Discovery demystifies origin of life chirality phenomenon

March 11, 2015 by Denise Henry, University of Akron
A composite image of the Western hemisphere of the Earth. Credit: NASA

The origin of life is still a mystery with many unsolved puzzles. How were molecules created? How did they assemble into large structures? Among the conundrums, the "homochirality" phenomenon upon which amino acids and sugars form is particularly fascinating.

University of Akron A. Schulman Professor of Polymer Science Tianbo Liu has discovered that Mother Nature's clear bias toward certain amino acids and sugars and against others isn't accidental.

Liu explains that all life are paired as left-handed and right-handed structures. In scientific terms, the phenomenon is called chirality.

Nature's selection of only right-handed sugars and left-handed upon which to build life might be much simpler than we expected before.

Liu found that any molecules, if large enough (several nanometers) and with an electrical charge, will seek their own type with which to form large assemblies. This "self-recognition" of left-handed and right-handed molecule pairs is featured in the March 10, 2015, issue of Nature Communications.

"We show that homochirality, or the manner in which molecules select other like molecules to form larger assemblies, may not be as mysterious as we imagined," Liu says.

While an understanding of how homochirality occured at the onset of life remains a mystery, this new finding emphasizes that Mother Nature's inner workings may not be as complex as we think.

Explore further: Chemists crack the chirality code

More information: "Chiral recognition and selection during the self-assembly process of protein-mimic macroanions." Nature Communications 6, Article number: 6475. DOI: 10.1038/ncomms7475

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syndicate_51
3 / 5 (4) Mar 11, 2015
Idle article.
big_hairy_jimbo
3.4 / 5 (5) Mar 11, 2015
I agree. That article was a waste of electrons.
Vietvet
2.6 / 5 (5) Mar 11, 2015
I'm guessing Phys.org didn't want to spend the $32 to actually read the study.
Whydening Gyre
3.4 / 5 (5) Mar 11, 2015
What a wierd article and presentation.....
Torbjorn_Larsson_OM
4.2 / 5 (5) Mar 12, 2015
This mechanism adds to many others known to induce choice of chirality, chiral breaking, in organisms. The press release is of course grasping over as much significance as it can (or more =D).

But the chiral choice was probably not done until evolution of coding, where protein function depends on it as the sequence of amino acids (AAs) has to map 1-on-1 to the geometry of folds and active sites. Modern tRNA - the "handles" that are used in the ribosome protein factory to translate rRNA code to protein sequences - has a frozen in preference for left-handed AAs. That preference is still there despite that modern cells seldom has much right-handed AAs present.

[tbctd]
Torbjorn_Larsson_OM
4.2 / 5 (5) Mar 12, 2015
[ctd]

And a month ago Joyce's lab showed how earlier replicators could assemble and persist in racemic (non-chiral) environments, and that it is even the preferred pathway. The shortest replicators yet seen are cross-chiral!

The trick is that replicators that needs less tight binding works better under these conditions, where the heteropolymers are used for both replication and enzymatic function. Right-handed sugar RNA replicates the left-handed strands and vice versa, and this work even in a racemic solution. "The team also showed that the new ribozyme could work without hindrance even when same-handed RNA nucleotides were present." [ http://www.scripp...yce.html ]

[tbctd]
Torbjorn_Larsson_OM
4.2 / 5 (5) Mar 12, 2015
[ctd]

[ Technically you also need an environment where the default tendency for strand shortening is reversed. But recent work has shown that it happens under PCR replication in hydrothermal vent pores. "Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length", Moritz Kreysing et al, Nature Chemistry.]
Torbjorn_Larsson_OM
3.7 / 5 (3) Mar 12, 2015
[ctd]

[ Technically you also need an environment where the default tendency for strand shortening is reversed. But recent work has shown that it happens under PCR replication in hydrothermal vent pores. "Heat flux across an open pore enables the continuous replication and selection of
oligonucleotides towards increasing length", Moritz Kreysing et al, Nature Chemistry.]
Whydening Gyre
3.7 / 5 (3) Mar 12, 2015
But the chiral choice was probably not done until evolution of coding, where protein function depends on it as the sequence of amino acids (AAs) has to map 1-on-1 to the geometry of folds and active sites. Modern tRNA - the "handles" that are used in the ribosome protein factory to translate rRNA code to protein sequences - has a frozen in preference for left-handed AAs. That preference is still there despite that modern cells seldom has much right-handed AAs present.

