Looking back 3.8 billion years into the root of the 'Tree of Life'

November 30, 2015
The ribosome grew by accretion of new RNA onto old RNA in a process reminiscent of nested Russian dolls. The most ancient part of the ribosome contains small RNA fragments and is represented by the smallest doll. Ever more recent additions to the ribosome increased its functionality, and are represented on dolls of increasing size. The largest doll represents the ribosomal RNA that is shared by all current forms of life. Credit: Courtesy Williams Lab

NASA-funded researchers at the Georgia Institute of Technology are tapping information found in the cells of all life on Earth, and using it to trace life's evolution. They have learned that life is a master stenographer - writing, rewriting and recording its history in elaborate biological structures.

Some of the keys to unlocking the origin of life lie encrypted in the , life's oldest and most universal assembly of molecules. Today's ribosome converts genetic information (RNA) into proteins that carry out various functions in an organism. But the ribosome itself has changed over time. Its history shows how simple molecules joined forces to invent biology, and its current structure records ancient biological processes that occurred at the root of the Tree of Life, some 3.8 billion years ago.

By examining variations in the ribosomal RNA contained in modern cells, scientists can visualize the timeline of life far back in history, elucidating molecular structures, reactions and events near the biochemical origins of life.

"Biology is a great keeper of records," said Loren Williams, a professor in the Georgia Tech School of Chemistry and Biochemistry, and principal investigator for the NASA Astrobiology Institute's Georgia Tech Center for Ribosome Adaptation and Evolution from 2009-2014. "We are figuring out how to read some of the oldest records in biology to understand pre-biological processes, the origin of life, and the evolution of life on Earth."

The study is scheduled to be reported November 30 in the Early Edition of the journal Proceedings of the National Academy of Sciences.

Like rings in the trunk of a tree, the ribosome contains components that functioned early on in its history. The center of the trunk records the tree's youth, and successive rings represent each year of the tree's life, with the outermost layer recording the present. Just as the core of a tree's trunk remains unchanged over time, all modern ribosomes contain a common core dating back 3.8 billion years. This common core is the same in all living organisms, including humans.

"The ribosome recorded its history," said Williams. "It accreted and got bigger and bigger over time. But the older parts were continually frozen after they accreted, just like the rings of a tree. As long as that tree lives, the inner rings will not change. The very core of the ribosome is older than biology, produced by evolutionary processes that we still don't understand very well."

While exploiting this record-keeping ability of the ribosome reveals how biology has changed over time, it can also point to the environmental conditions on Earth in which that biology evolved, and help inform our search for life elsewhere in the Universe.

"This work enables us to look back in time past the root of the tree of life - the ancestor of all modern cells - to a time when proteins and nucleic acids had not yet become the basis for all biochemistry," said Carl Pilcher, interim director of the NASA Astrobiology Institute. "It helps us understand some of the earliest stages in the development of life on Earth, and can guide our search for extraterrestrial environments where life may have developed."

By rewinding, reverse engineering, and replaying this ancient ribosomal tape, researchers are uncovering the secrets of creation and are answering foundational, existential questions about our place in the Universe.

By studying more additions to the ribosome, the research team - with key contributions by Georgia Tech Research Scientist Anton Petrov - found "molecular fingerprints" that show where insertions were made, allowing them to discern the rules by which it grew. Using a technique they call the Structural Comparative Method, the researchers were able to model the ribosome's development in great detail.

"By taking ribosomes from a number of species - humans, yeast, various bacteria and archaea - and looking at the outer portions that are variable, we saw that there were very specific rules governing how they change," said Williams. "We took those rules and applied them to the common core, which allowed us to see all the way back to the first pieces of RNA."

Georgia Tech Professor Loren Williams (left) and Research Scientist Anton Petrov in front of a large tree that symbolizes the growth and accretion of the ribosome over time. Credit: Credit: Rob Felt, Georgia Tech

Some clues along the way helped. For instance, though RNA is now responsible for creating proteins, the very earliest had no proteins. By looking for regions of the ribosome that contain no proteins, the researchers could determine that those elements existed before the advent of proteins. "Once the ribosome gained a certain capability, that changed its nature," Williams said.

While the ribosomal core is the same across species, what's added on top differs. Humans have the largest ribosome, encompassing some 7,000 nucleotides representing dramatic growth from the hundred or so base pairs at the beginning.

"What we're talking about is going from short oligomers, short pieces of RNA, to the biology we see today," said Williams. "The increase in size and complexity is mind-boggling."

