4-Billion-Year-Old Fossil Protein Resurrected 84
First time accepted submitter Zoë Mintz writes "Researchers have 'resurrected' a 4-billion-year-old Precambrian protein and found they resembled those that existed when life began, proving that protein structures have the ability to remain constant over extended periods of time."
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Re: Alive (Score:5, Funny)
Ever heard of weather being hellish, or the flight being a torture, a meal being an orgasm in the mouth, a person being an asspain or buttmad? Lauguage is strange thing, and as they say: time flies like an arrow, fruit flies like a banana.
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Re:Alive (Score:5, Informative)
It is implied by the usage of resurrected.
Actually, we use "resurrected" for lots of non-living things, e.g. a plan [google.com].
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Re:Alive (Score:5, Funny)
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I'd welcome you to Slashdot, but something about your UID makes me think that's redundant.
I still think he's new here.
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I once had a ten-post argument with someone about whether or not "weapon" could be applied to something that was not literally intended to cause physical injury.
I try not to go more than one or two rounds with idiots anymore. It's an utter waste of time, and usually leaves me looking like an idiot too.
Re:Alive (Score:5, Informative)
No it isn't. I'm a scientist and we use the word resurrected too. We are talking about molecular resurrection, not whole organism resurrection. The scientific community re-purposes common words to mean different specific scientific things all the time. We use the word resurrection to mean that we made an ancient protein in the lab, and the protein still has it's original function. There is a big difference between just making a predicted ancestral protein in the lab, and having it actually work the same way it used to. The protein needs to fold correctly and be in the correct environment.
For more details of the previous use of this word, google "Ribosomal Paleontology and Resurrection".
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What did the researchers do specifically?
Re:Alive (Score:5, Informative)
They traced back the mutations of every thioredoxin variation to a common ancestor 4bn years ago. If you have three close species: A, B, C. The three share a variation of a protein which is exactly the same at nucleotid level except for one site, lets say: A: CGCGTA, B: CGTGTA, C: CGCGTA. You know, because of the rest of the genome, that A and B had a common ancestor 2 million years ago, and that common ancestor had a common ancestor with C 3 million years ago. Chances are that the original protein was CGCGTA. In this case, the reconstructed protein is the same as the A and C proteins, but given enough species you can use this kind of reconstruction techniques to figure out how the ancient version of a specific protein looked like.
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No it isn't. I'm a scientist and we use the word resurrected too. We are talking about molecular resurrection, not whole organism resurrection.
No we're not. From TFA: Since the proteins are re-creations, scientists can’t be certain they are exact replicas of the originals.
There is no resurrection. Only educated guesses as to what it may have been. There is no such thing as fossilized protein, unless you mean a rock that is in the shape of the original protein.
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That's because you're an ignorant heathen.
"On the third day, he rose again."
... and then he saw his shadow, and we had six more weeks of winter.
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The title of TFA, 4-Billion-Year-Old Fossil Protein Resurrected, Thioredoxin May Have Lived On Mars
In the article, the word "resurrected " is in quotes, so I'll give then a pass on that, although they should have put them in the title. While one expects headlines to be dramatic, this is a science article and we want to be accurate. The "May Have Lived On Mars" part is interesting. I suppose if the protein was active inside a living organism, one could legitimately say it "lived".
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(LUCA = Last Universal Common Ancestor.)
I read a lot of conflicting info about the early Earth. Is the end of the Hadean Eon and beginning of the Archean supposed to be when life began? Or is some other event supposed to divide the two eons, like perhaps the emergence of conditions hospitable to life? I've read that it is 3.8 gya or 4.0 gya. Why not say 3.9+/-0.1 gya? Obviously 4 was picked for being a very round number, but settling on a single number however round seems a bad idea. Makes it sound like we're more certain of those dates than we really are.
Much of our knowledge is sketchy and speculative. No one really says whether the first life forms might be considered bacteria, or archaea. The archaean domain is still new to science. Was only in the late 1970s that archaea were recognized as being different enough to qualify as a separate domain and not part of the domain of bacteria. Then there are fun ideas like the RNA world hypothesis. There's the idea that life could have started and died several times before achieving permanence. Panspermia is another notion.
Re:Sorta (Score:5, Interesting)
The LUCA dates range from 3.5 to 4 gya, so it's even broader than that. Different estimates come from different sources and with different precision, though, so it's not quite right to give a single symmetrical error measurement. I'd personally vote for saying 3.8 +0.2/-0.3 gya. In the case of this article, however, they chose 4 exactly because of their molecular clock predictions.
