Scientists decipher 3 billion-year-old genomic fossils

Dec 19, 2010 By Denise Brehm
The figure shows the evolution of gene families in ancient genomes across the Tree of Life. The sizes of the little pie charts scale with the number of evolutionary events in lineages, slices indicate event types: gene birth (red), duplication (blue), horizontal gene transfer (green), and loss (yellow). The Archean Expansion period (3.33 to 2.85 billion years ago) is highlighted in green. Graphic: Lawrence David

(PhysOrg.com) -- About 580 million years ago, life on Earth began a rapid period of change called the Cambrian Explosion, a period defined by the birth of new life forms over many millions of years that ultimately helped bring about the modern diversity of animals. Fossils help palaeontologists chronicle the evolution of life since then, but drawing a picture of life during the 3 billion years that preceded the Cambrian Period is challenging, because the soft-bodied Precambrian cells rarely left fossil imprints. However, those early life forms did leave behind one abundant microscopic fossil: DNA.

Because all living organisms inherit their genomes from ancestral genomes, at MIT reasoned that they could use modern-day genomes to reconstruct the evolution of ancient microbes. They combined information from the ever-growing library with their own that takes into account the ways that genes evolve: new gene families can be born and inherited; genes can be swapped or horizontally transferred between organisms; genes can be duplicated in the same genome; and genes can be lost.

The scientists traced thousands of genes from 100 modern genomes back to those genes' first appearance on Earth to create a genomic telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being.

Eric Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering, and Lawrence David, who recently received his Ph.D. from MIT and is now a Junior Fellow in the Harvard Society of Fellows, have named this period the Archean Expansion.

Because so many of the new genes they identified are related to oxygen, Alm and David first thought that the emergence of oxygen might be responsible for the Archean Expansion. Oxygen did not exist in the Earth's atmosphere until about 2.5 billion years ago when it began to accumulate, likely killing off vast numbers of anerobic life forms in the Great Oxidation Event.

"The Great Oxidation Event was probably the most catastrophic event in the history of cellular life, but we don't have any biological record of it," says Alm.

Closer inspection, however, showed that oxygen-utilizing genes didn't appear until the tail end of the Archean Expansion 2.8 billion years ago, which is more consistent with the date geochemists assign to the Great Oxidation Event.

Instead, Alm and David believe they've detected the birth of modern electron transport, the biochemical process responsible for shuttling electrons within cellular membranes. Electron transport is used to breathe oxygen and by plants and some microbes during photosynthesis when they harvest energy directly from the sun. A form of photosynthesis called oxygenic photosynthesis is believed to be responsible for generating the oxygen associated with the Great Oxidation Event, and is responsible for the oxygen we breathe today.

The evolution of electron transport during the Archean Expansion would have enabled several key stages in the history of life, including photosynthesis and respiration, both of which could lead to much larger amounts of energy being harvested and stored in the biosphere.

"Our results can't say if the development of electron transport directly caused the Archean Expansion," says David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

David and Alm also went on to investigate how microbial genomes evolved after the Archean Expansion by looking at the metals and molecules associated with the genes and how those changed in abundance over time. They found an increasing percentage of using oxygen, and enzymes associated with copper and molybdenum, which is consistent with the geological record of evolution.

"What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of ," says Alm. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

Explore further: Automating the selection process for a genome assembler

More information: “Rapid evolutionary innovation during an Archean Genetic Expansion,” by Lawrence A. David and Eric J. Alm. Nature online Dec. 19, 2010.

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dogbert
1.5 / 5 (23) Dec 19, 2010
Scientists play with their computer models and pretend they have discovered something.
Quantum_Conundrum
1.6 / 5 (21) Dec 19, 2010
Scientists play with their computer models and pretend they have discovered something.


Yeah, basicly that's what it amounts to.

Some time in the past 20 years or so we transitioned to a state where anyone with a p.h.d. can make up a theory or a computer model, call it a discovery, and publish it, and it's immediately labeled as a "discovery", as if it were an actual, factual object. Additonally, if it insults "creationists" or something similar, they get bonus points.

Pretty much summary of modern scientific method.
StillWind
1.3 / 5 (15) Dec 19, 2010
This is a fascinating thought experiment, but like so much of what passes for "science" today, is nothing more than a video game.
It's no wonder that the average person is so misled.
Jotaf
4.9 / 5 (18) Dec 19, 2010
So they analyze actual genomic data that came from actual organisms, find some patterns, and you say they're making stuff up?

"New gene families can be born and inherited; genes can be swapped or horizontally transferred between organisms; genes can be duplicated in the same genome; and genes can be lost."

