The basic building blocks of life to be rethought after one discovered to be missing

Jun 12, 2012

(Phys.org) -- A gene thought previously to be present in all life on earth has been found to be missing in life near volcanoes.

The protein, thought to be one of the fundamental of life, is not present in certain volcanic .

The scientists studied , which are similar to bacteria, but have an independent evolutionary history, for the research. The research published in the Proceedings of the National Academy of Sciences (PNAS) found the expected gene missing and another in its place.

This missing protein, named SSB, performs an essential role binding DNA and protecting it from damage. Professor Malcolm White of the School of Biology at the University of St Andrews said: “All cells, whether they are microbial or human, have some things in common.

“These are the fundamental components or building blocks which were present in the first cells and have been passed on over 3.5 billion years.

“However, we have discovered that a gene normally thought to be absolutely essential and conserved throughout every form of life, is in fact lost in one group of volcanic bugs, and replaced by a completely novel gene we have christened ThermoDBP.”

The discovery has ramifications for understanding about how life has evolved on earth.

The new gene could have applications in biotechnology and the new scientific discipline of synthetic biology.

Explore further: Researchers successfully clone adult human stem cells

More information: Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales, PNAS, Published online before print November 21, 2011, doi: 10.1073/pnas.1113277108

Abstract
ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term “ThermoDBP,” exemplified by the protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a “ubiquitous” protein during evolution.

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msadesign
4.2 / 5 (16) Jun 12, 2012
Nor do they claim to know. In fact, it's a huge question, but remember this: while it's true that many things are unknown, it is also true that everything is knowable.
Might take a long time, is all.
In the end, to say that because 'evolutionists' can't say why life is here somehow negates evolution is just plain silly.
Eikka
3.9 / 5 (11) Jun 12, 2012
to explain just how it happens that another gene can be used in the place of another


Why not? Nobody has claimed that life can only work on a single set of genes, and there is no obvious reason why it should, which is why the fact that almost all life works on the same set is an indication that they have a common ancestor.

The only question is, which of those genes are truly essential and which are not.
Vendicar_Decarian
3.5 / 5 (8) Jun 12, 2012
This is bad news for anti-evolutionists.
Vendicar_Decarian
5 / 5 (7) Jun 12, 2012
Goodel disagrees with you.

"...it is also true that everything is knowable." - Msadesign
antialias_physorg
5 / 5 (20) Jun 12, 2012
Usually, what this means is that there are negative impacts with regard to how evolutionists thought life emerged on earth.

Get this through your thick skull: The theory of evolution makes no claim on how life got started on Earth. It ONLY makes claims on how life developed once it got started. Strawman much?

What the article says is that either archaea split off very early before the relevant mechanism was even in place OR it could mean that at some point SSB was replaced (through mutation) with ThermoDBP (or even vice versa depending on whether archaea were here first or the other kind was here first). This would be an example of convergent evolution in the former instance (where separate paths on the tree of life develop similar functions using different means) or divergent evolution in the latter instance (where species diverge through mutation)

"...it is also true that everything is knowable." - Msadesign

Gödel disagrees with you.

...and Heisenberg.
Eikka
3.8 / 5 (5) Jun 12, 2012


"...it is also true that everything is knowable."

Gödel disagrees with you.

...and Heisenberg.


And both are dealing with a much deeper meaning of "everything" than is necessary for understanding evolution.
jmcanoy1860
5 / 5 (7) Jun 12, 2012
This is very important but says nothing about either evolution or the origin of life. It MAY have some bearing on the last universal common ancestor hypothesis.

I notice the resident creationist got in first again. When are they going to get their own evidence to support their claims instead of bitching about evolution?
Anda
5 / 5 (5) Jun 12, 2012
Their own evidence is everywhere... Kinda old book...
Pkunk_
4.4 / 5 (14) Jun 12, 2012
Unhappy times for the evolutionists, since they haven't explained the existence of life here on earth in the first place yet.

The "evolutionists" , i.e the people who actually have a clue what is going on with the game of life have done a FAR better job explaining how life evolved and flourished on the Earth than the "people of the book" creationists.

