XNA? :-)

Kate asks:

Quoted message said:

A fellow science fiction fan once asked me why ribose was
the sugar in RNA - what was special about ribose? Could a
biology exist somewhere which was based around another
sugar, such as xylose? I was intrigued by the question,
but have never come across an answer in my reading. Can
anyone help?

Other sugars have indeed been considered. Ribose is
considered to be a difficult molecule to form abiogenically
(ribose, btw, derives its name from the "Rockefeller
Institute of Biology"😉, thus other, simpler sugars have been
investigated. See, e.g.:

nai.arc.nasa.govnews detail.cfmOpen ↗
189

Wirt Atmar

[email hidden] (Wirt Atmar) wrote in message news:<[email hidden]>...

Quoted message said:

Kate asks:

Quoted message said:

A fellow science fiction fan once asked me why ribose was
the sugar in RNA - what was special about ribose? Could a
biology exist somewhere which was based around another
sugar, such as xylose? I was intrigued by the question,
but have never come across an answer in my reading. Can
anyone help?

Other sugars have indeed been considered. Ribose is
considered to be a difficult molecule to form
abiogenically (ribose, btw, derives its name from the
"Rockefeller Institute of Biology"😉, thus other, simpler
sugars have been investigated. See, e.g.:

nai.arc.nasa.govnews detail.cfmOpen ↗
D=189

If you limit yourself to the 5 carbon (furanose) ring
sugars, you have 16 to choose among. 4 names, times 2 for
chirality, times 2 again for the alpha/beta configuration of
the ring formation.

As far as anyone knows, the choice of chirality is
arbitrary. But there is something a bit special about the
ribose ring. If you consider the ring as defining a plane,
the hydroxyl groups from the first three carbons all point
in the same direction (down, say). The fourth carbon doesn't
have a free hydroxyl - it is attached to the ring oxygen,
which can also pucker downward. The fifth carbon is above
the plane, but its attached phosphate group may also be
oriented downward.

Is this just a coincidence? Maybe. But it is possible that
this particular sugar arrangement is ideally suited for
hydrogen bonding to a flat surface - perhaps water ice or a
mineral crystal. Make it a crystal of a phosphate mineral,
maybe one whose metal ions are able to perform
photoreductions of CO2, and you may have something
interesting.

Nature doesn't always choose the best technology or material
for a job. It picks something that is easy to construct and
works reasonably well, then it builds from there. Not too
different from human technology.

[email hidden] (Wirt Atmar) wrote in message news:<[email hidden]>...

Quoted message said:

Kate asks:

Quoted message said:

Quoted message said:

A fellow science fiction fan once asked me why ribose was
the sugar in RNA - what was special about ribose? Could a
biology exist somewhere which was based around another
sugar, such as xylose? I was intrigued by the question,
but have never come across an answer in my reading. Can
anyone help?

Quoted message said:

Other sugars have indeed been considered. Ribose is
considered to be a difficult molecule to form
abiogenically (ribose, btw, derives its name from the
"Rockefeller Institute of Biology"😉, thus other, simpler
sugars have been investigated. See, e.g.:

nai.arc.nasa.govnews detail.cfmOpen ↗
D=189

Thanks Wirt - that's fascinating! (And the origin of the
name "ribose" is hilarious. :-)

Cheers,
- Kate

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

As far as anyone knows, the choice of chirality is
arbitrary.

Many theorise that it is not arbitrary:

ch.cam.ac.ukajm.htmlOpen ↗

abc.net.aus924661.htmOpen ↗
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

As far as anyone knows, the choice of chirality is
arbitrary.

Many theorise that it is not arbitrary:

Tim and Jim - many thanks indeed for the info and links!

- Kate

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

As far as anyone knows, the choice of chirality is
arbitrary.

Many theorise that it is not arbitrary:

ch.cam.ac.ukajm.htmlOpen ↗

abc.net.aus924661.htmOpen ↗

*Some* theorise that it is not arbitrary. The second link
actually agrees with me:

"But why the left path and not the right? It could be
simply chance. "We're not sure whether left-handed
serine's dominance in the earliest period of life's
prehistory was arbitrary," Cooks said.