Are those events made up as well?
StillWind
1.8 / 5 (20) Dec 19, 2010
re Jotaf, apparently you don't understand the scientific method, and what constitutes actual "science".
The scientific method intails observing a phenomenon, speculating about cause and effect, setting up an experiment to recreate the conditions that are involved with the proposed theory, and verifying the hypothesis.
None of this, beyond the existence of the phenomenon, can be verified. Just because a computer model can be constructed to spit out the similar results, does not mean that it actually happened that way.
All we have is an unverifiable theory.
That is not science.
That is a nice story, but in any other circumstance, we'd call that a myth.
It is in no way different from ancient Greeks stories about gods hurling thunderbolts from Mt Olympus.
trekgeek1
4.9 / 5 (11) Dec 19, 2010
I'm pretty sure when MIT does it, it's not some hokey study. Perhaps it's not the classic definition of science, but it is science. They took data and mathematical models that were proven to work on that data and then applied it to interpolating data that was missing. This isn't fact, just a theory that allows more research to be done. Just as we theorize about what will happen tomorrow based on data we have now, we can theorize about the past.
StillWind
1.5 / 5 (16) Dec 19, 2010
Just because MIT puts out a myth does not make it "science", any more than when NASA or some other group puts out a theory about "Global Warming", or any of the other non-science computer programs that have been used to rout public opinion.
Garbage in/garbage out.
If it can't be verifeid, then it aint science.
210
1.5 / 5 (8) Dec 19, 2010
I'm pretty sure when MIT does it, it's not some hokey study. Perhaps it's not the classic definition of science, but it is science. They took data and mathematical models that were proven to work on that data and then applied it to interpolating data that was missing. This isn't fact, just a theory that allows more research to be done. Just as we theorize about what will happen tomorrow based on data we have now, we can theorize about the past.

A man fathers a child in Australia: goes to WWII is killed in Norway.
(Ancient dinosaurs could travel 1000 miles in a week - Pterosaurs).
His brother marries widow and both child and father die in Sydney after long life; We find DNA of father son, make linkage; REAL father never found so even with DNA we cannot know what genes were EXPRESSED! DNA IS THE LIBRARY, which books were 'checked out?'
MIT needs MORE DNA AND NEEDS technique for ancient life gene repression and expression...my friends...we have a LONG way to go !
ubavontuba
2.2 / 5 (5) Dec 19, 2010
Extravagant speculation or not, that's one nifty looking chart!

Jotaf
5 / 5 (15) Dec 19, 2010
Bioinformatics is a whole field of study that has been around for 30 years. This is statistical analysis; just because a computer crunched the numbers doesn't make it less valid. If all your research's calculations can be done by hand, sir, then you're discovering pre-school level self-evidences. Have you published anything noteworthy in a reputable journal? Someone who talks so big must have something to show for it. "All scientists are dumb" -- show me your PhD and then we'll talk.

And garbage in/garbage out applies much more to the process by which you arrived at your opinions than it applies to these MIT fellas' research.
fmfbrestel
4.9 / 5 (8) Dec 19, 2010
[sarcasm]
Easy explanation: God caused all life to evolve millions of times faster for the first thousand years the earth has existed.

or

Easy Deflection: These scientists are either incompetent, or atheistic deceivers.
[/sarcasm]

Ethelred
5 / 5 (11) Dec 19, 2010
Scientists play with their computer models and pretend they have discovered something.

Yeah, basicly that's what it amounts to.
No. Its a MAP. A map of genetic change. Which tells us rather a lot. Of course it tells us things you don't like so you feel obligated to invite some sort way to sneer at it. Tbat sort of active ignorance you both engage in is NOT going to make reality go away.

Pretty much summary of modern scientific method.
Well that post was a pretty good example of Active Ignorance in action.

Lets watch you ignore this question?

When was the Flood? Why isn't there any evidence for it?

If you have to avoid those questions then your beliefs are simply wrong.

Ethelred
StillWind
1 / 5 (15) Dec 19, 2010
re Jotaf, ad hominem attacks do not make your case, sir. It only shows that you are able to come up with insults, while being blissfully unaware of the substance involved.
Typical of the dumb masses.
Since you don't have a clue, I'll explain it for you again, although I have little hope that you can grasp, even this simple analogy.
Simply creating a computer program that will give you the results that you program it to, proves nothing at all.
I'm glad that you're impressed with nothing, but some of us actually have a clue, and aren't impressed with shiny objects.
It also makes no difference how long this pseudoscience has been around.
StillWind
1.3 / 5 (16) Dec 19, 2010
Eugenics has been around longer than this tripe, and although it is stronger than ever, it still has no real validity.
I could also point out that Tarot card reading has been around for thousands of years, but I doubt that anyone who cares about science is about to pull out a Waite deck and get started writing papers about the "results" that they come up with.
Pity, though, they'd probably be as valid as the paper that started this thread.
Finally, a long time ago, a very wise man pointed out that there are 3 kinds of lies. Lies, damned lies, and statistics.
True then, true now.
Once these guys come up with some real evidence and actually have something tangible to support their theories, then we can call it science.
The sad fact is that folks like you will still not understand the difference.
StillWind
1.4 / 5 (14) Dec 19, 2010

