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4-Billion-Year-Old Fossil Protein Resurrected

samzenpus posted about a year ago | from the back-in-the-day dept.

Science 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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Alive (0)

Anonymous Coward | about a year ago | (#44517133)

Hows a protein alive?

Re:Alive (3, Informative)

GigaplexNZ (1233886) | about a year ago | (#44517147)

Nowhere in the title, summary or article was the word "alive" mentioned.

Re: Alive (0)

Anonymous Coward | about a year ago | (#44517167)

It's implied on the "ressurrected" word?

Re: Alive (2)

Anonymous Coward | about a year ago | (#44517283)

Ever had an old clunker of a car die and get resurrected by mechanics?

Re: Alive (5, Funny)

Anonymous Coward | about a year ago | (#44517849)

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.

Re: Alive (0)

Anonymous Coward | about a year ago | (#44519337)

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.

My favourite is "Hurry the fuck up"
1. Hurry (to get away from) the fuckup
2. Hurry (along) the (really bad person what a total) fuck up.
3. Hurry the (sexual act) fuck (in the) up(ward direction)
4. (The man named) Hurry (is the ultimate) fuck up

Re: Alive (0)

Anonymous Coward | about a year ago | (#44520197)

Grow the fuck up.

Re: Alive (1)

Anonymous Coward | about a year ago | (#44522021)

Grow's not a fuck up. I heard he's doing well these days.

Re:Alive (0, Interesting)

Anonymous Coward | about a year ago | (#44517183)

It is implied by the usage of resurrected.

Re:Alive (4, Informative)

Black Parrot (19622) | about a year ago | (#44517287)

It is implied by the usage of resurrected.

Actually, we use "resurrected" for lots of non-living things, e.g. a plan [google.com] .

Re:Alive (2)

Samantha Wright (1324923) | about a year ago | (#44517419)

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'd welcome you to Slashdot, but something about your UID makes me think that's redundant.

Re:Alive (5, Funny)

fellip_nectar (777092) | about a year ago | (#44518089)

Our chief weapon is surprise...surprise and fear...fear and surprise.... Our two weapons are fear and surprise...and ruthless efficiency.... Our *three* weapons are fear, surprise, and ruthless efficiency...and an almost fanatical devotion to the Pope.... Our *four*...no... *Amongst* our weapons.... Amongst our weaponry...are such elements as fear, surprise.... I'll come in again.

Re:Alive (1)

Kinthelt (96845) | about a year ago | (#44519519)

I'd welcome you to Slashdot, but something about your UID makes me think that's redundant.

I still think he's new here.

Re:Alive (2)

Kozar_The_Malignant (738483) | about a year ago | (#44521699)

Similar to the old definition of Usenet being a bunch of people with sticks beating a muddy spot on the ground where a dead horse used to be.

Re:Alive (1)

Black Parrot (19622) | about a year ago | (#44522359)

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 (0)

Anonymous Coward | about a year ago | (#44518351)

When a plan is resurrected, it means it was dead before and now it's alive again.

Re:Alive (5, Informative)

Anonymous Coward | about a year ago | (#44517317)

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".

Re:Alive (2)

Internetuser1248 (1787630) | about a year ago | (#44517803)

If you are a scientist, maybe you can explain what this article is even about. I read the summary and just boggled. So I went and read TFA. That was not very enlightening either. I went to the wikipedia article about Thioredoxin which turns out to be a useful and common protein.

What did the researchers do specifically?

Re:Alive (5, Informative)

Anonymous Coward | about a year ago | (#44518115)

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.

Re:Alive (1)

Princeofcups (150855) | about a year ago | (#44520689)

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.

Only foolish and unimaginative people do that. (0)

Anonymous Coward | about a year ago | (#44523771)

Perhaps one might say "reinstantiated" or "recreated" instead of "resurrected" if what one actually means is "recreated" or "reinstantiated". I mean, instead of purposely using an incorrect term and claiming Humpty-dumpty's right of random redefinition.