"But serine can switch its chirality under mild
conditions. If somehow polarised light, for example, or a
swirling motion in water were present at a critical
moment, some of the right-handed clusters could have
become left-handed. This could have cascaded into other
prebiotic reactions and set the pace for a billion years
of evolution."

As far as I can tell, this guy says it is arbitrary, but he
knows who made the arbitrary decision - it was serine.

The ideas expressed in the first link have been around since
parity-violation in the weak interactions was first
discovered back in 1954-56. They also assume 1950s ideas on
the origin of life from a pre-biotic soup of amino acids:

Due to the weak force, L and D molecules have slightly
unequal energies because they are not in fact true mirror
images: the true enantiomer of an L-amino acid is the D-
amino acid made of anti-matter.

We calculate these small energy differences between
enantiomers using ab initiomolecular orbital methods. In
most cases our calculations do indeed predict the
correct sign: not only are the L-amino acids more stable
than the D, but the natural D-sugars are more stable
than the L, and the right-hand DNA double helix is also
more stable than its left-hand mirror image. We believe
the slight enantiomeric excess from these "parity-
violating energy differences" could be amplified
kinetically in the pre-biotic soup to preferentially
select today's L-amino acid/D-sugar biochemistry over
D-amino acid/L-sugar "mirror life".

The key thing is that you have to have a "slight
enantiomeric excess" that gets "amplified kinetically". And
I have never seen a weak-force paper that says just how big
the excess is to begin with and how much more likely it is
that this global excess will be amplified - rather than a
local fluctuation being amplified. In any case, her results
only "predict the correct sign" in "most cases" - but we are
far from understanding which case is the important one. My
OOL theories suggest that it would be a chiral transition
metal ion. Yours suggest that it would be a flawed silicate
crystal. Other people agree with her that it would be a
sugar or amino acid. It still seems fairly arbitrary to me.

It seems to me that the choice of chirality is one of the
first choices made by natural selection. Was it made by r-
selection or K-selection? If K, then the weak force may be
significant. But if r-selection was involved, and I believe
it was, then we have "survival of the first", and arbitrary
local fluctuations are probably more significant than a
deterministic global bias.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

As far as anyone knows, the choice of chirality is
arbitrary.

Many theorise that it is not arbitrary:

ch.cam.ac.ukajm.htmlOpen ↗

abc.net.aus924661.htmOpen ↗

*Some* theorise that it is not arbitrary. [...]

Quoted message said:

The ideas expressed in the first link have been around
since parity-violation in the weak interactions was
first discovered back in 1954-56. They also assume 1950s
ideas on the origin of life from a pre-biotic soup of
amino acids:

Not really. The basic idea is that there is an asymmetry
between left- and right- handed molecules that stems from
the weak force, and that this contributed significantly to
the origin of biological chirality.

As for quantifying the issue:

``The ascent of parity-violation: exochirality in the solar
system and beyond''

- calorierestriction.orgpmidOpen ↗

...says that excesses of L-amino acids have been found in
meteorites.

``Non-racemic amino acids in the Murray and Murchison
meteorites''

- calorierestriction.orgpmidOpen ↗

...offers:

``Small (1.0-9.2%) L-enantiomer excesses were found in six
alpha-methyl-alpha-amino alkanoic acids from the Murchison
(2.8-9.2%) and Murray (1.0-6.0%) carbonaceous
chondrites [...]''

...but says it might have been significant:

``The alpha-methyl-alpha-amino alkanoic acids could have
been significant in the origin of terrestrial homochirality
given their resistance to racemization and the possibility
for amplification of their enantiomeric excesses suggested
by the strong tendency of their polymers to form chiral
secondary structure.''

Of course the founder effect may also have been involved.

However if there is a bias in the fundamental physics then
"arbitrary" seems like an unsuitable word to use - since the
choice has some significant consequences.