TL,
If you wouldn't mind - do you mean left chiral is counter clockwise and right is clockwise?
I've always been a little confused by the terms and relationships (at least in regard to biology)...
Are we even talking helicity?
Dethe
2.3 / 5 (6) Mar 12, 2015
that article was a waste of electrons
On the contrary, it's a shift toward paradigm, that the homochirality of life has its origin in the intrinsic asymmetry of chemical molecules itself, not the external cosmological etc.. influences. Before some time I realized, that the chiral molecules aren't equivalent with respect to their superhydrophobic properties, i.e. with respect the ability to adhere on highly curved cellular membranes. The proteins and aminoacids are often hydrophobic molecules, whereas the sugars are rather hydrophillic. Such a compound would collect at the outer side of hydrophobic membranes, whereas the aminoacids will seek the opposite side. If these membrane will be highly curved, it will spontaneously prefer the homochiral molecules and this effect will become negligible for flat membranes. In the above study the adsorption properties of anions were tested on model example of highly curved geometry - the donut skeleton of inorganic iron polytartarate.
Dethe
1.8 / 5 (5) Mar 12, 2015
This theory could be tested rather easily, if we should shake the mixture of oil, excess of soap and racemic mixture of proper hydrophobic or hydrophilic compound. After shaking the D-hydrophobic molecules should collect inside of resulting micelles, the L-hydrophobic molecules outside of them. The hydrophilic molecules should separate in the opposite way. I presume, this similar effect did happen with coacervates (simplest protein miceles) during formation of organic life. This model is interesting by the fact, that the RNA is actually a compound of sugar and aminoacids. The RNA molecules would preferentially collect at the micellar membranes and serve as a memory for sugar and aminoacid molecules chemisorbed there. If the micelles would split with their shaking, their surface RNA molecules will be inherited into resulting halves of original micelles.
Dethe
2.3 / 5 (3) Mar 12, 2015
We could illustrate the above explanation with following analogy: the molecules are behaving like an insect with four legs arranged into vortices of tetrahedron. One of its leg is oiled and as such hydrophobic and the another ones are hydrophilic. To give a chirality to such a molecule, we can imagine, the whole body of insect is hydrophilic (sugar molecule) or hydrophobic (aminoacids molecules). The hydrophilic molecules would climb more easily around positively curved hydrophilic surface represented with sphere (biological cell formed with lipidic bilayer), where the higher number of hydrophilic parts of its body would get into contact with the surface of sphere. Whereas the hydrophobic molecules would prefer the internal negatively curved surface of the sphere from the same reason. For hydrophilic molecules it would be advantageous to have oiled leg oriented outside of sphere, for second ones toward center of sphere. Their separation would increase with decreasing radius of the celt
JVK
1.8 / 5 (5) Mar 14, 2015
Dethe or anyone else.

How can the fact that glycine is the only achiral amino acid be placed into the context of your details? I've seen others ignore it, but it is linked from physics and the chemistry of protein folding to RNA-mediated cell type differentiation in all vertebrates.
Dethe
3 / 5 (2) Mar 14, 2015
Glycine is not only achiral, but also the simplest aminoacid and it's also sweet, i.e. sugar-like, as its name implies. So it represents a sorta transition between aminoacids and sugars. The consequence for above theory is, it serves as both source of energy, both the raw material for peptides, so that the organisms can occasionally produce it themselves, i.e. synthesize it with their bodies.
JVK
1 / 5 (4) Mar 14, 2015
Thank you. It appears to link the balance of sugars to amino acids in all vertebrates via substitution in the gonadotropin releasing hormone decapeptide.

Is there a likely link to the formation of glycine from the sun's biological energy via contact with water that slows the speed of light? Electrostatic charges?

For some reason, theoretical physicists refuse to answer any questions I've asked about how light-induced amino acids arise. Perhaps they do not know.