The article doesn't clarify between the Archean and Hadean periods, however, and it's probably bad to equate the LUCA with the beginning of life because we have pretty strong evidence that the LUCA was already a very well-developed organism, with a complete central dogma, hundreds of enzymes, and a preference for potassium ions over sodium ones. Wikipedia cites several science journalism pieces that argue for a Palaeoarchaean LUCA.
As for what the LUCA actually looked like, I would say somewhere between Archaea and Bacteria, but defying both categories. Archaeans have a number of later innovations that definitely disqualify them from being good representatives, since they can do sophisticated chromatin modelling (folding DNA to make gene transcription more efficient) and have a unique membrane composition (which I personally like to imagine may be evidence of multiple abiogenesis events, but that's a bit of an uninformed theory.) Bacteria, on the other hand, are known to have a tendency towards simplifying their genomes. If anything the bias seems to be toward Bacteria as the root; no one has recently proposed that Archaeans pre-date Bacteria.
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Not being any kind of Biology geek, please excuse if the question is dumb, but what makes you so sure that there is actually a LUCA? Considering that our cells contain mitochondria that, at least to my understanding, must have evolved separately before they somehow "got together" with other cells, wouldn't that, too, be some kind of hint that life as we know it was the fusion of various different random "chemical machines" (I'll use the term here, lacking a better one, to describe some molecules or combinat
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Mitochondria are thought to be a (relatively late) Major Event - the genetic and biosynthetic pathways were already fairly advanced.
The major idea behind a LUCA is that you can 'work the clock back' with DNA sequencing to something around 4 billion years ago AND that all life-as-we-know-it relies on a fairly specific set of chemical reactions. It's pretty clear that modern organisms are a mismash of A+C+B+x - nature hates to throw genetic material away. It's also perfectly reasonable to assume that life started / stopped multiple times and that bits of earlier life were indeed incorporated into later critters. When you start talking about that, you get into some terribly annoying semantic arguments (perfect for Slashdot).
The Holy Grail would evidence of organisms using wildly different chemistry (like incorporating arsenic into the DNA backbone [arstechnica.com] instead of Phosphorus) or some molecule that transferred genetic information without DNA or RNA entirely.
This is one strong reason why we should get our respective asses towards Mars. It offers the closest laboratory for finding off-world life. What that looks like (if it exists) is going to be one of the biggest scientific discoveries ever.
So, for life on earth, it's pretty clear that there is one LUCA - something started us along the pathway to RNA and DNA based life (I'm personally a proponent of RNA World [wikipedia.org]). And TFA implies that that this enzyme was present fairly early on. But something further back had to set the stage for the ability of an organism to fold amino acids into proteins, etc. TFA doesn't even begin to discuss what the chemistry would have been - that''s another story - but by the time Thioredox was on the scene, something was making RNA and there was something that looked like a ribosome - pretty advanced functions. How they got there is pretty much hand waving.
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ColdWetDog pretty much nailed it: endosymbiosis is believed to have happened [pnas.org] in the Proterozoic era, only 2.5 billion years ago, based on DNA evidence. This is also the same period [fossilmuseum.net] that the archaeological record suggests. Mitochondria and other plastids are actually just bacteria that hitched a ride; the mitochondrion is from a purple sulphur bacteria, the chloroplast is from cyanobacteria, and so on.
Personally, I don't believe that a lack of wildly different chemistry is proof there was a LUCA, although it
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A team of scientists from Columbia University, Georgia Institute of Technology and the University of Granada in Spain have successfully reconstructed active enzymes from four-billion-year-old extinct organisms.
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In their study, published in the journal Nature Structural & Molecular Biology, the researchers used vast amounts of genetic data to computationally reconstruct the genes of extinct species, a technique known as ancestral sequence reconstruction. The researchers then went a step further and synthesized the proteins encoded by these genes. They focused their efforts on a specific protein, thioredoxin, which is a vital enzyme found in all living cells.
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Much better source. Thank you.
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Yeah, that was funny after dismissing "trying to understand the evolution of birds by comparing several living birds".
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They took present-day versions of the protein in living organisms, used a computer to interpolate a hypothetical common ancestor, then 'found' sequence homology
Did they fill in the gaps with frog DNA?
"resembled those that existed when life began" (Score:3)
Which implies that we must know what proteins looked like 4Bn years ago.
Zoà Mintz overstated the ibtimes piece so extremely that she must be a "journalism" student jonesing for a job at Fox News.
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I'm thoroughly underwhelmed by this article.
Re:"resembled those that existed when life began" (Score:5, Interesting)
I can't sort out why. The statistical tools they used seem little different from how the proto-languages of major language families are reconstructed. In both cases you look at the genomic unit (in molecular biology that is genes and the proteins they encode, in comparative linguistics it's words, or more specifically cognates). In either case you cannot state with absolute certainty that the proposed progenitor unit (gene or cognate) has been reconstructed absolutely, but you can say with a reasonably high probability that you're pretty close.