All the creationists have is nonsense written in their holy books with nothing to back it up with facts. More of "Let the earth produce every type of living creature: every type of domestic animal, crawling animal, and wild animal" . Of course it happened the way they claim just cause "the lord said so".
Mike_Massen
3.5 / 5 (13) Jun 12, 2012
kevinrtrs tried to provoke
..since they haven't explained the existence of life here on earth in the first place yet.


Its evolutionary biologists you want to speak to Eg Dawkins & more so physicists who understand & continue to research fundamental atomic & intra-molecular interactions.

Its interesting all life on earth has a reliance on amines !

ie We all need amino acids in our food, they make us, our proteins.

Amines derive from Ammonia, the early earth had a tremendous amount of Ammonia, some methane, water and lightning.

There have even been spectral signatures of some amino acids beyond our solar system in Ammonia gas clouds.

Isnt there a well defined series of experiments where you start with a sterile chamber with Ammonia, water, methane with varying temperatures and when you pass electrical discharges through it then organic compounds are created including amino acids.

Time, the huge permutation space & wide environments on Earth offer such huge opportunities.
pauljpease
5 / 5 (5) Jun 12, 2012
Their own evidence is everywhere... Kinda old book...


Yep, and as we know, the older the knowledge the better, right? Forget the THOUSANDS of years of accumulated experience since then.
Torbjorn_Larsson_OM
5 / 5 (4) Jun 12, 2012
This is one of those results that are inflated by the researchers. Yes, it speaks to the ability for extremophile adaptation in archaea and the ability of evolution to change essential functional roles. Only in a very loose sense is the later important for the process of chemical to biological evolution outside of evolution proper.

Oh, and creationists shouldn't comment on science! Learning more is bad apparently, laughable. Well it is, for them.
Torbjorn_Larsson_OM
5 / 5 (2) Jun 12, 2012
Let us put the finding in perspective. Recent mass sequencing and data handling has made abiogenesis undergone massive testing. The RNA-protein world stands for ~ 20 % of the protein fold time proxy. ["The evolution and functional repertoire of translation proteins following the origin of life", Goldman et al, Biology Direct, 2010.]

After RNA evolved to couple to proteins, a deterministic cycle is predicted to take us up to a fully evolved translation system. This takes us between ~ 4.1 (likely) to ~ 3.5 Ga bp [billion years before present] which is right before the Archaean Expansion. ["Rapid evolutionary innovation during an Archaean genetic expansion", David et al, Nature, 2010.]

At this time the DNA LUCA evolved between ~ 20 to ~ 40 % of the time proxy, calibrated to be between ~ 3.5 to 2.5 Ga bp. DNA deoxy nucleotides need proteins to be converted from RNA precursors. The increased ability of DNA to code for large genomes predicts the AE genetic expansion.
Mike_Massen
2.8 / 5 (9) Jun 12, 2012
pauljpease offered some sarcasm
Yep, and as we know, the older the knowledge the better, right? Forget the THOUSANDS of years of accumulated experience since then.
It gets worse, the deity that supposedly spoke to Moses only chose one racial group, ie. he/she/it is clearly Racist !

And didnt xerox copies to other cultures anywhere, therefore lazy & impotent.

Clearly, there cannot be any true religion ever, all deities claimed by all major religions show by the deity's actions and rather definitively that they cant communicate effectively and are *completely* impotent.

If someone has a skill or power then why do they need to be constantly reminded of it, isnt that a classic sign of insecurity & with who knows what unclear psychological problems.

So the 'god is great' cry of emotionally rattled peoples comes across as an arbitrary selfish means to ingratiate in front of a deity to gain favour, in other words childish hope arising from the worst evil kind of emotional hypnosis...
Torbjorn_Larsson_OM
5 / 5 (3) Jun 12, 2012
At ~ 2.5 Ga bp the atmosphere oxygenated, and the earlier robust CO2 fixing metabolism of pre-LUCA diversified due to oxygen and energy stress. ["The Emergence and Early Evolution of Biological Carbon-Fixation", Braakman et al. PLoS Comp Bil, 2012.] This is where the article result fits in, after ~ 40 % of evolutionary history.

Parallel to this is research testing the preceeding RNA world directly. Before atmosphere oxygenation, iron could help RNA catalyze without as today produce lethal hydroxides. Turns out that Fe-RNA is at least an order of magnitude more efficient than today in Mg-RNA cases. This predicts that the RNA world latest disappeared when oxygen became plenty.