But, one of them took everything I have published or presented on RNA-mediated cell type differentiation and incorporated it into his model of simultaneous hen and egg emergence.
Vietvet
1.8 / 5 (5) Mar 14, 2015


But, one of them took everything I have published or presented on RNA-mediated cell type differentiation and incorporated it into his model of simultaneous hen and egg emergence.


Have a link to his "model"? Maybe at https://answersin...olution/ ?

I really would like to read what he has to offer.

I love to laugh my ass off.
JVK
1 / 5 (4) Mar 14, 2015
http://matpitka.b...tor.html

Excerpt: "Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously."

Vietvet
2.1 / 5 (7) Mar 15, 2015
@JVK

Thanks for the laughs!

There is nothing in Pitkanen's blog post to suggest he has ever heard of you or your "works".

There is a commonality though. You both push pseudoscience bullshit.

Dethe
2 / 5 (4) Mar 15, 2015
Was ribosome the first self-replicator?
Pitkannen is a lone genius mathematician, but completely separated from real life, physics in particular. Above I just explained, that the first replication served the membrane of eobionts itself. If we split pair of droplets, their surface (and its chemisorbtion properties selected with evolution) will get also inherited - no ribosomes or similar (extremely complicated cellular organelles btw) are required for it.
JVK
1 / 5 (4) Mar 15, 2015
Vietvet is Steven Taylor who asked Greg Bear about my claims but never reported this to anyone else. http://www.gregbe...?id=8064

From: Steven Taylor
Location: United States
Date: 01/28/2015

James V. Kohl claims you incorporated his model of nutrient dependent, pheromone ecological adaptation in your Darwin novels. Any truth to that?
Re: James V. Kohl

From: Greg Bear
Date: 01/29/2015
There's more than a hint of pheromone-HERV and cortico-steroid interaction in DARWIN'S RADIO. And James is certainly a pioneer in the pheromone world! We've corresponded for years on these subjects. I'm not sure about the nutrient angle, however. Interesting to follow that track as well!'

Unlike Pitkanen, Greg Bear did not steal the information from me. Instead, he acknowledged me as a source. Much more is now known about the biophysically constrained chemistry of protein folding but Greg's representations remain accurate more than a decade later.
JVK
1 / 5 (4) Mar 15, 2015
Dethe.
I think that with you as a co-author, I could polish off the invited review on nutritional epigenetics that I submitted to "Nutrients."

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281

I'm not going to submit the invited review to any other publication, because it was returned without review.

I know that means the reviewers are theorists and they are not ready to learn anything about top-down causation -- or to let anyone else learn about it.

However, the "critical mass" of experimental evidence that will drive the paradigm shift is rapidly accumulating -- as you know. Perhaps someone else you know would be interested in collaboration if you are not.
Dethe
5 / 5 (4) Mar 16, 2015
Nutrient-dependent pheromone-controlled ecological adaptation
It sounds like another Sokal article for me.... Are you completely sure, you haven't use any random world generator?
Dethe
5 / 5 (5) Mar 16, 2015
Try to for example decipher this
I mentioned the moth larvae that ate leaves contaminated with lead and manganese. Their fawn color changed to a peppered color, which appears to be an example of nutrient-dependent pheromone-controlled plant-animal mutualisms in the context of ecological adaptations and color changes that are controlled by the physiology of reproduction in all animal species
Where we can find a top-down causality in this? I can see only random string of words. Moth larvae were poisoned with lead and they changed color. How is it supposed to serve as a pheromone? (not to say, you're telling "that was dismissed when a replication attempt failed"). Man, this is dense...
anonymous_9001
5 / 5 (4) Mar 16, 2015
Good luck trying to converse with him clearly, Dethe. Once he finds out you don't agree with him, all he'll do is call you a science idiot and copy and paste things at you instead of holding a reasonable discussion.
Dethe
2.3 / 5 (3) Mar 16, 2015
I've been banned long time here, so I've sorta understanding for desperate out-of-box thinkers, I can even understand the role of emergent top-down causation in future science - but we cannot pretend causality, where none exists at all.
Dethe
2 / 5 (4) Mar 16, 2015
why on planet Earth do not exist organisms with proteins containing only right handed amino acids
The right-handed aminoacids are preferentially bound onto OUTER surface of lipidic membranes of small micelles - which is just the opposite side, where they're needed with living cells for building of proteins. This difference is small, but it does represent a true evolutionary disadvantage at the very basic molecular level. If the evolution of life would start from its very beginning again, it would probably repeat itself with the same result. The above study just tried to illustrate it with model system - so it's Nobel prize worthy, given the theoretical significance of explanation of life homochirality..