The scientific community re-purposes common words to mean different specific scientific things all the time.

The insufferably lame portion of the scientific community, you mean. Here in computer science we occasionally have a few people who can understand the value of semantics, so we have virii instead of viruses, bytes instead of bites, and gibibytes just to drive the SI boys nuts.

Sam Watterson had something to say about this [coimbra.lip.pt] .

Quark, quark, quark, quark.

Re:Alive (0)

Anonymous Coward | about a year ago | (#44517799)

surrection - n. A rising; an insurrection. (from The Century Dictionary and Cyclopedia)

I don't see how resurrected could imply alive. I do however see how it could imply that a similar process has happened before.

Re:Alive (0)

Anonymous Coward | about a year ago | (#44518509)

I don't see how resurrected could imply alive.

That's because you're an ignorant heathen.

"On the third day, he rose again."

Re:Alive (1)

redneckmother (1664119) | about a year ago | (#44522507)

I don't see how resurrected could imply alive.

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.

Re:Alive (0)

Anonymous Coward | about a year ago | (#44518625)

Implied, Lisa... or implode?

Re:Alive (2)

invid (163714) | about a year ago | (#44518813)

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".

Re:Alive (0)

Anonymous Coward | about a year ago | (#44520035)

Like a bad dream from the movie young Frankenstein a researcher yells "It's ALIVE". However in this dream the fossil's protein structure's DNA made a clone of one of my dinosaur fuck witch face grade school teachers. She was great horror movie material, complete with crooked yellow teeth, bad breath, strange hair and that voice.. like scraping nails across the chalk board..

Yeah, tell me about it... (-1)

Anonymous Coward | about a year ago | (#44517149)

The bastard runs News Corp. and a slew of shitty tabloids.

Sorta (5, Insightful)

dnadoc (3013299) | about a year ago | (#44517181)

They took present-day versions of the protein in living organisms, used a computer to interpolate a hypothetical common ancestor, then 'found' sequence homology - but people already knew the sequence was highly conserved, it's evident in modern organisms. There were no "fossils" involved. And conserved sequences make for poor molecular clocks, so who knows if it was 4 billion years ago.

Re:Sorta (5, Informative)

Samantha Wright (1324923) | about a year ago | (#44517255)

The key is that because thioredoxins are found in all of the kingdoms, and are so conserved, the authors are assuming this is what the thioredoxin in the LUCA looked like. Even if the molecular clock isn't accurate over this one protein because of masked mutations, the number's most likely sound. (To one significant figure, anyway, since the LUCA is held to be 3.5 to 3.8 gya.)

Re:Sorta (5, Informative)

bzipitidoo (647217) | about a year ago | (#44517695)

(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 (5, Interesting)

Samantha Wright (1324923) | about a year ago | (#44517789)

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.

Re:Sorta (2)

Opportunist (166417) | about a year ago | (#44518145)

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 combination of molecules that have an effect on its surroundings that allow it to reach a state of higher energy), and the forms that actually gained a benefit from each other survived?

That doesn't necessarily lead up to a LUCA, though, since molecule groups A+B could form "Lifeform" X, A+C form Y and A+B+C form Z.

Re:Sorta (2)

Sique (173459) | about a year ago | (#44518355)

Read that post again, she actually hinted at possible evidence for multiple abiogenesis.

Re:Sorta (4, Interesting)

ColdWetDog (752185) | about a year ago | (#44520337)

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.

Re:Sorta (1)

Samantha Wright (1324923) | about a year ago | (#44528123)

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 its existence would be strong evidence of disproof. The reason we believe in a single LUCA is quoted really well in the appropriate Wikipedia article [wikipedia.org] : the number of genes in common between Archaea and Bacteria is much too high for them to have been shared later.

Re:Sorta (5, Informative)

c0lo (1497653) | about a year ago | (#44517289)

Better source [columbia.edu]

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.
[...]
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.

Re:Sorta (1)

quax (19371) | about a year ago | (#44517431)

Much better source. Thank you.