The idea that amino acids were chosen without their
handedness being considered seems most likely in "amino-acid-
first" scenarios.

If there's an existing complex adaptive system, then it can
try using both types, and then adopt the better one.

I tend to favour the latter view - if there's an amino-acid
chiral asymmetry, then by the time living systems came to
choose their amino acids, then they would have been smart
enough to pick the best ones.

According to my first link
["]http://www.ch.cam.ac.uk/CUCL/staff/ajm.html] that seems to
be what happened:

``We calculate these small energy differences between
enantiomers using ab initiomolecular orbital methods. In
most cases our calculations do indeed predict the correct
sign: not only are the L-amino acids more stable than the D,
but the natural D-sugars are more stable than the L, and the
right-hand DNA double helix is also more stable than its left-
hand mirror image.''

I.e. not arbitrary - by design.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

(Jim Menegay) said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

As far as anyone knows, the choice of chirality is
arbitrary.

Many theorise that it is not arbitrary:

ch.cam.ac.ukajm.htmlOpen ↗

abc.net.aus924661.htmOpen ↗

The ideas expressed in the first link have been around
since parity-violation in the weak interactions was
first discovered back in 1954-56. They also assume 1950s
ideas on the origin of life from a pre-biotic soup of
amino acids:

Due to the weak force, L and D molecules have slightly
unequal energies because they are not in fact true
mirror images: the true enantiomer of an L-amino acid is
the D-amino acid made of anti-matter.

Nitpick: the true mirror image of an L-amino acid is the D-
amino acid made of antimatter, travelling backward in time.
I.e., physics is invariant under CPT transformations, but
not CP transformations. Not that you'd ever be able to tell
the difference in practice.

--
Steve Schaffner [email hidden] Immediate assurance is an
excellent sign of probable lack of insight into the topic.
Josiah Royce

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or
quoted:

Quoted message said:

Quoted message said:

> As far as anyone knows, the choice of chirality is
> arbitrary.

Many theorise that it is not arbitrary:
ch.cam.ac.ukajm.htmlOpen ↗ ww-ww-Open ↗
w.abc.net.au/science/news/stories/s924661.htm

*Some* theorise that it is not arbitrary. [...]

As for quantifying the issue:

``The ascent of parity-violation: exochirality in the
solar system and beyond''
- calorierestriction.orgpmidOpen ↗ ...says
that excesses of L-amino acids have been found in
meteorites.

Yes, but did the weak force cause that excess?

Quoted message said:

``Non-racemic amino acids in the Murray and Murchison
meteorites''
- calorierestriction.orgpmidOpen ↗
...offers:

``Small (1.0-9.2%) L-enantiomer excesses were found in six
alpha-methyl-alpha-amino alkanoic acids from the Murchison
(2.8-9.2%) and Murray (1.0-6.0%) carbonaceous chondrites
[...]''

These are HUGE excesses. Too big, IMHO, to have been caused
by the weak force. And, in fact, the authors suggest a
completely different explanation in the part of the abstract
that you clipped:

These amino acids [2-amino-2,3-dimethylpentanoic acid
(both diastereomers), isovaline, alpha-methyl
norvaline, alpha-methyl valine, and alpha-methyl
norleucine] are either unknown or rare in the
terrestrial biosphere. Enantiomeric excesses were
either not observed in the four alpha-H-alpha-amino
alkanoic acids analyzed (alpha-amino-n-butyric acid,
norvaline, alanine, and valine) or were attributed to
terrestrial contamination. The substantial excess of
L-alanine reported by others was not found in the
alanine in fractionated extracts of either meteorite.
The enantiomeric excesses reported for the alpha-
methyl amino acids may be the result of partial
photoresolution of racemic mixtures caused by
ultraviolet circularly polarized light in the
presolar cloud.

