Chirality of life: Another false positive?

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Creationists have considered the ‘mystery’ of the chirality of life a problem inaccessible to scientific explanation. Of course, science as usual takes little notice of claims to ignorance and has provided yet another explanation for the chirality of life.

Point in case, a recent paper in Nature shows that:

Chirality, the molecular version of right- and left-handedness, has intrigued chemists ever since Pasteur found mirror-image tartaric acid crystals. The synthesis of molecules in a single chiral form is usually achieved by using a chiral entity from the outset. But in some reactions the formation of a chiral product seems to be further amplified. Most current explanations implicate autocatalysis as the source of this asymmetry. An alternative mechanism is demonstrated this week. This new approach generates a strong bias towards one chiral form from a small initial imbalance, based on the equilibrium solid–liquid phase behaviour of amino acids. As this takes place in aqueous solution, the process might explain how a prebiotic world, with left- and right-handed molecules present in equal numbers, could turn into a living world where biomolecules favour one chiral form.

Editor’s Summary ‘Chemistry mirrors life’

The paper in question is:

Martin Klussmann, Hiroshi Iwamura, Suju P. Mathew, David H. Wells, Jr Urvish Pandya, Alan Armstrong and Donna G. Blackmond Thermodynamic control of asymmetric amplification in amino acid catalysis Nature 441, 621-623 (1 June 2006)

Based on the work by Dembski, this ‘researcher’ concludes that

So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism

So let’s look at the ‘design inference’ in more detail

Let’s first establish that the chirality of life matches the definition of complex specified information.

Complexity

However, this does not solve the mystery of where the optical activity in living organisms came from in the first place. A recent world conference on ‘The Origin of Homochirality and Life’ made it clear that the origin of this handedness is a complete mystery to evolutionists.4 The probability of forming one homochiral polymer of N monomers by chance = 2–N. For a small protein of 100 amino acids, this probability = 2–100 = 10–30. Note, this is the probability of any homochiral polypeptide. The probability of forming a functional homochiral polymer is much lower, since a precise amino acid sequence is required in many places. Of course, many homochiral polymers are required for life, so the probabilities must be compounded. Chance is thus not an option.

All that is needed is a polymer of length 500 (500 bits) to meet Dembski’s stringent limit but Dembski also seemed satisfied with 40 out of 41 in the Caputo case. In other words, the complexity criterion in met. But what about specification?

Specification The specification is simple. In biology a function is all that is needed for specification to exist and thus any functional polymer will do. But in addition, another specification is a “Sorted set of amino-acids where all amino acids posess a left chirality”.

Based on the observation that chirality of life is complex and specified I conclude, and various other creationists and ID activists agree, that there exists a design inference that chirality of life required a designer.

So if in fact the research turns out to be relevant, and chirality of life has been resolved, will ID accept that it has been falsified?

Or will it argue that

1. The original claim by the explanatory filter was flawed 2. ID is still a logical possibility (for instance via front loading) 3. Ignore the whole issue in the hope that it will go away 4. The scenarios proposed are not specific enough and are ‘just so stories’ as opposed to the story about the unembodied designer.

And will someone explain to me how ID would explain chirality of life?

The authors conclude:

Here we have established that the coupling of solid–liquid phase behaviour and amino acid catalysis results in an efficient and robust mechanism for asymmetric amplification. This finding suggests that amino acids may have played a role in the evolution of biomolecular homochirality23. One can easily imagine the coexistence of solid and dissolved amino acids under a range of environmental conditions in a prebiotic landscape, and high ee could then evolve from an initially small imbalance in ee if (1) the amino acid forms a racemic compound rather than a conglomerate; (2) the amino acid exhibits high enantiopurity at its eutectic; and (3) the amino acid acts with high selectivity as an asymmetric catalyst in solution phase transformations. In fact, our studies show that serine meets the first two criteria, and recent work24 has demonstrated that serine catalyses certain asymmetric aldol reactions with high enantioselectivity; it has also been highlighted as one of a small number of amino acids likely to have played an important role in prebiotic chemistry25, 26. A scenario for homochiral evolution based on our amplification mechanism was hinted at some years ago27, and it also shares some similarities with the suggestion that chiral enrichment may result from the selective dissolution of only one (enantiopure) crystal of a conglomerate in a microenvironment28, but seems ultimately much simpler. A particularly appealing feature of the scenario we outline here is that it is based on an equilibrium mechanism, in contrast to the far-from-equilibrium environments invoked in kinetically induced amplification via autocatalytic reactions or crystallizations29, 30. Finally, we note that further enhancements in solution-phase enantiomeric excess may be discovered in more complex multi-component systems with a greater number of equilibrium solid and liquid phases. This possibility and the influence of interactions between different amino acids and between amino acids and other molecules such as sugars is the subject of ongoing investigations by our group, as is the search for high selectivity in amino-acid-catalysed reactions of potential biological relevance.