Re: Sorta (0)

Anonymous Coward | about a year ago | (#44517533)

They're exaggerating here too.

By resurrecting proteins, we are able to gather valuable information about the adaptation of extinct forms of life to environmental alterations that cannot be uncovered through fossil record examinations

Reconstructions of highly divergent sequences don't produce functional proteins. Reconstructions of conserved sequences are going to be stable in a wider range of environments because of all the bottlenecks over billions of years - they say nothing about particular time periods. The whole field is riddled with assumptions not found in the rest of biology, especially with respect to linear mutation rates.

Re:Sorta (1)

Black Parrot (19622) | about a year ago | (#44517295)

Yeah, that was funny after dismissing "trying to understand the evolution of birds by comparing several living birds".

Re:Sorta (1)

Hatta (162192) | about a year ago | (#44520879)

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" (2)

Nutria (679911) | about a year ago | (#44517193)

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.

Re:"resembled those that existed when life began" (0)

O('_')O_Bush (1162487) | about a year ago | (#44517243)

"Since the proteins are recreations, scientists can’t be certain they are exact replicas of the originals. "There is no way to make absolutely certain unless we invent some kind of time machine," Sanchez Ruiz said. "

I'm thoroughly underwhelmed by this article.

Re:"resembled those that existed when life began" (4, Interesting)

MightyMartian (840721) | about a year ago | (#44517335)

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" (5, Informative)

Samantha Wright (1324923) | about a year ago | (#44517357)

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" (4, Interesting)

MightyMartian (840721) | about a year ago | (#44517411)

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.

Re:"resembled those that existed when life began" (2)

Samantha Wright (1324923) | about a year ago | (#44517441)

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 boring. Xenophilia, probably.)

Related factoid: the first phylogenetic constructions of biological sequences were based on principles borrowed directly from stemmatics.

Re:"resembled those that existed when life began" (3, Interesting)

khallow (566160) | about a year ago | (#44517569)

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" (4, Informative)

Samantha Wright (1324923) | about a year ago | (#44517649)

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:

  • - The researchers were acutely aware of the exact problem you described, and spent several paragraphs on it in their background section.
  • - Their way of getting around it was to ensure consistency at various time-steps, which revealed a gradual change in the shape of the protein overall that wouldn't have been evident if they'd just used a multiple sequence alignment and gone with the maximum parsimony route.
  • - The models they ended up generating are extremely high-precision and based on a ton of data.
  • - The final results perform optimally in an environment similar to ones from 4 gya according to archaeological evidence. They didn't try to force that, which means they must've gotten it very close to right.

In the future, here's how to read scientific news stories (at least molecular biology ones):

  • - If the article was published in Nature or Science, it's a really big deal. Any shortcomings you can see are probably failures on the part of the journalist. I think PNAS is in this category, too, but as a bioinformatician I don't know quite enough to comment.
  • - If the article was published in Cell, it's also almost certainly really serious, although you should note that the authors have no scruples because they're publishing in an Elsevier journal.
  • - If the journal name sounds like it's just a description of the field with no organization attached ("Journal of Microbiology") then it's probably from a fake journal. (But not necessarily. Tread with caution. In particular, one-word journal titles don't fall in this category.) Any exciting claims made by the journalist are probably exaggerations.
  • - If the article came from PLOS ONE (and only that journal; there are lots of good PLOS journals) it was terrible or boring science and couldn't cut it anywhere else. Anything exciting in PLOS ONE is probably a typo.
  • - Any other journal (e.g. Oxford Bioinformatics) is fairly reputable but not infallible. It's unlikely that the journalist understands more than half the article.
  • - If the source is a university press release, it's complete crap. Unless you're a potential donor, in which case you should eat it up.

Re:"resembled those that existed when life began" (2)

khallow (566160) | about a year ago | (#44519253)

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 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.