The researchers obtained their ribosomes from structure and sequence databases that have been produced to help scientists identify new species. Ribosomes can be crystallized, which reveals their three dimensional structures.

Beyond understanding how evolution played out over time, this knowledge of the ribosome's development could have more practical modern-day health applications.

"The ribosome is one of the primary target for antibiotics, so understanding its architecture and consistently throughout biology could be of great benefit," said Williams. "By studying the ribosome, we can start thinking about biology in a different way. We can see the symbiotic relationship between RNA and proteins."

As a next step, Williams and colleagues are now using experiments to verify what their model shows.

"We have a coherent and consistent model that accounts for all the data we have going all the way back to a form of biology that is very primitive compared to what we have now," Williams explained. "We plan to continue testing the predictions of the model."

Explore further: Evolution of life's operating system revealed in detail

More information: History of the ribosome and the origin of translation, PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1509761112

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Nik_2213
4.6 / 5 (11) Nov 30, 2015
Astonishing work...

It's going to show some surprises, that's for sure !!

Sad there's no comparable 'dig site' for viruses-- They're honed too sharp.
Torbjorn_Larsson_OM
4.6 / 5 (9) Nov 30, 2015
It is very exciting that Petrov et al's 2014 model with insertion fingerprints remains viable and gathers adherents! As the accompanying video implies, it is very informative on the UCA lineage from RNA/RNA cells over RNA/protein cells to the DNA/protein LUCA. [ https://astrobiol...of-life/ ; note that the video gets the universal tree and Crick's central dogma wrong.]

But that group could also improve on the emergence estimate, now that mineral data shows habitability before 4.3 billion years ago and - indeed - putative fossil finds support the molecular clock estimates of emergence before 4.2 billion years ago. The 3.8 billion year date is arguable too and a much looser upper limit, so why not dip into the full data set?

@Nik: Agreed, in spades! Though Koonin has convincingly (IMO) tied some major virus clades to much the same UCA genetic machinery evolution.
Torbjorn_Larsson_OM
4.5 / 5 (8) Nov 30, 2015
[ctd] But as you say, not much extraneous data to dig into there. Extant viruses are streamlined parasites by excellence.

The new work is paywalled. The earlier work could be tied to pre-code ribosome use to produce dipeptide cofactors for ribozymes and eventually longer random protein nests for metal atom catalysts as primitive generic enzymes. That is feasibly what the evolution of "peptidyl transferase center" and the "exit tunnel" the abstract tells of could produce before ordered proteins by evolving the triplet code happened. [ http://www.pnas.o...abstract ]

I hope they have added a timeline for the small ribosomal unit SSU evolution. (The old work could pinpoint the co-option of it.) Also, the video hints that it was co-opted from the same "peptidyl transferase center" nick of a double strand (to shield from chemical attack) ribozyme as the LSU was.
Vietvet
4.4 / 5 (13) Nov 30, 2015
It's a pleasure to read an article like this knowing JVK can't comment while serving her temporary ban. I'm dreading the 12th of Dec.
ichisan
1.8 / 5 (16) Nov 30, 2015
"But the ribosome itself has changed over time. Its history shows how simple molecules joined forces to invent biology, and its current structure records ancient biological processes that occurred at the root of the Tree of Life, some 3.8 billion years ago."

There is no science in this pile of crap. Just stories, or rather, myths. Popper is turning in his grave.
BartV
1.6 / 5 (21) Nov 30, 2015
So sad that there is basically no science in this article. Just some comments thrown around a theory called evolution that has never been observed nor proven. Interesting how the atheist scientists jump to try to support it or somehow make some kind of distinguished comment regarding it.

True scientists would reject evolution.

Vietvet
4.1 / 5 (13) Dec 01, 2015
@ichisan
@BartV

Thanks for demonstrating you have IQs lower than a turnip, no insult intended to turnips.
Vietvet
4.1 / 5 (14) Dec 01, 2015
I should have known the creationist, anti-science trolls would would make an appearance.
yep
4.3 / 5 (13) Dec 01, 2015
@ichisan
@BartV

Thanks for demonstrating you have IQs lower than a turnip, no insult intended to turnips.


You would think believing in a Sky Daddy with no physical proof would be harder then believing in evolutionary theory with millions of years worth of fossil evidence? Or why believing in a Sky Daddy would preclude evolution to begin with?
jsdarkdestruction
5 / 5 (11) Dec 01, 2015
Bart

You don't want to see it or read the evidence proving it so you have not.