Relevant Links

Update:

Complex forms in proteins, enzymes, DNA, and other biological structures demonstrated by their constituent molecules in regard to size, shape, quantity, orientation, sequence, chirality, and integration imply intelligent design was necessary for the first life on earth. Intelligence is capable of designing complex form;

HOUSE BILL NO. 911, 92ND GENERAL ASSEMBLY, INTRODUCED BY REPRESENTATIVES COOPER (155) (Sponsor), REINHART, DAVIS (19), NIEVES, PHILLIPS, EMERY AND HUNTER (Co-sponsors). Pre-filed December 19, 2003, and copies ordered printed.

Also HOUSE BILL NO. 1722, 92ND GENERAL ASSEMBLY INTRODUCED BY REPRESENTATIVES COOPER (155) (Sponsor), DAVIS (19), NIEVES, EMERY AND STEVENSON (Co-sponsors). Read 1st time April 7, 2004, and copies ordered printed.

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Chirality - panda’s thumb from Sciencebase Science Blog on June 7, 2006 7:50 AM

The chirality of life, an issue I’ve discussed on numerous occasions in these and other pages, emerges as yet another source of pseudo-science for the intelligent design lobby. Apparently, the bias in handedness among the molecules of life - am... Read More

17 Comments

This is an interesting paper, but chiral ampification in highly cooperative processes has been known for a long time, as Dembski would know if he knew any science. A small level of enantiotopic deuterium labeling of polyalkylisocyanates -say 10%, an incredibly small perturbation - causes the helical polymers to be wound entirely in one sense. Bill McBride showed about 10 years ago that if you stir a solution of sodium chlorate while it crystallizes, the crystals will all have the same handedness.

So in other words when creationists claim that chirality is a problem for science they are unfamiliar with the science? Perhaps it’s time for ID to teach the reality.

So in other words when creationists claim that chirality is a problem for science they are unfamiliar with the science?

hmm. It seems to me that 99.99% of the time, this pattern holds regardless of topic at hand.

check out AFDave over at ATBC for a perfect case on point.

He hasn’t made one single argument over a period of months that doesn’t fit the pattern noted above.

that’s literally over hundreds of pages of posts, btw.

PvM Wrote:

And will someone explain to me how ID would explain chirality of life?

Switch the chirality of one of your amino acids. You die! Therefore, ID.

So in other words when creationists claim that chirality is a problem for science they are unfamiliar with the science?

That did seem to be the case when we explored the issue in the last Berlinski comments thread. There’s an embarrassment of possible mechanisms for chiral amplification, with new ones being proposed all the time. Of course, the more that are found, the wider the possibilities for which one or combination actually contributed, and creationists make the usual “Well, if scientists can’t stop arguing over which one happened, then they don’t actually know anything, do they?” argument.

It’s precisely analogous to the transitional fossils situation. We find a bajillion birdish-dinosaurish-species, therefore it becomes unlikely that any one of them can be established as the ancestor to modern birds, therefore, saith the creationist, there are no transitional fossils. That much irony could kill a man, but they’ve built up resistance.

So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism

Wtf? Talk about your false dichotomy!

From one of the quotes in the main post:

the origin of this handedness is a complete mystery to evolutionists.

It’s a ‘mystery’ to the IDists too. The difference is that scientists are productively trying to solve it, rather than thinking a lack of knowledge is somehow informative in itself.

Arthur Asuncion Wrote:

All of this analysis leads to a contradiction. One out of the two propositions below must be wrong:

1. Obtaining homochirality through stochastic processes is virtually impossible. 2. The feature of homochirality is observed today and is abundant in life.

Since proposition 2 has been empirically proven and cannot be wrong, proposition 1 must be wrong.

Indeed, proposition 1 is wrong; homochirality through stochastic processes is not virtually impossible.

Either homochirality is not virtually impossible, or homochirality did not come from undirected, stochastic processes

But, as he just noted, homochirality is not virtually impossible, since it is observed and abundant. Thus, there is no reason to conclude that homochirality did not come from undirected, stochastic processes.