For example, maybe they're actually reconstructing a much later period where universal selection pressure shifted all organisms a certain way. And there's the possibility that there were considerably more protein changes per unit time in the past (which had a more radioactive environment than today, both in background decay radiation on Earth and likely a higher cosmic ray background as well).

The procedures you describe wouldn't have gotten around the inherent biases of evolution. In language where the technique started, there isn't an inherent survival value to how you pronounce "father". Tribes who pronounced words in a certain way weren't more likely to die off. I don't think such evolutionary biases would show up in this method because organisms exhibiting those weaker protein patterns would have billions of years to go extinct and hence wouldn't be around to be measured today. And no matter how detailed a reconstruction you do, you aren't going to reconstruct extinct branches from existing organisms.

In the future, here's how to read scientific news stories

This is just the argument from authority fallacy.

I have no issue with speculative research like this or where it was published. What I have problems with is the considerable degree of false confidence associated with such research in this thread. For example, your complaint that "reasonably scientifically-minded people" are "bewildered" by this research is unfounded. The research has huge problems which you are downplaying.

Re:"resembled those that existed when life began" (1)

Samantha Wright (1324923) | about a year ago | (#44528035)

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 ago, which is an extrapolation based on a wide range of evolutionary and fossil-record evidence, not just the molecular clock.

For example, maybe they're actually reconstructing a much later period where universal selection pressure shifted all organisms a certain way. And there's the possibility that there were considerably more protein changes per unit time in the past (which had a more radioactive environment than today, both in background decay radiation on Earth and likely a higher cosmic ray background as well).

Fluctuations in the Earth's magnetic field are so frequent and minor that they're already averaged out across the molecular clock, which greatly diminishes the potential for changes in cosmic ray impact. Geologically, it is evident that the magnetic field is at least 3.54 billion years old, which limits the potential range in which anything so dramatic could happen. It is perhaps possible that isotopic decay has had a significant impact on the global rate of evolution, and that DNA repair mechanisms took time to evolve, but an underestimate is more likely due to saturation of mutations. I'm not a complete expert on the molecular clock, and it's possible that the 4 Gya figure is a little controversial, but since we have evidence [berkeley.edu] for 3.8 billion-year-old archaean fossils, which would have to be after the LUCA split by most theories, it's not an unreasonable figure.

The procedures you describe wouldn't have gotten around the inherent biases of evolution. In language where the technique started, there isn't an inherent survival value to how you pronounce "father". Tribes who pronounced words in a certain way weren't more likely to die off. I don't think such evolutionary biases would show up in this method because organisms exhibiting those weaker protein patterns would have billions of years to go extinct and hence wouldn't be around to be measured today. And no matter how detailed a reconstruction you do, you aren't going to reconstruct extinct branches from existing organisms.

There definitely are evolutionary pressures in tribal pronunciation choice, although they're not very common: on one extreme, you have the shibboleth [wikipedia.org] , where intertribal pressure forces conservation of pronunciation, and on the other, a language can only tolerate so many homophones.

Extinct branches are of no interest to this reconstruction. They're trying to find the ancestor of the current surviving crop, not rediscover what all life was like at the time. A more serious concern is that some convergent mutation occurred in all descendants where they all eliminated an old residue in favour of a new one at the same time; the authors have done their best to control for this possibility, and concluded that the risk of significant change is minimal or non-existent, given that the ancient protein appears to be stronger and more stable than the 200 or so that they extrapolated it from.

This is just the argument from authority fallacy.

No, there's justification for why these journals are the authorities. Nature, Science, PNAS, and Cell have more rigourous editing standards and are able to hire more experts to verify and ensure that claims made in their articles are correct. As a result, they only publish what they consider important—they may miss some important stuff because of personal bias, but they generally don't include unimportant stuff. In contrast, the "generic-sounding" journal claim is based on this list [scholarlyoa.com] , which we discussed on Slashdot a few months ago [hhttp] . PLOS ONE actually is an open-publication journal and there is little editorial oversight as to what is permitted, and so frequently contains only very unimportant articles that no editorial board anywhere took any interest in. Hence, reporters commenting on exciting stories can be judged based on this pattern.

