Slashdot Mirror


Scientists Decipher 3-Billion-Year-Old Genomic Fossils

hnkstrprnkstr writes "MIT scientists have created a sort of genomic fossil (abstract) that shows the collective genome of all life underwent an enormous expansion about 3 billion years ago, which they're calling the Archean Expansion. Many of the new genes appearing in the Archean Expansion are oxygen related, and could be the first biological evidence of the Great Oxidation Event, the period in Earth's history when oxygen became so plentiful that many anaerobic life forms may have become extinct."

21 of 217 comments (clear)

  1. At last! by lpaul55 · · Score: 3, Funny

    I can breathe!

    --
    ... now back to the bit mines.
  2. For the "but it's just a computer model!" trolls by Daniel+Dvorkin · · Score: 3, Insightful

    Go here. Follow, read, and understand the links on the first, say, three or four pages of search results. Then, maybe, you'll know enough to have a meaningful opinion on the subject.

    --
    The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
  3. Wait, what? by WD · · Score: 3, Funny

    I'm confused. So they were on the Ark or what?

    1. Re:Wait, what? by garyisabusyguy · · Score: 4, Interesting

      really, creationism is the 'elephant in the room' whenever you start talking about the fossil record

      what I find interesting about the article is the layering effect of life. how the anerobic life got pushed out by the oxygen breathers and relegated to living in the cracks. good for us, but an extinction event for them. there have been many big extinctions, and each allowed some hardier form of live to make it to the next expansion. we are in a current extinction event (holocene), and have started to worry about an asteroid or some such wiping us out.

      even that worry over our own 'extinction' bumps up against any number of religious beliefs, even if they seem to have an unrealistic timescale of tens of years, when any historical events have been separated by millions of years

      so, gimmee something here, how do you discuss geologic events when people seem so driven to think in terms of their own lifespans?

      --
      Wherever You Go, There You Are
    2. Re:Wait, what? by Black+Parrot · · Score: 3, Funny

      I'm confused. So they were on the Ark or what?

      Why do you think they call them 'Archean'?

      --
      Sheesh, evil *and* a jerk. -- Jade
    3. Re:Wait, what? by ColdWetDog · · Score: 5, Funny

      so, gimmee something here, how do you discuss geologic events when people seem so driven to think in terms of their own lifespans?

      Very, very slowly.

      --
      Faster! Faster! Faster would be better!
    4. Re:Wait, what? by ralphdaugherty · · Score: 3, Interesting

      what I find interesting about the article is the layering effect of life. how the anerobic life got pushed out by the oxygen breathers and relegated to living in the cracks. good for us, but an extinction event for them. there have been many big extinctions, and each allowed some hardier form of live to make it to the next expansion. we are in a current extinction event (holocene), and have started to worry about an asteroid or some such wiping us out.

      even that worry over our own 'extinction' bumps up against any number of religious beliefs, even if they seem to have an unrealistic timescale of tens of years, when any historical events have been separated by millions of years.

      I'm a programmer but just happen to be reading Nick Lane's books on this. If I get something wrong please biologists jump in and correct me. :)

      I only read a page or two a day (first "Oxygen", and now "Power, Sex, Suicide" - and yes, that's all based on oxygen). But the revelation I had yesterday was that anaerobic bacteria essentially drown in oxygen, just as we would suffocate with too little oxygen, which by the way is not that much below the historic percentage of atmosphere for last several hundred million years of 21%. Dropping below about 15% of atmosphere would kill all oxygen breathing life.

      So anaerobic life which ruled the world didn't get pushed out by oxygen breathing life, it got pushed "out", or down into stagnant places rather, by oxygen, which was created by photosynthesis. Almost all the oxygen over .1% of the atmosphere was created by photosynthesis in plant life.

      And what became of that anaerobic life in the sea with .1% oxygen? It exists to this day in our cells, which are in the same salt water of the sea in our body and exposed to .1% oxygen delivered by hameoglobin in the blood. It also exists in our intestines among other places with little oxygen, such as bottoms of swamps.

      The kicker? People talk of evolution and they have no idea. All current life was set in place nearly three billion years ago. Every complex thing you ever read about in the human body cells is in every cell of every life form for almost three billion years.