(or we are extremely lucky, but we can reject this notion because we have already curbed our luck through the statistical analysis above). As we have seen in the analysis above, the statistical results convincingly show that chance chemistry cannot produce homochirality.

Only under unwarranted assumptions such as independence of events.

So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism.

Only as a leap of faith; certainly not as a matter of logic.

“As this takes place in aqueous solution, the process might explain how a prebiotic world, with left- and right-handed molecules present in equal numbers, could turn into a living world where biomolecules favour one chiral form.”

No doubt by invoking the coriolis effect, one could even infer in which hemishere this occurred:

http://www.snopes.com/science/coriolis.htm

One must question Dembski’s ability to count, also. Let’s take another instance of chirality: sugars. The D and L stereoisomers of the basic sugars and the chirality of amino acids are intimately interrelated, especially thermodynamically, when those amino acids interact with the sugars. Dembski’s “count” would include every atom as an independent element in determining the “complexity” of the molecule.

However, the complexity of a thermodynamically stable sugar stereoisomer has only two possibilities: D or L (depending upon whether the C-O ring bond points “up” or “down”). A one in two chance certainly doesn’t point toward “complexity”, let alone “design”!

Further, the {t=0} = {t=n} identity implied by these calculations omits a critical factor that anyone who has even cursorily studied biochemical systems (as opposed to test-tube reactions) is all too aware of: positive feedback selectivity. Consider a species that is attempting to obtain energy by breaking down sugars in its environment. If its immediate environment has even a slightly greater than equal distribution of D sugars, individual organisms whose enzymes more efficiently metabolize D sugars will be selected. Further, the breakdown products will, at some stages, themselves be optimized to form more D sugars by simple reversal of equilibrium… and since those sugars are used by the same organism for energy storage, the organism has a “motive” to expend the least possible energy in reconstituting the sugars. And that’s the positive feedback loop.

Dembskian counting is rather like claiming that an aircraft’s structure and complexity are determined by the number of rivets used to attach the wings to the body, without regard to the number or shape of the wings (or, for that matter, the possibility of welding…). It conflates structural considerations of inherently different orders; if we’ve learned nothing else from quantum chemistry, it’s that we don’t get accurate results or predictions when we do that.

Some wannabe undergrad wrote; So we are left to conclude that homochirality came about by some directed, non-stochastic mechanism. No. All that you have shown is the small probability of an event. The false dichotomy is not even hinted in the analysis. We must pity this kid already in a path of clueless assumptions and faulty logic so early in his career. That is unless he just wants to be an apologetic for pseudo-religion-science.

Oh, BTW, all the assumptions made by Asuncion are completely independent of the environment. That is to say that the poor kid never considered what the statistical analysis would be once you place the crystalls in a context!!! Statistics can tell you a whole lot but YOU have to use your brains and knowledge about the event you are studying to properly assess the results obtained through the statistical analysis. Obviously this kid did not think about consulting with Francisco Ayala or any of the other good scientist at the Eco/Evo department at UCI before posting such a ridiculous analysis. But, hey! he is a mathematician and computer wizz kid. Who needs biologists? My poor wife must be shivering in a dark corner of the bedroom just thinking that UCI will graduate such a midget brain.

hmm. It seems to me that 99.99% of the time, this pattern holds regardless of topic at hand.

check out AFDave over at ATBC for a perfect case on point.

300 posts by that guy, without a single intelligent statement. That’s why he won the vote :-)

we are left to conclude that homochirality came about by some directed, non-stochastic mechanism

Such as . … . … ?

On UncommonDescent Dembski claims that he personally has not personally argued that homochirality triggers a design inference. In addition, Dembski’s response shows how the EF will never be allowed to fail by moving the goalposts to another area of our ignorance. Since I did not argue that it was Dembski himself who had argued in favor of chirality showing design I fail to see the relevance of him distancing himself from the work of other ID activists. If Dembski were interested in the scientific validity of the claims of other ID activists, he could for instance point out the scientific problems with the young earth IDists claims. Teach the controversy I’d say. But I digress.

What lessons have we learned here? That the EF is scientifically vacuous either because it leads to false positives (which would make the method useless since it does not provide any way of estimating the likelihood of a false positive and can thus not even compete with ‘we don’t know’) or it cannot be falsified because the goalposts can always be moved to another gap in our knowledge.

Dembski Wrote:

But the chirality problem pales in comparison to the problem of sequencing amino acids to form functional proteins. That’s where Steve Meyer and I have always focused our attention. Let the Thumbsmen at PT come up with a plausible mechanism for protein generation along with a detailed account for how this proposed mechanism could generate a modest sized 250-amino acid protein, and I’ll take notice. Until then, indulge your homochiral fantasies.