IMO this breaking of symmetry represents an analogy of CP symmetry breaking at the atomic level. From my theory follows, such a CP violation should occur at least at four distance scales inside of our Universe.
syndicate_51
1 / 5 (2) Mar 16, 2015
"While an understanding of how homochirality occurred at the onset of life remains a mystery, this new finding emphasizes that Mother Nature's inner workings may not be as complex as we think."

Waiting............. Waiting..............

More should have been discovered before reporting on this. At this point the article is inert.
Torbjorn_Larsson_OM
5 / 5 (4) Mar 16, 2015
@WG: There are several kinds of chemical chirality (mirror configuration D/L, local configurations R/S and optical configuration +/-), which may or may not overlap. [ http://en.wikiped...emistry) ] There is a choice in cellular metabolism of mirror chirality (L amino acids and D sugars).

@Dethe: "chiral molecules aren't equivalent with respect to their superhydrophobic properties".

Wrong. Don't you think such simple solutions has been considered and tested? Look into a basic astrobiology text book and you will see long treatments on this.

The problem isn't to get local chiral breaking as such - you can do it while growing crystals - but to square the break with the evolutionary history. See my longish comment on ways to do that.
JVK
1 / 5 (3) Mar 16, 2015
Are you completely sure, you haven't use any random world generator?


The invitation to submit the review was based on my history of publications. For comparison to your ridiculous opinion, see this article on top-down causation, co-authored by George FR Ellis: http://rsfs.royal...abstract

See also the comments section of: Understanding and accounting for relational context is critical for social neuroscience http://journal.fr...127/full

I wrote: "Animal models reaffirm..."

George FR Ellis wrote: "This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics."

AND

"I'm intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems..."

You wrote:
It sounds like another Sokal article

JVK
1 / 5 (3) Mar 16, 2015
I wrote:
...fawn color changed to a peppered color, which appears to be an example of nutrient-dependent pheromone-controlled plant-animal mutualisms in the context of ecological adaptations and color changes that are controlled by the physiology of reproduction in all animal species...


Interpretation by Dethe:
Moth larvae were poisoned with lead and they changed color. How is it supposed to serve as a pheromone?


Notice how quickly all other "...plant-animal mutualisms in the context of ecological adaptations..." are dismissed. Ask, why didn't George FR Ellis also dismiss them. Instead, he put them in the context of top-down causation, which is what I expect serious scientists to do.

This is what I expect a biologically uninformed science idiot, like anonymous_9001 to say:
Moth larvae were poisoned with lead and they changed color. How is it supposed to serve as a pheromone?


Good luck trying to converse with him clearly, Dethe.
JVK
1 / 5 (3) Mar 16, 2015
More news stories here at phys.org

Unlikely hydrogen bond discovered
'Quantum jitters' could form basis of evolution, cancer
Protein mimic shows promise as tissue engineering glue

More integration of physics, chemistry, and conserved molecular mechanisms of biologically-based cause and effect from the same author or co-author:

Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment http://rsta.royal...abstract

Learning from Bacteria about Natural Information Processing
http://dx.doi.org....05022.x

MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
http://www.pnas.o...abstract

How can someone like Eshel Ben-Jacob, George Ellis, me, or Guenther Witzany grasp the obvious fact that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570 when science idiots cannot?
anonymous_9001
4.5 / 5 (2) Mar 16, 2015
Ellis has also confirmed that he does not reject mutation and selection. Why are you continuing to cite the peppered moth example when multiple follow-up studies have confirmed that the lead and manganese did not CAUSE the color change?
JVK
1 / 5 (3) Mar 16, 2015
Why are you continuing to cite the peppered moth example when multiple follow-up studies have confirmed that the lead and manganese did not CAUSE the color change?