      DNA, RNA, mitochondria, conversion of glucose to storage of energy in ATP molecules using an extremely complex 12 step process, manufacture of the same proteins with ribosomes, fermentation to create energy without even that .1% of atmosphere oxygen when necessary (such as our muscles which fermentation kicks in when needed and creates a byproduct lactic acid which eventually causes cramps), respiration using haemin which is haemoglobin in blood and clorophyll in plants, everything was set almost three billion years ago.

      Nothing has evolved, it has only specialized.

      The bigger question is how this complex machinery of life developed in the first billion years of Earth amidst massive meteor impacts. People can call it what they want, but knowing that all life that has ever existed has existed essentially unchanged from three billion years ago defies explanation of "evolving" in first one to two billion years to the amazing complexity of how cells work and then staying pat for almost three billion years and only losing capabilities, not gaining new and more complex capabilities as one assumes from casual science study and reading.

      I am not religious and do not consider religious arguments against evolution as anything but pedantic handwaving, but what we call evolution is really rather trivial specialization implemented by the ancient common embryo genes.

      I could go on and I'm probably leaving out even more stuff that took my breath away when I read it but people have no idea the ancient universality of all life forms from the same unbelievably complex cell from three billion years ago.

        rd

    5. Re:Wait, what? by Lloyd_Bryant · · Score: 4, Insightful

      Nothing has evolved, it has only specialized.

      The bigger question is how this complex machinery of life developed in the first billion years of Earth amidst massive meteor impacts. People can call it what they want, but knowing that all life that has ever existed has existed essentially unchanged from three billion years ago defies explanation of "evolving" in first one to two billion years to the amazing complexity of how cells work and then staying pat for almost three billion years and only losing capabilities, not gaining new and more complex capabilities as one assumes from casual science study and reading.

      Why would you expect the "gaining of new and more complex capabilities"? Evolution is not oriented towards perfection. It's oriented towards "good enough". So it's quite possible that all those 3 billion year old mechanisms have been "good enough" to meet all conditions encountered since then, in which case unless the "new and more complex capability" provided a substantial survival advantage, it won't have become commonplace. And since "more complex" generally means "more expensive in terms of energy consumption", any mutations in that direction could quite likely have been a survival *disadvantage*.

      --
      Don't tell me to get a life. I had one once. It sucked.
    6. Re:Wait, what? by Black+Parrot · · Score: 5, Insightful

      The bigger question is how this complex machinery of life developed in the first billion years of Earth amidst massive meteor impacts. People can call it what they want, but knowing that all life that has ever existed has existed essentially unchanged from three billion years ago defies explanation of "evolving" in first one to two billion years to the amazing complexity of how cells work and then staying pat for almost three billion years and only losing capabilities, not gaining new and more complex capabilities as one assumes from casual science study and reading.

      a) How long should we have expected that first billion years of evolution to take?

      b) You should rephrase "not gaining new and more complex capabilities" to say "at the cellular level". At higher levels, progress has been phenomenal. (How much smarter are you than a single-cell organism?)

      The origin of cellular machinery is indeed impressive, but unfortunately "I can't believe it could happen by natural causes in a billion years" tells us a little about the speaker's beliefs, and nothing at all about what actually happened.

      As to why not much new has been added to that machinery since, maybe we have more basis for speculation. Competition from all-new "designs" is probably impossible, because the necessary building blocks would probably be oxidized, or digested by current organisms, before it could bootstrap itself into a new cell type. For variants on what we have, evolution is not a reversible process, so we can't expect cells to undo part of their history and try something else, any more than birds would evolve back into dinosaurs and go then forward again down a different path.

      So we're probably stuck with consideration of add-ons to the current machinery. But there's no guarantee that something nifty would happen in that regard within any bounded period of time. Evolution doesn't provide organisms with things just because they are needed or would be useful. Possibly cellular evolution has reached a "local maximum" on the fitness landscape, from which there is no easy jump to something better.

      And who knows... some of the past jumps may not have been particularly easy either, but merely fortuitous one-time events.

      And evolution of macroscopic organisms has certainly gotten a lot of mileage out of the existing cellular machinery. Maybe it's good enough?