That is, they postulate a physical chirality (polarized
light) which results not from the weak force, but from
macroscopic geometric chirality. That is, they think it was
arbitrary. (Thanks for making my case for me Tim. That is
twice now you have done it ;-)

[snip]

Quoted message said:

However if there is a bias in the fundamental physics then
"arbitrary" seems like an unsuitable word to use - since
the choice has some significant consequences. [snip rest
of post]

I'll accept this restriction on the use of "arbitrary". So,
the question between us is whether biochirality results from
fundamental physics or from some local arbitrary physical
asymetry such as polarized light or the orientation of a
crystal face. Personally, I happen to like the crystal face
idea (and I'm surprised you don't as well). Here is a link
to such a theory:
pubmedcentral.govarticlerender.fcgiOpen ↗

Well, since you didn't provide information on how large the
weak-force effect is, I went looking and came up with this:

pubmedcentral.govarticlerender.fcgiOpen ↗

It references the weak force sources that you favor:

From the works of Mason, Tranter, and MacDermott (11–15),
we know that the value of PVED is ≈1 × 10^−17
kT for the amino acids, the L-amino acids having the
lower energy.

PVED = parity-violating energy difference between
enantiomers. As I'm sure you are aware, 10^-17 kT is a tiny
effect. Completely unmeasurable.

Despite the smallness of PVED there have been suggestions
that PVED is in fact the cause of the homochirality of
biomolecules. Although the existence of a PVED between
enantiomers is theoretically certain its experimental
confirmation is still missing. ...

However, these authors come up with a way of amplifying
it, and actually detect it in a non-biologically
relevant system!

There is hope of detecting PVED in crystallization
because macroscopic crystals consist of a large number of
molecules. If there is strong enantiomeric selection in
crystallization from a racemic solution, a mixture of
pure right and left crystallites will be separated. PVED
could increase the number of crystallites of the
enantiomer that has lower energy.

The extremely small value of [epsilon] probably rules out
the possibility of observing PVED in the case of carbon-
centred enantiomers. Its value, however, increases in
proportion to the sixth power of the atomic number Z of
the element in the asymmetry center. In our experiments
enantiomers with Co (Z = 27) or Ir (Z = 77) at the
asymmetry center were chosen for the crystallization
procedures.

Exciting stuff, though the effect they got was at the
borderline of detectability.

So, how does the (global) weak force compare in strength
with the (very local) crystal face or the (astronomically
local) polarized light ideas. I found the following review
which claims that polarized light can explain enantiomeric
excesses on the order of 1%, and that crystals can do that
well too, or better. However, the weak force seems to be
limited to excesses on the order of 10^-12 or less.

pubmedcentral.govpicrender.fcgiOpen ↗
ion=stream&blobtype=pdf

"Jim Menegay" <[email hidden]> wrote in message
"]news:[email hidden]...

Quoted message said:

From the works of Mason, Tranter, and MacDermott
(11–15), we know that the value of PVED is ≈1 ×
10^−17 kT for the amino

acids,

Quoted message said:

the L-amino acids having the lower energy.

Sorry about the garble. The lines should read:

Quoted message said:

From the works of Mason, Tranter, and MacDermott
(11–15), we know that the value of PVED is about 10^-17
kT for the amino acids, the L-amino acids having the
lower energy.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...
> Jim Menegay <[email hidden]> wrote or
> quoted:

Quoted message said:

Quoted message said:

Quoted message said:

> > As far as anyone knows, the choice of chirality is
> > arbitrary.
>
> Many theorise that it is not arbitrary:
> ch.cam.ac.ukajm.htmlOpen ↗ --Open ↗
> www.abc.net.au/science/news/stories/s924661.htm

*Some* theorise that it is not arbitrary. [...]

As for quantifying the issue:

[...]

Quoted message said:

Quoted message said:

``Non-racemic amino acids in the Murray and Murchison
meteorites''
- calorierestriction.orgpmidOpen ↗
...offers:

``Small (1.0-9.2%) L-enantiomer excesses were found in
six alpha-methyl-alpha-amino alkanoic acids from the
Murchison
(2.8-9.2%) and Murray (1.0-6.0%) carbonaceous
chondrites [...]''