Re:"resembled those that existed when life began" (Score:5, Informative)
With protein sequence evolution it's a little more controlled: the modifications occur more-or-less randomly, and there are almost no cases where a letter (residue) is replaced throughout the entire vocabulary (proteome) due to phonological shifts. As a result, if you have enough datapoints to work from, like with the thioredoxins, it's simply a matter of picking the version most commonly agreed upon by all of the branches. In that sense, it's more like textual criticism than historical linguistics, particularly since you can also use the requirement of "it has to be well-formed language" (i.e. a working protein) to weed out obviously bad combinations of changes.
For some reason, that bewilders a lot of reasonably scientifically-minded people.
Re:"resembled those that existed when life began" (Score:5, Interesting)
I didn't mean to say they were identical, but still, at least in the Indo-European languages (and I'm sure it can be found in other language families) there are some pretty highly conserved cognates, like pHtér (father). In most cases throughout the various Indo-European families one can trace pretty predictable sound changes to explain why pHtér became pater in the Italic languages. pitár in Sanskrit and father/fadar in the Germanic languages. Yes, there's a good deal more horizontal transfer in languages, and indeed in some cases words will disappear from some members of the family, but in general, the core vocabulary of the proto-language is pretty highly conserved in its descendants. Even in English, with its vast importation from the Norman invasion onward of Romance and Greek words, the core vocabularly remains Germanic, and the sound shifts from the Proto-Germanic thru West Germanic thru to Modern English tend to follow regular rules. It's actually kind of cool, because even where you have a word that was adopted from another language, you can usually determine when roughly it happened by the way in which it was or was not effected by the sound changes going at the time.
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Yeah, I'm actually a fan. I wanted to be an historical linguist when I was a teenager, but I was worried about job security and ended up in evolution as a result. There are lots of different sophisticated evolutionary systems out there that all obey the same basic structure (governments, cultures, religions, public-domain code snippets, Linux distros...) and the little nuances that distinguish them from each other can be downright mesmerising. (But to be honest I find the whole Germanic language family bori
Re:"resembled those that existed when life began" (Score:4, Interesting)
For some reason, that bewilders a lot of reasonably scientifically-minded people.
Just because you can come up with one or more best fit versions from what currently survives, doesn't mean that they resemble the original source of the evolutionary pattern.
Re:"resembled those that existed when life began" (Score:5, Informative)
To be fair, the IB Times article doesn't do a very good job of explaining the lengths the researchers went to in order to avoid that. Here's a summary:
In the future, here's how to read scientific news stories (at least molecular biology ones):
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To be fair, the IB Times article doesn't do a very good job of explaining the lengths the researchers went to in order to avoid that.
In other words, it's yet another research paper where they claim to have dealt with an problem without actually having done so. For example, high precision results which are compared and fitted to an extremely poorly understood past.
Their way of getting around it was to ensure consistency at various time-steps
While I agree that this is an attempt to deal with my final concern below (about the biases that evolution puts into place) this is also a great way to introduce researcher biases into the final results. Recall that "time steps" are degree of change of the protein and have at be
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In other words, it's yet another research paper where they claim to have dealt with an problem without actually having done so. For example, high precision results which are compared and fitted to an extremely poorly understood past.
The results are not fitted; the observation that the enzyme performs better under an acidic environment was spontaneous and unguided.
While I agree that this is an attempt to deal with my final concern below (about the biases that evolution puts into place) this is also a great way to introduce researcher biases into the final results. Recall that "time steps" are degree of change of the protein and have at best a vague positive correlation with the passage of time. So what "time steps" are important and how to group that high precision data? These are subjective choices that can influence the outcome.
The time steps are actually the most recent common ancestors of various clades, and are not arbitrary at all. There is nothing subjective involved in this part of the process, and no dates for these are claimed explicitly in the paper; only the roots of trees. The only claim to a specific date being made is that the last universal common ancestor lived about four billion years
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+ 5 - If Slashdot had stickies, this would be up top on Biology / Molecular Biology articles. Tape this to your monitors, folks.
(Except as a caveat, even Nature / Science / PNAS and Cell have blown it big time on occasion. Nothing is certain. Eat dessert first. Do Not Taunt Happy Fun Ball.)
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You are judging it based on the press release. You haven't read the original article, and you are not an expert peer in the field. This is cutting edge research in the field done by world class research institutions. Figuring out what happened 4 billion years ago is not easy. One of the Principle Investigators on this paper is on my thesis committee. He is very rigorous, always telling us to do things more rigorously then we want to do. You can't judge an article based on the press release.