      --
      Sheesh, evil *and* a jerk. -- Jade
    7. Re:Wait, what? by Artifakt · · Score: 4, Insightful

      Except the original Hebrew word didn't mean a day, and was often used in other writings to mean an indeterminate period. If you're asking how you can trust a poor translation job, you may be on to something, but the original text didn't use the English word 'day' at all, let alone redefine it.
      Alternately, some people claim the account in Genesis is metaphorical. Now I'm not arguing that it definitely is or isn't, but your argument seems to be that if it is metaphorical, it's untrustworthy in some absolute sense. I.e. "Carl Sagan used a metaphor of the Milky Way as the Backbone of Night in Cosmos, so how can we trust anything else in Cosmos?" Or maybe you're going as far as "The discoverer of the Benzine ring used a metaphor of a snake devouring its tail to describe it, so how can we trust anything in organic chemistry?".

      --
      Who is John Cabal?
    8. Re:Wait, what? by Gogogoch · · Score: 5, Informative

      "All current life was set in place nearly three billion years ago". Absolutely not - your view of the history of biology is very warped. Study more biology itself to realize what 'current life' actually looks like. Some important points:

      1.7~2 Billion years ago: probable endosymbiosis of prokaryote into eurkaryotic cells, forming mitochonria. Much later than the 3 billion years you suggest, and an absolutely vital stage in the evolution of multicellular life. In fact, it is suggested that the emergence of mitrochondria is why we are here to day - without these powerhouses single-celled life did not have enough available energy to form multi-cellular organisms.

      1~1.3 Billions years ago: complex multi-cellular life: While the diversity, resilience, and ubiquity of single-celled life is amazing, I find complex multi-celled life much more astonishing. That colonies of cells can cooperate, specialise and form complex life is a wonderful achievement of evolution. Of course, it took a mind-boggling amount of time. Still, a significant step the results of which are quite distinct from life of 3 billions years ago. So your assertion is again inadequate.

      ~600 million years: emergence of the first neuron.

      ~580 million years: nerves and muscles, working together; first eyes

      ~550 million years: brains

      And so the list goes on. Perhaps a significant development every 10-20 million years.

      ~540 million years: hearts and circulatory systems

      There is a giant change from single-celled life to cats, dogs, and humans. What you should be saying is that, as a programmer, you are amazed that all life on Earth has the same genetic code - that the 3 base-pair codon is almost universal in every cell and organism on the plant. I suppose I do like you perspective though, when you look at a yeast cell, an oak tree, and a human and realise they are all related, all cousins, all derived from an evolutionary chain billions of years in the making.

    9. Re:Wait, what? by Graff · · Score: 5, Informative

      I only read a page or two a day (first "Oxygen", and now "Power, Sex, Suicide" - and yes, that's all based on oxygen). But the revelation I had yesterday was that anaerobic bacteria essentially drown in oxygen, just as we would suffocate with too little oxygen

      They don't "drown" in oxygen. Oxygen is a highly reactive substance, cut an apple and it browns fairly rapidly, expose iron to air and it will rust, those chemical hand warmers take oxygen from the air in order to produce heat. Some organisms, called obligate anaerobes, can't tolerate an environment with high oxygen content because it poisons them by destroying enzymes and interfering with key biological pathways in those organisms.

      When organisms came about that produced large amounts of oxygen (a byproduct of photosynthesis, as well as other reducing processes) they basically polluted the environment by producing so much oxygen. This oxygen "pollution" poisoned most of the organisms of the time until some evolved ways to break down and even use the oxygen. Once this happened there was an explosion of oxygen-using organisms. It turns out that since oxygen is so reactive it makes a great agent to "burn" (oxidize) other materials and produce energy.

      However, there are many anaerobes that can survive in an oxygen environment - some can even use a little of the oxygen when it's available. There's no hard and fast cutoff of how much oxygen is too much or too little. As levels rise there will be more wildfires and the less oxygen-tolerant organisms will struggle, as levels fall the more oxygen-reliant organisms will have problems. A partial pressure for oxygen of 0.15 kPa (15% at STP - standard temperature & pressure) will certainly cause a lot of problems for many oxygen-reliant organisms.

    10. Re:Wait, what? by Marcx77 · · Score: 3, Interesting

      The point is that this is extremely complex biochemical machinery that is mind boggling to even imagine how this somehow came together.

      I am more inclined to think it came from space than anything.