re: Ethelred

Kinda murky waters here, just trying to figure out the point that you're trying to make. I'd love to see you actually defend anything that you wrote, since you don't have a clue as to what any of us are saying.
Do you just enjoy making random pronouncements and insults for no reason?
Please do us all the honor of describing the scientific method in more appropriate terms than those already posted, explain just what results that you think that I, or anyone else would prefer, and show your work, since I'm sure we'd ll like to know the source of your clairvoyance, and finally describe which "flood" to which you are referring, and what relevance it has to this particular discussion.
vidar_lund
5 / 5 (10) Dec 19, 2010
re: StillWind

Physorg is obviously not a place for you, why don't you go somewhere else instead of just hurling insults.
Ethelred
5 / 5 (8) Dec 19, 2010
1/2
The scientific method intails observing a phenomenon
Which they did. Genes ARE phenomena.
, speculating about cause and effect,
Well in this case those are both known. Evolution is the effect and Natural Selection is the cause.
setting up an experiment to recreate the conditions that are involved with the proposed theory, and verifying the hypothesis.
Only true for some areas of science. Can't really be done in historical sciences.
None of this, beyond the existence of the phenomenon, can be verified.
Yes it can. YOU can go gather up all the genetic data available and make a map of genes vs. species like they did.

More
Ethelred
5 / 5 (10) Dec 20, 2010
2/2
Just because a computer model can be constructed to spit out the similar results, does not mean that it actually happened that way.
Its a MAP of genes not a simulation. A multidimensional map with a lot of data which would be rather hard to print out on 2d paper. That you didn't see this is evidence that you aren't interested in the actual science involved.
All we have is an unverifiable theory.
No. We have a verifiable map of genes across many species.
That is not science
Putting unordered data into a comprehensible order is most definitly science.
That is a nice story, but in any other circumstance, we'd call that a myth.
That is what the Bible has a lot of. This mapping technique is not a myth. They made reasonable conclusions based on that map.
It is in no way different from ancient Greeks stories about gods hurling thunderbolts from Mt Olympus.
Nonsense. However the Bible is not much different from Greek Mythology.

Ethelre
Ethelred
5 / 5 (10) Dec 20, 2010
Kinda murky waters here, just trying to figure out the point that you're trying to make
There was nothing murky there. I made my point. OC knows it.
I'd love to see you actually defend anything that you wrote, since you don't have a clue as to what any of us are saying
I know what OC and Dogbert were saying.
Do you just enjoy making random pronouncements and insults for no reason?
There weren't insults by me. I never say anything random.
and show your work,
I don't see any from you so that seems a touch hypocritical.
nce I'm sure we'd ll like to know the source of your clairvoyance
Didn't use any such thing. Just previous posts. OC and Dogbert are known Creationists.
and finally describe which "flood" to which you are referring, and what relevance it has to this particular discussion.
The people I was replying to know exactly which flood and I am positive you do as well so that seems a bit duplicitous of you to pretend you don't.

Ethelred
Jotaf
5 / 5 (12) Dec 20, 2010
"I could also point out that Tarot card reading has been around for thousands of years"
I was obviously speaking of an established science field, your comparison fails. Show me another one.

"Simply creating a computer program that will give you the results that you program it to, proves nothing at all."
It does if you program it with valid rules. Many discoveries nowadays begin with a simulation as a sort of "proof of concept", and though no one would call it "all the proof we ever need", it's still good evidence. If NASA's simulations tell us that an asteroid is going to hit the Earth, do you say it's bogus because a computer was involved in the process?

The statistical methods used in this paper are routinely used to discover cures for diseases. Some day you'll be treated by the same field you're badmouthing now. Our computational methods are getting pretty good, you're just jealous of how others are in the front line of discovery while you sit there and be cranky.
StillWind
1 / 5 (13) Dec 20, 2010
re: StillWind

Physorg is obviously not a place for you, why don't you go somewhere else instead of just hurling insults.


Kindly piss off.
StillWind
1 / 5 (12) Dec 20, 2010
re Ethelred

This is a battle of wits with an unarmed man, and it's not even fun anymore.