Thanks for asking. I cite it because, as everyone who is not a theorist already knows, it was the nutrient-dependent RNA-mediated physiology of reproduction that caused the color change. Only biologically uniformed science idiots attribute such things to mutations, which is why Denis Noble addressed that fact in: Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology? http://jp.physoc....007.full

"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." (p 1014)

Thanks for showing you are not aware of anything that's been learned in the past two decades about cell type differentiation.
JVK
1 / 5 (2) Mar 16, 2015
Ellis has also confirmed that he does not reject mutation and selection.


Do you think that he and Denis Noble argue about mutation-driven cause and effect -- after they co-authored "Top-down causation: an integrating theme within and across the sciences"
http://rsfs.royal...abstract

I think your claim
Ellis has also confirmed that he does not reject mutation and selection.
is an example of how biologically uninformed science idiots take anything anyone says and put it into the context of their ridiculous theories.

It matters not if Ellis or anyone else, like me, shows that mutations lead to loss of function and to the creation of pseudogenes. People like you and Masatoshi Nei will still claim: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." -- because you prefer to believe in theories.
anonymous_9001
5 / 5 (2) Mar 16, 2015
I'm not putting it into any context. That's what he directly said, almost verbatim.
Dethe
not rated yet Mar 16, 2015
"chiral molecules aren't equivalent with respect to their superhydrophobic properties". Wrong. Don't you think such simple solutions has been considered and tested?
I admit, it's a simple solution = but if you believe it has been considered before, you should prove it with link, not to ask me for it - don't you think? At any case, the authors of the above study are presenting it as a big finding (I proposed it in 2008). But IMO the similar chiral effect was observed before with water clusters, just misunderstood and ignored. The D-aminoacids are repelled with small hydrophobic micelles, but attracted preferably to hydrophilic water clusters and they're hydrolyzed faster. This effect has been used for explanation of homochirality before few years.
JVK
1 / 5 (2) Mar 16, 2015
I'm not putting it into any context. That's what he directly said, almost verbatim.


Tell us the question you asked him, and let others determine whether you placed his answer into the context of your question.

All you've done here is to continue to deceive others about the claims of Ellis that support mine, as do all the claims of anyone who understands how the the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man.
anonymous_9001
5 / 5 (3) Mar 16, 2015
I already posted our correspondence here:

http://phys.org/n...ive.html

Me: "He has also claimed that your recent work with the emergence of complexity and top down causation is evidence that you deny the contribution of mutation and selection to evolution."

Ellis: Certainly not. Natural selection as usually envisaged is a form of top down causation (because the environment is a major causal factor in the outcomes). Selection is a key process in the rise of complexity. That is quite clear in what I have written. Indeed I claim that multilevel selection is a key to complexity

I posted it verbatim. That's the complete opposite of deception.
JVK
1 / 5 (2) Mar 16, 2015
I never claimed that Ellis denied "...the contribution of mutation and selection to evolution." You approached him with your deceptive misrepresentation of what I claimed despite his response to me in the comments section of the open access article.

Understanding and accounting for relational context is critical for social neuroscience http://journal.fr...127/full

Multi-level selection is nutrient-dependent and pheromone-controlled. It's how selection for nutrients is linked from their metabolism to metabolic networks and genetic networks linked to health and physiopathology by RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize protein folding in the organized genomes of species from microbes to man.

Only a science idiot would approach Ellis with claims that someone else was misrepresenting him -- after he clearly stated: "This is absolutely correct..." in his response to me.
anonymous_9001
5 / 5 (4) Mar 16, 2015
It's implied heavily when you write things like

"What if biophysical constraints on the chemistry of protein folding, which are known to people like Professor Ellis eliminate theories about mutations and evolution."

despite his response to me in the comments section of the open access article


Only a science idiot would approach Ellis with claims that someone else was misrepresenting him -- after he clearly stated: "This is absolutely correct..." in his response to me.


Him agreeing with you on one point doesn't mean he agrees with you on all.
JVK
1 / 5 (2) Mar 16, 2015
Unlike it is with biologically uninformed science idiots, it is more important what serious scientists agree to than what they are not yet willing to agree to.

Eventually, all serious scientists agree to the facts that have been established by experimental evidence of biologically-based cause and effect.

Science idiots don't do that. They never have, and probably never will.

See, for example: Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility http://www.cell.c...ll%3Dtru
e

Tell us what you think it means to evolutionary theorists.

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