      How would that make it less mind-boggling? It just relocates the problem. Does it somehow make more sense to think that life had a few billion more years to evolve on some other planet than just 1.5 billion years here on earth? I'm not trying to be pedantic here, I'm genuinely curious as to how you'd think "space" is a better explanation...

  4. Re:Creationism by Daniel+Dvorkin · · Score: 5, Funny

    40% of US residents believe in creationism. What are you going to say to them, huh?

    As little as possible.

    --
    The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
  5. The Great Memory Leak by Anonymous Coward · · Score: 3, Funny

    This is what happens when you don't free() your genes after you're done with them.

  6. Re:Creationism by gman003 · · Score: 5, Insightful

    Simple. "God works in subtle, mysterious ways. Who is to say that He did not create the universe in such a way that the precise results He wished to occur would occur, like an intricate, universe-wide set of dominoes? Could not evolution be the means by which He created man?"

    If they continue to argue, hit them with a crowbar.

  7. Re:Creationism by PPH · · Score: 5, Insightful

    The overwhelming majority of human progress has come from people who were or are highly religious.

    Or claimed to be in order to escape the current Inquisition.

    --
    Have gnu, will travel.
  8. Re:Creationism by adamofgreyskull · · Score: 5, Insightful
    I'm sorry, but that's a ridiculous argument. So what? Newton was religious. Richard Feynman isn't. Richard Dawkins isn't. Thomas Edison wasn't. Sigmund Freud wasn't. Stephen Hawking isn't. Peter Higgs isn't. James Watson isn't. These people aren't/weren't. So what? People make discoveries and come up with inventions. Some of those people believe in religion, some of them don't. Measuring relgion's impact on progress by naming famous religious scientists/inventors...down that path lies madness.

    On the other hand, many murderers, mass murderers even, are/were "highly religious" and of course, in the middle of those two extremes, there are many many many many many many many other people who have made no impact on society whatsoever, doomed to be excluded from the annals of history by their mediocrity who are (or were) "highly religious". You can't just hold up an example of a great scientist who was also religious and say:

    "Look! That proves it!!! Human progress is impossible without Religion!!"

    I think if you replaced Newton's headstone with a magnet and wrapped his coffin in wire, you'd produce a measurable current every time you did say that.

    The "overwhelming majority of human progress" is in the past, due to the fact that the present is still happening and we can't see into the future. Society is becoming more secular. Many countries still have blasphemy laws. Some countries will stone you to death if you criticise a man who's supposedly an emissary of a prophet of a god. How many people were hanged/stoned/shot to death because of their godlessness who might have come up with calculus, or the "law of gravity" or the bagless vacuum cleaner or any one of a number of Really Great Things? How many were excluded from schools/universities because of accidents of birth, or because of their religious beliefs (which is pretty much the same thing).

    How many scientists paid lip service to God and religion because it was an established social convention. How many scientists paid lip service to God because the church was giving them money? If you were studying at one of the earliest 12th-14th century(I think) church-run universities would you come out with a heretical theory that suggested that God might not exist? No. No you wouldn't.

  9. Re:Creationism by c6gunner · · Score: 3, Insightful

    Nice logic! Got another one for ya: The overwhelming majority of murders and rapes were committed by people who were or are highly religious. Guess that proves that theists are inherently immoral, eh?

  10. Re:For the "but it's just a computer model!" troll by pinkushun · · Score: 4, Informative

    Wow, the first result is very interesting, and mostly understandable, because the ideas read much like similar programming concepts. And it even contains a car analogy!

    The character ’existence of engine’ is compatible with the tree of Figure 2.1 (a) as the
    motor is invented once in the edge connecting the root and the common ancestor of car and
    motorcycle. The same character is not compatible with the tree in Figure 2.1 (b) where the
    engine is invented twice. The character ’number of wheels’ is compatible with both trees.

  11. Re:Let's get rid of that oxygen by h00manist · · Score: 3, Insightful

    Shut down the coal mines. Yes, coal, gas and oil have to go - basically carbon from underground that people burn. Limited resources, causing dispute, war, monopolies, smoke, soot, noise. Nuclear and hydroelectric works just fine, most of NYC trasportation runs on electric power. Millions of people get to work and back every day, fast with no traffic - on electric power. Get PRT and it'll be faster than any car-based system can ever be.

    --
    Build your own energy sources from scratch. http://otherpower.com/