It is suspected that RNA was selected over other nucleotides because it handles the ubiquitous iron well. An implication, if this tests out well, is that the process from chemical to biological evolution is both generic and mostly deterministic on habitable terrestrial planets!
Terriva
3.4 / 5 (5) Jun 12, 2012
The basic building blocks of life to be rethought after one discovered to be missing
This is exaggerated sensationalism of finding, which will be forgotten in few days. The archaea differ from other organisms in many different ways, so it's not surprising when they have some gene replaced with another ones. After all, what we are supposed to expect, when they have different nuclei, cytoskeletons and internal membranes? Of course they must have different genes for these structures, which will unique between all other organisms, after then.
TheGhostofOtto1923
3.5 / 5 (11) Jun 12, 2012
In this case it means that now the tooth fairy has to called in ANOTHER time to explain just how it happens that another gene can be used in the place of another if life arose spontaneously from the ground up.
Naw kev it just means we continue to learn, while you and your buds continue to refuse to learn.

As always thanks for showing up and giving us the opportunity to point out this disparity.
bob456789
5 / 5 (8) Jun 12, 2012
Thank you for sharing your utter ignorance of science with us Kevin.
Now if you can explain how being shaped out of dirt by an invisible space wizard makes more sense we'd be much obliged.
MandoZink
5 / 5 (4) Jun 12, 2012
Usually, what this means is that there are negative impacts with regard to how evolutionists thought life emerged on earth.

Unhappy times for the evolutionists, since they haven't explained the existence of life here on earth in the first place yet.

What? This is more good news for evolution! More pieces of the overall picture are being discovered.

It's like discovering something we misunderstood about earthquakes. It sure doesn't mean earthquakes aren't real. We then know even more about earthquakes.

It's not even a setback - it's an expansion of our understanding.
How in the hell can you possibly think fine-tuning or improving what we know correlates to a notion of "See, it's was all wrong to begin with" ?

Good grief! Do you not understand anything about the process of learning and growing smarter?
aroc91
5 / 5 (8) Jun 12, 2012
This site is run by a bunch of idiots. They've yet to ban kevin, no matter how many reports he gets and no matter how clear his religious trolling is. I've had comments deleted for less. Feedback is never addressed or answered. Fuck phys.org's administration/moderation. They're all completely inept.
MandoZink
5 / 5 (1) Jun 12, 2012
This is exaggerated sensationalism of finding, which will be forgotten in few days.

I agree that the headline was overdramatic. It's important knowledge, but just more info to add to the mountain of understanding we already have about evolving life.
Jonseer
2.3 / 5 (3) Jun 13, 2012
The basic building blocks of life to be rethought after one discovered to be missing
This is exaggerated sensationalism of finding, which will be forgotten in few days. The archaea differ from other organisms in many different ways, so it's not surprising when they have some gene replaced with another ones. After all, what we are supposed to expect, when they have different nuclei, cytoskeletons and internal membranes? Of course they must have different genes for these structures, which will unique between all other organisms, after then.


It is NOT a sensationalist headline. The reasons you give for your cynicism are not grounds for declaring this finding "just more of the usual", but they do reveal your utter lack of understanding of genetics, cellular biology, the scientific method and science in general, and that you know just enough to think you know a lot, but far to little to actually know what you are talking about.
Deesky
5 / 5 (4) Jun 13, 2012
@kev,
Usually, what this means is that there are negative impacts with regard to how religionists thought life was created on earth. Hence the total absence of what those ramifications are.

In this case it means that now the god fairy has to be called in ANOTHER time to explain just how it happens that another creation myth can be used in the place of my (one true) creation myth, if life arose spontaneously from a sky fairy.

Unhappy times for the religionists, since they can't explain the existence of life here on earth, even with dozens of religions to choose from.

PhotonX
4 / 5 (4) Jun 13, 2012
what this means is that there are negative impacts with regard to how evolutionists thought life emerged on earth.
And the same negative impacts with regard to how auto mechanics thought life emerged on earth. Not to mention janitors, taxi drivers, and pharmacists. Because none of them deal with how life began on Earth. Why can't this twit and the rest of his cult understand this?
TheGhostofOtto1923
3.5 / 5 (8) Jun 13, 2012
This site is run by a bunch of idiots. They've yet to ban kevin, no matter how many reports he gets and no matter how clear his religious trolling is. I've had comments deleted for less. Feedback is never addressed or answered. Fuck phys.org's administration/moderation. They're all completely inept.
You do not appreciate the VALUE of debating religionists in a public forum. Superstition is a very dangerous thing. It threatens not only science but our continued existence.