These are HUGE excesses. Too big, IMHO, to have been
caused by the weak force. And, in fact, the authors
suggest a completely different explanation in the part of
the abstract that you clipped:

These amino acids [2-amino-2,3-dimethylpentanoic acid
(both diastereomers), isovaline, alpha-methyl
norvaline, alpha-methyl valine, and alpha-methyl
norleucine] are either unknown or rare in the
terrestrial biosphere. Enantiomeric excesses were
either not observed in the four alpha-H-alpha-amino
alkanoic acids analyzed (alpha-amino-n-butyric acid,
norvaline, alanine, and valine) or were attributed to
terrestrial contamination. The substantial excess of
L-alanine reported by others was not found in the
alanine in fractionated extracts of either meteorite.
The enantiomeric excesses reported for the alpha-
methyl amino acids may be the result of partial
photoresolution of racemic mixtures caused by
ultraviolet circularly polarized light in the presolar
cloud.

That is, they postulate a physical chirality (polarized
light) which results not from the weak force, but from
macroscopic geometric chirality. That is, they think it
was arbitrary. (Thanks for making my case for me Tim. That
is twice now you have done it ;-)

Several other references attribute the asymmetry to
polarised light:

``Photochemical concepts on the origin of biomolecular
asymmetry.''

- calorierestriction.orgpmidOpen ↗

``Circular polarization in star-formation regions:
implications for biomolecular homochirality.''

- calorierestriction.orgpmidOpen ↗

One that attributes it to a heavy star:

``Supernovae, neutron stars and biomolecular chirality''

- calorierestriction.orgpmidOpen ↗

*If* the polarisation stems from one particular rotating
object, then it might well be arbitrary. Otherwise, the weak
force and existing living systems seem like possible casuses
of the asymmetry.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Quoted message said:

However if there is a bias in the fundamental physics
then "arbitrary" seems like an unsuitable word to use -
since the choice has some significant consequences.
[snip rest of post]

I'll accept this restriction on the use of "arbitrary".
So, the question between us is whether biochirality
results from fundamental physics or from some local
arbitrary physical asymetry such as polarized light or the
orientation of a crystal face. Personally, I happen to
like the crystal face idea (and I'm surprised you don't as
well). Here is a link to such a theory: pubmed-pubmed-Open ↗
central.gov/articlerender.fcgi?artid=33239

As far as I'm concerned there are basically two options for
the origin of homochirality - the weak force, and chance.

The subsequent prevalance of molecules of one sort or the
other is a consequence of one of these (plus - of course -
common descent, the fact that complex machines need to be
chiral and the fact that componenets of the same handedness
sometimes associate).

The weak force is indeed weak. The hypothesis that it is
involved really depends on the presence of mechanisms that
could magnify it.

Natural selection could magnify it - but that could also
magnify any bias present due to differential destruction of
left- and right- enantiomers by polarised light emitted from
something like a neutron star.

I suspect living systems will *eventually* use whichever set
of molecules that are of the chirality which is most
suitable -
i.e. I have faith that evolution is sufficiently powerful to
escape from any local minima on this front - even if
the selection pressures involved are very small.

I *expect* this will mean that the weak force will
eventually win out over any local biases caused by spinning
objects - on the grounds that living systems are more likely
to want universal homochirality than the benefits of using a
chirality to suit local conditions.

The only question in my mind is whether this has
happened already.

*Hopefully* some empirical data will one-day be available on
the issue:

``If the observed molecular parity violation on Earth was
mainly caused by random mechanisms one would expect to find
enantiomers of different handedness on different planetary
or interstellar bodies. If homochirality was determined by
circularly polarized radiation from a passing neutron star,
all planets within a given solar system would have been
affected by its same pole, and would therefore produce
biomolecules of the same hand. And if biology?s optical
activity was determined by the universal chiral influence of
the weak force, one would expect to find the same type of
enantiomers throughout the entire universe.''

- chiralitaet.demh(ol1.htmlOpen ↗

However, today, I have to admit that the case for the weak
force being involved seems far from proven.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.