Why do you believe it's only atheists scientists who support evolution? Do you believe everyone follows your specific sect of christianity or whatever you are? I'll bet others who worship the same God as you believe in evolution. Probably most of them on some level or another.

You already ignore any transitional fossils we've found and would probably still deny it even if we could find every single species that ever existed and show them to you. Your faith blinds you and covers your ears too strongly for any objective reasoning from you.
antialias_physorg
4.6 / 5 (9) Dec 01, 2015
True scientists would reject evolution.

It's only in the US that some christians reject evolution (the official church stance is an acceptance of evolution as a natural process within creation*) - and that's only because the education system in the US is rather...lacking. If there were any in depth teaching of why we think evolution is a very good theory this would change...from handedness of molecules to the DNA record to observed adaptations - even speciations - to leftover DNA 'junk'...which would make no sense if there was a creator/designer.
Alas, understanding such 'complex' things cannot be expected of the average high school student (nor of the average adult, it seems).

*It should also be noted that the guy who co-authored the paper with Darwin that proposed evolution/natural selection was a deist.
jsdarkdestruction
4.6 / 5 (11) Dec 01, 2015
Anti, I disagree. A large part of it is people like Bart who don't want to believe it so they don't. You could explain it to these people all day long about evolution and they still will choose their religious/personal beliefs over evidence. Our system needs improvement but we can only do so much. I've been out of high achool 12 years almost and even back then our evolution unit was fairly detailed and thorough enough anyone who wasn't biased by religious views understood it.
jsdarkdestruction
5 / 5 (5) Dec 01, 2015
Disagree about in depth teaching helping the problem that is.
Torbjorn_Larsson_OM
4.7 / 5 (12) Dec 01, 2015
The Way of The Crank. So JVK is banned!? Also good news!

The creationist cranks didn't read the comments or the article. Since the ribosome evolution could be ordered like Russian dolls, it is yet another successful test of, and observation on, the scientific theory. Precisely these types of phylogenetic tests, that play out on a combinatorial space, makes evolution the best observed, best tested science we have.

In fact, evolution has passed at least 1.5 million individual tests!

"Evolution is a cornerstone of modern science, accepted as one of the most reliably established of all facts and theories of science,". [ https://en.wikipe...volution ]

[tbctd]
Torbjorn_Larsson_OM
5 / 5 (8) Dec 01, 2015
[ctd]

"Keep in mind that about 1.5 million species are known currently, and that the majority of these species has been discovered since Darwin first stated his hypothesis of common ancestry. Even so, they all have fit the correct hierarchical pattern within the error of our methods. ... the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants." [ http://www.talkor...ierarchy ]

Not that facts or other forms of truth bother the Crank. He or she must troll the annoying sites that tell them their preferred - often religious - crankhood is wrong, despite that the Crank 'know I am right no matter the evidence'.
FredJose
1.3 / 5 (13) Dec 01, 2015
all modern ribosomes contain a common core dating back 3.8 billion years.

How does the scientist know this? Is there any documented history that shows this statement to be true? Was he there? When it comes to eliciting historical progress and given the same evidence, one can interpret it anyway one wants according to one's worldview.
makes evolution the best observed, best tested science we have

Let's test that assertion shall we? Who observed that life arose from dead materials all by itself some billions of years ago? Who observed the progress from a single cellular thing to current lifeforms? How can we test and verify the Darwinian assertion that it actually happened?
A belief in Darwinian evolution is the same as believing that the dead can come to life all by itself. Have you or anyone else EVER seen that happen? I don't think so.
FredJose
1.3 / 5 (13) Dec 01, 2015
only in the US that some christians reject evolution (

You do your reputation a great disservice by spouting such nonsense, anti-alias. There are millions of Christian people all over the world who totally reject the notion that life arose from dead material all by itself and then proceeded to built itself up from a single cellular type into the current lifeforms we see today.
You either have to be a complete dunce or totally ignore and reject even the most basic of biochemical and physics rules to believe in the fairy tale of Abiogenesis and Darwinian evolution.
If you are unable to demonstrate that abiogenesis occurred, you have no chance with Darwinian evolution either since they both rely on the creation of abstract rules of logic and of storage of vast amounts of abstract information.
How does the abstract arise from purely mechanical and materialistic processes?
FredJose
1.3 / 5 (13) Dec 01, 2015
Since the ribosome evolution could be ordered like Russian dolls,

This is only if you assume that it evolved in the first place. Since these researchers are trying to establish the history of the ribosome, one has to question their assumptions. I do not see them mentioning what it was that they assumed regarding the origin of the ribosomes in the first place. How and when did it get created originally? No one can tell that by just looking at the present instance without making undue simplifying assumptions. In this case those assumptions will be steeped in the evolutionary / humanistic worldview of which the basis is that life arose from dead materials all by itself and then proceeded to develop via Darwinian evolution.
One can make an even better case for special creation and development, given exactly the same evidence.
antialias_physorg
4.6 / 5 (9) Dec 01, 2015
Anti, I disagree. A large part of it is people like Bart who don't want to believe it so they don't.