Religion cannot be ignored. It needs to be addressed and exposed whenever possible. Kevin and all his friends graciously present the unique opportunity to do this here in the context of a scientific news site, where it's artifice can most easily be exposed.

Attacking religionists in public can be considered a community service. Let them speak out so we can see what they really are.
PussyCat_Eyes
1 / 5 (10) Jun 13, 2012
....says the GhostofCrappo
Vanity of vanities...how vain art thou
Actually, fat and ugly TheGhostofOtto1923 suffers from Multiple Personality Disorder....aka Dissociative Identity Disorder, which is why he fights with himself in his identity of dick_wolf et al. Some of his other identities are CardacianNeverid, FrankHerbert, bewertow, otto1923, otto1932, otto1882, TheGhostofOtto1932. Yuppers, this GhostofBlotto has a whole slew of alts that emerge and then recede back according to his mental disease.
From: http://www.medici...icle.htm

Dissociative identity disorder (DID) is a mental illness that involves the sufferer experiencing at least two clear identities or personality states, also called alters, each of which has a fairly consistent way of viewing and relating to the world. Some individuals with DID have been found to have personality states that have distinctly different ways of reacting, in terms of emotions, pulse,...........
ryggesogn2
1.5 / 5 (6) Jun 13, 2012
it is also true that everything is knowable.


"Science cannot solve the ultimate mystery of nature. And that is because, in the last analysis, we ourselves are a part of the mystery that we are trying to solve.
Read more at http://www.brainy...hjpx6.99
"
Deesky
4.4 / 5 (5) Jun 13, 2012
it is also true that everything is knowable.


"Science cannot solve the ultimate mystery of nature. And that is because, in the last analysis, we ourselves are a part of the mystery that we are trying to solve.
Read more at http://www.brainy...hjpx6.99
"

This misstatement was already pointed out, twice. Not paying attention?
aroc91
5 / 5 (4) Jun 13, 2012
History has been made, ladies and gentlemen. A post of kevin's has been deleted. My numerous, angry, previously unanswered feedback submissions and emails have been answered. Hallelujah.
Deesky
5 / 5 (2) Jun 13, 2012
History has been made, ladies and gentlemen. A post of kevin's has been deleted. My numerous, angry, previously unanswered feedback submissions and emails have been answered. Hallelujah.

Well done. I too have been reporting him, as I'm sure many others have also. But alas, it makes my parodies of his posts seem a bit out of context now.
aroc91
5 / 5 (2) Jun 14, 2012
True. One deleted post doesn't necessarily mean he's finally been banned, either. Time will tell.
Cornelius2008
3 / 5 (2) Jun 16, 2012
Religion is a belief system that at its heart does not require nor warrent proof or evidence in the traditional sense. I believe that science is the means that we understand the universe we live in, from physics to sociology, but I believe that from the big bang to an unknowable future all of this was set into motion by a conscious entity some know as God. Science and religion are not opposites, because the days that man fit Gods and dieties into the cracks in our understanding are long gone. Its unfortunate that in their insecurity some religious people seek to silence science but as well its unfortunate that some believers in science (I didnt want to call them scientists), in their arrogance try to dismiss and belittle the beliefs of others.

Great article though, really brings the robustness of life itself into light, as well as that words definition.
aroc91
5 / 5 (2) Jun 17, 2012
Well, shit. It seems kevin hasn't been banned after all. Like I said, one deleted post doesn't necessarily mean he's been banned. Again, you're completely inept, phys.org staff.

@GhostofOtto,

There would be value in debating and exposing kevin, but I don't think he's sincere. I've been keeping track of kevin's posts for a long time and, as time progresses, Poe's law has taken over. 6-12 months ago, I came to the conclusion that kevin is here as a parody. Pay close attention to how he words things involving "pseudo-science" and anything he claims doesn't have proof. It's clear to me that he's here to get a rise out of people, as he never seriously debates. Once again: Fuck the phys.org staff.

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