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Technically there is a bit of a limit—it's probably more like 3.5 to 3.8 billion years ago and not four. A pretty severe mistake, yes, but technically the exact date of the last universal common ancestor is still under debate.
And yes, we do have the knowledge to infer, to within a relatively modest degree of error, the correct sequence and structure of certain extremely well-conserved proteins all the way back that far. It's called multiple sequence alignment, and it's honestly pretty basic.
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we do have the knowledge to infer, to within a relatively modest degree of error, the correct sequence and structure of certain extremely well-conserved proteins all the way back that far
It's too easy to make the mentally lazy step from "we infer to within a relatively modest degree of error" to "we know".
That kind of hubris shakes laypeople's trust that what scientists say is to be believed, when the "relatively modest degree of error" turns into out and out "wrong".
Re:"resembled those that existed when life began" (Score:4, Informative)
Re:"resembled those that existed when life began" (Score:4, Informative)
...sorry, I've read the article a little more closely and I made a couple of factual errors in my other reply to you and the one before it. There were small structural changes, and the primary purpose of this paper was to investigate ways of detecting them. Convergent evolution (every copy changes at once after a split) does occur in protein structure and sequences, primarily due to large-scale environmental changes.
The paper's primary contribution is that they stepped back gradually, rather than doing a bulk sequence alignment (what they called a "vertical" approach rather than a "horizontal" one) and found that to maintain function, certain shifts had to occur. (The details of which are rather boring.) Rather encouragingly, they found that, by the time they'd stepped back all the way to the beginning, the changes the protein experienced meant that it would perform optimally in a chemical environment much like the one archaeology has shown us was ubiquitous in the Precambrian era. Not only does this support the idea that their results are very close to being correct, it also tells us that the LUCA probably had a fair amount of time to evolve its thioredoxin to that environment.
Does anyone, and i mean ANYONE, question the age (Score:1)
Re:Does anyone, and i mean ANYONE, question the ag (Score:5, Funny)
It's faintly possible that an absolutely essential component of cellular function suddenly worked its way into the genomes of every single organism on Earth one Tuesday afternoon, and that despite every indication of all copies being descendant from a single master source, they were simply made to look that way after the fact, and that the last universal common ancestor got along just merrily without it, despite it being much more logical that this one particular protein happened to be there alongside all the other ancient essential proteins we know and cherish... but that would require an incredibly petty and childish divine being, or one with terrible planning skills. Possibly the divine being that buries dinosaur bones to test the faith of His followers.
So, no; not really. Why do you ask?
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Is it possible something got uploaded to a torrent (or the other thing that we don't talk about) that contained watermarks so He could catch the infringers?
I figure it wasn't a meteorite that did for the dinosaurs; they got sued to death by the RIAE.
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I really have to be more careful about making glib off-the-wall comments. This isn't the first time I've said one that was true.
One place I worked at a long time ago had an informal taboo against saying "But nobody would ever be stupid enough to ..." on the grounds that on uttering it somebody would do precisely that.
I'm wondering if there's some underlying mechanism behind this, and that rule 39 is just another manifestation of it.
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"Men rarely (if ever) manage to dream up a god superior to themselves. Most gods have the manners and morals of a spoiled child. "
Heinlein
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To be fair to the journalists, it wasn't them doing the rounding: Conservation of Protein Structure over Four Billion Years [sciencedirect.com].
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To be fair to the journalists, it wasn't them doing the rounding: Conservation of Protein Structure over Four Billion Years [sciencedirect.com].
OK, then, let's look at the first sentance of the summary of the source:
"Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales."
^^^^^^^^^^^^^
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Yes, relatively little compared to a lot of biology. This is origin of life, or in another word, abiogenesis research. This is a very young and small field. The field is wide open for ground breaking discoveries. The research community is just beginning to organize. Abiogenesis is hard. How do you create life from no life, without the interference of God? The answer is that there are hundreds, thousands of steps, and each one has to be figured out, and it can take years of work and millions of dollars. The
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Right, but the object of the paper is to then advance what is known in that very area, in which I think it is highly successful. Varieties of thioredoxins are present in every free-living organism on earth. One of their many functions is to donate electrons to an enzyme called ribonucleotide reductase which converts ribonucleotides into deoxyribonucleotides, so in a roundabout way, working thioredoxin proteins are necessary to make DNA. Between its ubiquity and general structural similarities in modern orga
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We have a pretty good idea of the minimum genome needed for a free-living organism, and even if we figure out what that possible ancestral genome looks like, we still know nothing of how it came to be. Any cell is a spectacularly complicated machine, and for it to fall together spontaneously is improbable b