I think it's connected with a lack of education. Because people who cannot think for themselves then have to resort to being literalist (and these people don't even realize that their 'literal' interpretation is based off of a badly translated and multiply edited book...it would be funny if it weren't so sad to watch.)

You could explain it to these people all day long about evolution and they still will choose their religious/personal beliefs over evidence

The sad thing is that evolution isn't even at odds with their religion. Only with their overly naive/literal way of what they _think_ is belief. Their god didn't say "be dumb". But for some reason they choose to be.
antialias_physorg
4.6 / 5 (9) Dec 01, 2015
Let's test that assertion shall we? Who observed that life arose from dead materials all by itself some billions of years ago?
...
A belief in Darwinian evolution is the same as believing that the dead can come to life all by itself.

Ah...here we go. You don't really know what evolution is, do you? The theory of evolution or Darwinism says nothing about how life got started (the theory that says something about this is called abiogenesis).
You also don't even realize that there is no physical/chemical distinction of 'alive'/'not alive' apart from the label. The same chemical, physical, quantum-mechanical, ... laws that operate in 'alive' materials operate in 'non-alive' ones. If you have a measurable/verifiable observation to the contrary I'm sure the scientific world would be happy to see it (as the definition of 'life' is still something that no one has nailed down - and plenty of very smart people - religious and not - have had a go at it over the centuries)
Zzzzzzzz
4.6 / 5 (9) Dec 01, 2015
You will never convince a psycho that the maintenance and defense of the delusion his veneer of sanity requires to remain in existence is an exercise in futility. The threat of the impending chaos of complete mental dissolution is a very powerful motivator, much like a loaded and cocked revolver with a hair trigger held to his head.
antialias_physorg
4.6 / 5 (10) Dec 01, 2015
You will never convince a psycho that the maintenance and defense of the delusion his veneer of sanity requires to remain in existence is an exercise in futility.

You're right, but it would be somewhat less insane if they'd actually know that the arguments they field (as insane as these arguments are) aren't even relevant to the subject but at something entirely unrelated.

It's like watching someone arguing that 2 plus 2 cannot possibly be four "because grass is green". The sheer stupidity of it coupled with the misplaced surety of self is mindboggeling.

Zzzzzzzz
4.2 / 5 (10) Dec 01, 2015
That is why the creationists are drawn to science sites - the desperation to defend the delusion is very strong, and opportunities to feed the desperation are searched for with every waking moment.
PhotonX
4.6 / 5 (11) Dec 01, 2015
Was he there?
Anyone who says this is automatically an idiot. Were you there when Christ was crucified, Fred? No? Must not have happened, then. Can't you realize how stupid you make yourself look by saying things like this?
.
.
my2cts
4 / 5 (8) Dec 01, 2015
True scientists would reject evolution.

Of course , the word "true" coming form you means "in agreement with BartV's preferred delusional (interpretation of a) text".
my2cts
3.9 / 5 (7) Dec 01, 2015
all modern ribosomes contain a common core dating back 3.8 billion years.

How does the scientist know this? Is there any documented history that shows this statement to be true?

Its all in the bible. Jimmy Swaggart said it, too.
Was he there?

No but his imaginary friend was. He's dead now but that is only temporary. Also we have hundreds of reliable long dead witnesses. Somebody wrote everything down long after the facts. We choose believe them. Life is life !

When it comes to eliciting historical progress and given the same evidence, one can interpret it anyway one wants according to one's worldview.

That's exactly what we are doing. We cherry pick and fabricate, brainwash our children starting at birth, and then call it the truth.
yep
3 / 5 (2) Dec 01, 2015
This is another area I belive historical perspective can help people place their belief system into context.
The lead scholar on the Dead Sea scrolls, John Allegro wrote one of my favorite books on the subject : The Sacred Cross and the Mushroom
This video is one of the best I have seen on the subject by a gentlemen whose childhood inspiration was Dr. Gordon Wasson. http://youtu.be/_VcC--cxQHc
DavidW
1.6 / 5 (7) Dec 02, 2015
True scientists would reject evolution.

