe that one or two methane utilizing bacteria combined to produce a eukaryotic cell that is oxygen based.

No he doesn't. You're wrong on the methane, and you're wrong in claiming that the author in any way asserts that the first eukaryotic cell had an oxygen-based metabolism. Clearly, oxygen consumption was developed long after the first eukaryote.

I don't think so.

And neither does the author.

[Ichneumon]

That's like pulling thirty people off the street and, by examining their DNA, declaring two of them my "most likely ancestors."

No it isn't, but it's nice that you're trying.

[tallhappy]

Too lazy to follow the links?

No, I followed the link. I am not as stupid as you to not understand the link did not discuss criticism of the actual study but was about political issues relating to the paper's publication. Big difference you are clearly not bright enough to understand. Buts that's OK. You're special in your own way, I'm sure.

[Ichneumon]

My problem with cellular evolution is a little earlier: how did we go from non-life to life?

That depends on where you choose to draw the line between "non-life" and "life". Define your question more specifically and I'll be glad to answer.

The general answer is that "life" as we think of it includes many properties, but early "life" (or proto-life, or whatever you want to call it) wasn't that complicated. So while it seems baffling to think of "life" (*as we now know it*) arising *poof* from "non-life", instead the process was a much more gradual accumulation of properties, and there was no *poof* instant, nor any point where the preceding step was obviously "non-living" and the following step was obviously "alive" by our standards.

And how come all proteins are left handed, when the proteins we synthesize in vidrio are left and right handed?

They aren't all left-handed, just most of them. Numerous living things produce and incorporate right-handed amino acids. As for why, because things work out more neatly when working with building blocks that are mostly of the same handedness, so evolution favored processes of life which specialized in one "hand" (left, or right).

[Ichneumon]

[Too lazy to follow the links?]

No, I followed the link. I am not as stupid as you to not understand the link did not discuss criticism of the actual study but was about political issues relating to the paper's publication. Big difference you are clearly not bright enough to understand. Buts that's OK. You're special in your own way, I'm sure.

You followed "the link", eh? There were "linkS", plural, Einstein. Try the other one and you'll see plenty of "criticism of the actual study".

I'll accept your apology any time you're ready, dunderhead.

[ScuzzyTerminator]

Does the article say that Archaea is anything but a better candidate than the other microbes?

This study assumes, a priori, that endosymbiosis is true and eukaryote ancestors are in the group. It does not even claim to prove whether endosymbiosis is true.

[tallhappy]

Please.

Provide a serious criticism of the methods and approach.

Not some web site. And even that wasn't a comment on the methods. It was a comment on not citing or accepting other published articles.

First off in this article-- what were the methods?

Can you or anyone tell me what the article was about?

[Junior]

The latest release from the journal says the article in question got by their otherwise good peer-review process and that the journal in question regrets publishing the article. 'Course, you'll never post that -- creationists prefer partial truths, as they help the creationist cause.

[Junior]

No it wasn't. There were lots of pre-Cambrian multicellulars.

[VadeRetro]

Mitochondria.

And chloroplasts.

[VadeRetro]

I thought these guys were rather gentle in their review.

Down the page, some people mention that. This is only the first-cut high-level treatment, anyway. A more detailed dissection has been promised.

[tallhappy]

The latest release from the journal says the article in question got by their otherwise good peer-review process

How?

It's all politics.

Administrative bureaucrat types generally have no spine whatsoever and never take responsibility. Like democrats.

My guess is there are many articles that have been published in this "low impact" journal that have similarly skirted past the "otherwise good" peer review process.

[tallhappy]

I read -- or looked at and read one section -- of Meyer's article. It's 23 pages.

It's not really an article, its an essay. I also read the "criticism" from the web site. It's not so much a criticism as a rebuttal.

The Meyer article really was pretty much the same ol same ol and so was the "criticism."

Since it is not a study and is more an essay there isn't all that much method to criticize. The criticisms thus are the same ol same ol. It comes down to one side saying this is how they see it and the other saying I don't see it that way and you are wrong and stupid and have no right to talk or say anything because you are stupid.

To the extent that method was presented, such as the section on "amino acid space" the criticisms did not address or criticize Meyer's methods. They criticized his analogies and assumptions, e.g. the analogy to human written language. The criticizers also criticized the writer for not citing what they felt he should cite. Yet their comments were not directed to what the writer was trying to say. They pointed to articles about gene shuffling and modifications of existing genes whereas the writer was not addressing that issue.

This is what I note of these "debates". To the extent that the sides try to argue science, they talk past each other.

The conclusion is that no one here has said anything about Jame's Lake's article and have chosen to focus on a meaningless "debate" regarding differing religious beliefs.

These threads and the subject in general remains bald men fighting frantically over a comb.

[Michael_Michaelangelo]

The latest release from the journal says the article in question got by their otherwise good peer-review process and that the journal in question regrets publishing the article. 'Course, you'll never post that -- creationists prefer partial truths, as they help the creationist cause.

Those pesky creationists! The way you talk, one would hardly know you were Catholic!

This is, of course, false.

[Michael_Michaelangelo]

NCSE Flip-flops As Controversy Over Peer-Reviewed Article Continues

The folks at the NCSE seem to embrace peer-review only when it confirms their pre-determined conclusions,” adds West. “Their goal isn’t peer-review, it’s censorship. They want to squelch the scientific debate. Fortunately, there are lots of scientists who still support free discussion.”

West also points out the spurious nature of the NCSE’s previous claim that supporters of intelligent design have not produced peer-reviewed publications. Mathematician William Dembski published a peer-reviewed monograph with Cambridge University Press, The Design Inference (1998). Biochemist Michael Behe has published his ideas recently in the peer-reviewed science journal Protein Science as well as previously in Philosophy of Science (2000) and And Stephen Meyer edited an entire volume of peer-reviewed articles with Michigan State University Press, Darwinism, Design, and Public Education (2003).

[stremba]

Your problem then is that this is not cellular evolution, but rather abiogenesis. Abiogenesis is on a much more speculative footing than the theory of evolution (not to say that there's no evidence favoring it). Once more for those who haven't been listening to these threads: Evolution is only concerned with what happens once a viable cell exists. It isn't concerned with how that cell came to be.

[Junior]

This is, of course, false.

Ahem. Check again:

Meyer's ID Paper Embarrassing Society Which Published It

by Glenn Branch
email lists

NCSE's Glenn Branch reports that the Biological Society of Washington has distanced itself from Steven Meyer's ID-friendly paper, strongly implying that it somehow got by their usual peer review process.