I have no issue with speculative research like this or where it was published. What I have problems with is the considerable degree of false confidence associated with such research in this thread. For example, your complaint that "reasonably scientifically-minded people" are "bewildered" by this research is unfounded. The research has huge problems which you are downplaying.

I think you're being presumptuous about your own understanding of the material at hand. It's not false confidence, you just aren't quite aware of how big the gulf between your knowledge and the state of the art really is. I'm encouraged by your enthusiasm for the topic and the amount of thought you've put into interpreting the facts you were able to make sense of, but sometimes you need to trust authority a bit more, if only to avoid a lot of tedious research and awkward conversations like this one.

Re:"resembled those that existed when life began" (0)

ColdWetDog (752185) | about a year ago | (#44520433)

+ 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.)

Re:"resembled those that existed when life began" (1)

Samantha Wright (1324923) | about a year ago | (#44521817)

Yeah, all journals have retractions, and they've been getting worse for a while as people become more pressured by lazy employers with shallow performance metrics. I think there's some sampling bias that makes it less likely such stories will hit the mainstream press (perhaps a case of science journalists not messing up?) but they do happen; mounting pressure to get high-profile publications is met with mounting editorial rigour.

Re:"resembled those that existed when life began" (2, Informative)

Anonymous Coward | about a year ago | (#44517365)

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.

Re:"resembled those that existed when life began" (2)

Samantha Wright (1324923) | about a year ago | (#44517337)

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.

Re:"resembled those that existed when life began" (2)

Nutria (679911) | about a year ago | (#44517369)

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" (3, Informative)

Samantha Wright (1324923) | about a year ago | (#44517413)

Save your cynicism for other headlines. The amount of potential variability in this situation is genuinely minuscule, and it is inappropriate to worry about the predicted structure being 'out and out "wrong".' Claiming knowledge of the original structure is not that much of an exaggeration; the researchers demonstrated that none of the differences in the various versions of thioredoxin had a significant impact on its shape.

Re:"resembled those that existed when life began" (3, Informative)

Samantha Wright (1324923) | about a year ago | (#44517539)

...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.

Re: "resembled those that existed when life began" (0)

Anonymous Coward | about a year ago | (#44517379)

let me translate:

they found the protein they reconstructed resembled the protein they reconstructed

But it's not her fault, the press release didn't explain it well.

my balls sure are itchy tonight... (-1)

Anonymous Coward | about a year ago | (#44517233)

and now it will be recorded by the NSA for all future generations to know the state of ball itch in 2013.

Re:my balls sure are itchy tonight... (0)

Anonymous Coward | about a year ago | (#44517347)

seems like a reasonable use of tax payer money....

Does anyone, and i mean ANYONE, question the age (1)

InPursuitOfTruth (2676955) | about a year ago | (#44517343)

of this protein?!?

Re:Does anyone, and i mean ANYONE, question the ag (4, Funny)

Samantha Wright (1324923) | about a year ago | (#44517381)

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?

Re:Does anyone, and i mean ANYONE, question the ag (0)

Anonymous Coward | about a year ago | (#44517995)

Hilarious!

Re:Does anyone, and i mean ANYONE, question the ag (1)

Hognoxious (631665) | about a year ago | (#44518573)

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.

Re:Does anyone, and i mean ANYONE, question the ag (0)

Anonymous Coward | about a year ago | (#44520259)

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.

I think you're onto something here. We used to get many instances of miracles and divine interventions in the past: plagues, floods, burning bushes, lightning bolts smiting the wicked, immaculate conceptions, etc

Perhaps the copyright lawyers invaded the heavens, and nowadays gods can't manifest themselves physically on us mortals for fear of infringing some patent

Re:Does anyone, and i mean ANYONE, question the ag (1)

Samantha Wright (1324923) | about a year ago | (#44521717)

Don't be so hard on the RIAE; they were simply exercising their legal freedom to shoot themselves in the foot by destroying their whole industry. (Although if you're semi-vaguely-actually curious, the Venter Institute put a watermark in the Mycoplasma laboratorium genome a couple of years ago, which everyone thought was in terribly bad taste. Such sequences usually mutate randomly into illegibility in a few decades because nothing depends on them staying put.)