I am not sure what Dembski means by the problem of sequencing amino acids to form functional proteins. Is Dembski saying that a 250 amino acid protein could not form naturally? Perhaps he could clarify his position?

Let’s explore Dembski’s arguments a bit further based on his public statements. Ironically, Dembski comments on the imprecise nature of probabilistic reasoning in the creationist literature and thus must have included his imprecise and incomplete ‘calculations’ for the formation of a flagellum protein in “No Free Lunch”.

Dembski argues also that specification is needed to deal with the problem of rejecting small probabilities but in biology function IS a specification and thus natural selection cannot be excluded as the ‘designer’ since it is exactly function which arises under the processes of variation and selection.

Dembski Wrote:

Nonetheless, I found the probabilistic reasoning in the creationist literature incomplete and imprecise. For instance, authors often referred to the probability of the chance formation of a particular protein, but failed to note that the relevant probability was that of any protein that performed the same function (this is a much more difficult probability to calculate, and one with which recent ID research has been having some success). Another problem was taking the small probability of events as sufficient reason to rule out their chance occurrence without acknowledging that small probability by itself is not enough to rule out chance. What else is needed? In my theory of design detection, I argue that what’s needed is a specification, that is, a type of pattern with certain mathematical and logical characteristics.

Even ID is claimed to have at most ‘some success’ in this area. So where is the beef?

Re “So where is the beef?”

Wendy’s?

Henry

I don’t normally have access to Nature, but I ran across two other articles (apparently) dealing with the same phenomena some time ago.

See for example:

“Hegstrom et al. [3], as well as Mason and Tranter [4], have calculated PVED [parity violation energy difference] for chiral carbon molecules, like amino acids, and found that for such molecules, at around room temperature, PVED is in the order of 10^−17 kT or 10^−17 RT per mole. More recent elaborate calculations [5, 6, 7] suggested that PVED in such molecules is actually greater by about one order of magnitude, i.e, PVED=10^−16 kT . In other words, one enantiomer will be of a lower energy state of 10^−17 − 10^−16 kT .”

Subtle differences in structural transitions between poly-L- and poly-D-amino acids of equal length in water Yosef Scolnik, Irina Portnaya, Uri Cogan, Saar Tal, Rachel Haimovitz, Mati Fridkin, Avshalom C. Elitzur, David W. Deamer and Meir Shinitzky Physical Chemistry Chemical Physics, 2006, 8, 333 - 339 http://www.rsc.org/publishing/journ[…]doi=b513974k

See also:

P-Violation Manifested at the Molecular Level - A Simple Means for an Absolute Definition of “Left” vs. “Right” Avshalom C. Elitzur and Meir Shinitzky arXiv:physics/0601010 v1, 3 Jan 2006 http://arxiv.org/PS_cache/physics/p[…]/0601010.pdf

In essence, it seems that the structure of water itself is amplifying the weak force parity violation to a level that affects the relative rates racemization of left-handed and right-handed amino acids. This potential for amplification may be related to the higher-than-expected sensitivity of water to electric fields – which has been demonstrated by water being frozen at room temperature in electric fields which are 1/1000 of the strength that was expected.

Please see:

Freezing Transition of Interfacial Water at Room Temperature under Electric Fields Eun-Mi Choi, Young-Hwan Yoon, Sangyoub Lee, and Heon Kang PRL 95, 085701 (2005) Department of Chemistry, Seoul National University, Kwanak-Ku, Seoul 151-747, Republic of Korea (Received 25 March 2005; published 19 August 2005) http://chem3.snu.ac.kr/~surfion/Him[…]nsition).pdf

In any case, once the break in symmetry is amplified such that the balance for serine is tipped, it should be tipped for all other amino acids – given the strong bonds which serine forms for amino acids of the same chirality.

Please see:

SHORT COMMUNICATION Chiral Enrichment of Serine via Formation, Dissociation, and Soft-Landing of Octameric Cluster Ions Sergio C. Nanita, Zoltan Takats, and R. Graham Cooks J Am Soc Mass Spectrom 2004, 15, 1360-1365 CHIRAL ENRICHMENT OF SERINE VIA ION SOFT-LANDING 1363 http://www.indiana.edu/~clemmer/pub[…]pub%2098.pdf

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This page contains a single entry by PvM published on June 5, 2006 6:23 PM.

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