...which would make no sense if there was a creator/designer.


"which would make no sense if there was a creator/designer. "

Just because others associate the words creator and designer with a true living god, does not make your understating of what was meant when someone did have it correct, correct.

Having the quality of completely true means completely innocent. Is a baby responsible for it's birth? No. Just by being true and being alive, there is true glory. Hence, why we are here. And hence why we cannot blame a true living god for anything, as the true living god holds innocence.

Every other possibility is actually ruled out, if you honestly ponder what is truthfully possible. Yet, loving as an example seems to help life more, as that is the only way to love this true living god. We can not get further than each other, as we have equality
DavidW
1.6 / 5 (7) Dec 02, 2015
Intelligent design does not mean it was intentionally intelligently designed. Even though many people have preached it this way and believe it.

Look at general relativity. See the = sign. One does not exist without the other. It is the same relationship as truth and life. Yet, with truth and life we see that there is true glory. General relativity exists because true glory exists. Anything less and we would not be alive. We have to have been here to witness this true glory or the glory wouldn't be true, as far as we can ever discern. This mechanism unpins all things we can ever perceive. It also does not mean that a true living god is to blame. Just that the true living god is the true living god AND holds innocence of whatever things we think of as bad that might ever occur.

True innocence means always innocent. We can't truthfully blame a true living god for what others say and do. No matter what it is or how ridiculous it sounds. It's a hypocritical position to attempt that.
DavidW
1.8 / 5 (5) Dec 02, 2015
You will never convince a psycho that the maintenance and defense of the delusion his veneer of sanity requires to remain in existence is an exercise in futility.

It's like watching someone arguing that 2 plus 2 cannot possibly be four "because grass is green". The sheer stupidity of it coupled with the misplaced surety of self is mindboggeling.


Yes, but that is only because people do not accept, 100%, that life is most important in life.

When we fail at that, then the result is people who can't think properly. This is the cause of all of our problems that we make. That's a terrible thing to have told another that their ability to understand truth is incorrect, or never reminding another why they truly are most important.

When we fail at this, we are the ones that cause the stupidity to happen. We risk breaking the minds of others when we don't uphold the truth. How smart is that compared to the one doing stupid things?
leetennant
3.7 / 5 (6) Dec 02, 2015
What a pile of gibberish.

It's like watching someone arguing that 2 plus 2 cannot possibly be four "because grass is green". The sheer stupidity of it coupled with the misplaced surety of self is mindboggeling.


Exactly.
Torbjorn_Larsson_OM
3.7 / 5 (3) Dec 05, 2015
@FredJose: "How does the scientist know this? Is there any documented history that shows this statement to be true? Was he there?"

It is known by observation, the (arguable fossils) from 3.8 Ga bp are used as date and the RNA/RNA cells ("RNA world") that preceeded the RNA/protein and later the DNA/protein cell shows the evolution of the ribosome. (I.e.from having none to having one.) Yes, the scientist was there, or rather the system he or she studies.

"Who observed that life arose from dead materials". That isn't what goes into testing evolution, but the cases of speciation (say) that gives the observed phylogerentic trees. See the provided link before spouting inanities!

Testing life emergence on the other hand is done by the fossils (and extant life). We can see the early Earth was inhabitable (molten), today it is habitable and indeed inhabited. In between life had to emerge to fit the observations.
Torbjorn_Larsson_OM
3.7 / 5 (3) Dec 05, 2015
@DavidW: "Intelligent design". There you go with your unwarranted religion inserted into a discussion of science. Just stop, no one is interested if your religious magic has 'gods' with horns or clay feet or is claimed to 'design'.
FredJose
1 / 5 (2) Dec 10, 2015
Humans have the largest ribosome, encompassing some 7,000 nucleotides representing dramatic growth from the hundred or so base pairs at the beginning.

There is no supporting documented evidence that this "growth" process actually occurred. This is a mythical, non-science statement made out of thin air.

@Torb:
"It is known by observation..."

Please, man, that is exactly why I asked the question - there has been no observation, it's impossible to go back into the past. No one saw and documented this supposed small beginning and superlative growth. Get real.
That isn't what goes into ....
Typically sidestepping the issue that life cannot arise from dead materials. Ever.
Answer the very basic question in a peer-accepted scientific way: Where and how did life originate on planet earth? No scientist can answer that question in a definitive way according to the currently accepted scientific methodology. Hence you require faith to BELIEVE life started off by itself.

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