How sad for you.

Best of luck in life, you're going to need it.
Ethelred
5 / 5 (11) Dec 20, 2010
This is a battle of wits with an unarmed man, and it's not even fun anymore.
I disagree, I like teaching the ignorant. Not my fault you didn't come armed with evidence or reason and have only managed insults and the automatic gainsaying of whatever I say.
How sad for you.
I am sad that anyone would be so aggressively ignorant. It is my hope that you learn.
Best of luck in life, you're going to need it.
Ahh the standard surrender post of the ignorant. I see it a lot. Mostly from Cranks and Creationists. Some are made of sterner stuff. Zephyr for instance. He doesn't quit. Ever. Doesn't learn either. You do have that in common with him.

No guts no glory.

Everyone needs luck in life. Perhaps when you reach my age you will have managed to learn that. I hope you manage to learn SOMETHING.

In any case I thank for your clear surrender to a superior force. Anytime you want to try REASON or EVIDENCE do let me know. Its much more fun but so rare.

Ethelred
fmfbrestel
5 / 5 (10) Dec 20, 2010
Ahh, i see the young earthers are going the "researcher is incompetent" route. It is a very strong criticism since non of us have first hand knowledge of this particular research beyond the press release above. However, since any poster claiming deception/incompetence from the researcher also has no first hand knowledge of the methods (beyond what is included in this press release) they have even less ground to stand on then those trying to defend the researchers.
Javinator
5 / 5 (5) Dec 20, 2010
Typical of the dumb masses.


Facepalm.
CHollman82
4.6 / 5 (10) Dec 20, 2010
I don't know whether to laugh or cry after reading the first couple of comments... you would think this of all news sites would be relatively immune from the general public stupidity that permeates our society today, I guess I was wrong.

It's almost gotten to a boiling point, this conflict between the anti-intellectual and the educated, it will be nothing if not interesting to see what becomes of this social divide in the future.

"I'm an idiot and I hate everyone who isn't. Scientists from MIT are the enemy, they don't like to watch daytime television in their underpants. They understand things that no one needs to know and they try to bore everyone with it! Their fancy computer models are no match for my unwavering ability to deny anything and everything that conflicts with my simple and baseless beliefs! DEATH TO THE SCIENTISTS!!!
Jotaf
5 / 5 (7) Dec 20, 2010
fmfbrestel: I do have first-hand knowledge with some of this research so I can tell you I'm not defending it on a whim; it is worth the trouble :)

CHollman82: The first time I read comments like that I was baffled too. How can it be? What can they possibly gain by attacking people who are making discoveries and sharing?

StillWind: It's funny that your comment was several hours after mine, so there's no way you missed it -- I just composed a nice reply with no insults and defending these scientists. It means you found no flaw in my reasoning; thank you!
A_Paradox
5 / 5 (3) Dec 25, 2010
@Stillwind:
If it can't be verifeid, then it aint science.


Well that statement is actually wrong in one very important respect:
To be scientific a statement must be capable of falsification, in other words it must be that the statement can be used to make a prediction about part of the real world so that if the prediction is wrong then either part or all of the statement can be deduced to be wrong.

It occurred to me not long ago [I'm a slow learner :-] that if you ignore the supernaturalism of the cultural context, then the teachings of Jesus of Nazareth contain an important analogue of scientific method: forgiveness.

Scientific method proceeds by eliminating statements which are wrong. The person/s who made and defended the statement which turned out to be wrong will have made a very real contribution to human knowledge. [ ....cont]
A_Paradox
5 / 5 (2) Dec 25, 2010
Forgiveness ...cont
There is a very deep issue here about the nature of human knowledge. Those who understand the issue of falsifiability as the basis of science will probably tune in well to the idea that all human knowledge is actually of this nature. I mean human experience is _about_ the world, but in fact is [much of] what the brain is doing. So the experience is actually _in_ the brain but _about_ the world.

Before the advent of scientific method and its clear efficacy, people in general had no way of knowing that _all_ knowledge is constructed. Scientific method has allowed us to discover that naive realism - the basis of all traditional and assumed certainty - is normally practical but none the less deeply flawed. One of these flaws is the psychological projection which underpins supernaturalism.
Parsec
5 / 5 (4) Dec 25, 2010
Stillwind: its ok that you just do not understand the nature of this research. The mathematics of complex patterns is beyond the capability of most. However you seem unusually insulting and arrogant to those that do. In addition, you seem to have a mindset that excludes an understanding of what science is, and how scientific research is constructed.

One thing I agree with you about however, is that this research is conjecture, and until I see a solid prediction or piece of collaborating physical evidence, while I see it as quite reasonable; its still speculative.