Re:Does anyone, and i mean ANYONE, question the ag (1)

Hognoxious (631665) | about a year ago | (#44588595)

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.

Re:Does anyone, and i mean ANYONE, question the ag (1)

Samantha Wright (1324923) | about a year ago | (#44590963)

It's probably the same fundamental principle that causes there to be no original ideas.

Re:Does anyone, and i mean ANYONE, question the ag (2)

ColdWetDog (752185) | about a year ago | (#44520549)

"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

Re:Does anyone, and i mean ANYONE, question the ag (0)

Anonymous Coward | about a year ago | (#44517399)

Any protein that existed in LUCA has to be at least as old as LUCA. That's somewhere around 3.5BYA. The journalists rounded that up to 4.

Re:Does anyone, and i mean ANYONE, question the ag (2)

reverseengineer (580922) | about a year ago | (#44517473)

To be fair to the journalists, it wasn't them doing the rounding: Conservation of Protein Structure over Four Billion Years [sciencedirect.com] .

Re:Does anyone, and i mean ANYONE, question the ag (2)

Samantha Wright (1324923) | about a year ago | (#44517509)

Which is quite honestly a reasonable thing to say, as that's what the molecular clock dictates. It probably means that thioredoxin was a little more variable at first than it is today.

Re:Does anyone, and i mean ANYONE, question the ag (1)

InPursuitOfTruth (2676955) | about a year ago | (#44517591)

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."
^^^^^^^^^^^^^

Re:Does anyone, and i mean ANYONE, question the ag (1)

Anonymous Coward | about a year ago | (#44517745)

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 BioTech companies patent and proprietarize everything. They charge you hundreds of dollars for a few dollars worth of chemicals. Evolution from LUCA forward is very mature. Chemical evolution, essentially, abiogenesis, is an immature field. If you don't want to follow along, come back in 25 years and a billion dollars later for a progress report.

Re:Does anyone, and i mean ANYONE, question the ag (2)

reverseengineer (580922) | about a year ago | (#44517961)

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 organisms, there is reason to think that the general structure of thioredoxins was settled long ago in the history of life, before archaea and eukaryotes split off from bacteria. As other posters have noted, the timeframe of this event is generally held to have been ~3.5-3.8 billion years ago.

Re:Does anyone, and i mean ANYONE, question the ag (1)

Biosci777 (2785273) | about a year ago | (#44520823)

This research was successful in determining what may have been an ancestral form of one protein, and that's interesting. But if you want to talk about abiogenesis, this doesn't even address the issue.

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 beyond all reason.

And blaming aliens or even a transfer from Mars is only kicking the proverbial can down the road.

Re:Does anyone, and i mean ANYONE, question the ag (0)

Anonymous Coward | about a year ago | (#44518643)

I heard they found it in some freezer in China, along with tons of chicken. I'm sure it'll be fine after some bathing in peroxide...

JM (0)

Anonymous Coward | about a year ago | (#44517489)

"We spared no expense."

aren't we forgetting something? (0)

Anonymous Coward | about a year ago | (#44517517)

I for one welcome our new Precambrian Protein Overlords... in whatever form they may take!

Sample taken from Hugh Hefner? (1)

SplashMyBandit (1543257) | about a year ago | (#44518165)

.. and I won't speculate what kind of sample.

Yum! (0)

Anonymous Coward | about a year ago | (#44521987)

Now we need to insert it into a bovine stem cell taken from fetal blood, grow that in a culture until we have a suitable amount and voila... dinoburgers!

I don't believe it (0)

Anonymous Coward | about a year ago | (#44522039)

How can you find something that's 4 billion years old when the universe is only 7000 years old? Hard to believe if you ask me
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