Silicon in Life

Diatoms Using Silicon

Diatoms Using Silicon

Original Image

Recently there was a NASA press conference about finding that some life could tolerate arsenic and perhaps substitute it for phosphorus in some biochemicals. (There is a tiny bit of controversy of the method used to demonstrate that the arsenic was USED as opposed to just tolerated).

This has caused some folks to prattle on about other potential forms of life using other substitutions (me included, though only in a comment or two) including the staple of Sci-Fi: silicon based life.

What many folks may not realize is that life already uses silicon.

It’s not like it has to have whole new processes invented to absorb & utilize it.

So I thought I write a little article about the simple way it’s used, how we don’t know much about it, and that it’s largely in plants, like Bamboo, so herbivores will avoid the leaves. (One of the ‘issues’ in grazing stock and in my bunny ‘herd’ is that high silica plants wear the teeth too fast and somehow the herbivores know to avoid them. So I’ve a stand of tall timber bamboo, but few of the leaves are eaten, even when I present them to the bunnies.)

Nice idea for a simple and quick little article. But somehow these things never work out that way… Right off the bat, I run into a “scholarly article” that connects silicon to carbon utilization. So I’ll do that “simple bit” further down, but first we’re going to take a detour through diatoms…

Diatoms, Silicon and Carbon

From this article:

http://www.ifa.hawaii.edu/users/akboal/abjc18feb0502.pdf

we have in the opening paragraph:

Diatoms are the world’s largest contributors to biosilicification and are one of the predominant contributors to global carbon fixation. Silicon is a major limiting nutrient for diatom growth and hence is a controlling factor in primary productivity. Because our understanding of cellular metabolism of silicon is limited, we are not fully knowledgeable about intracellular factors that may affect diatom productivity in the oceans.

Well.

Here we are smack up against all that “settled science” again. Predominant carbon fixer. Don’t know what controls its productivity. Understanding is limited. Silicon is limiting (and I wonder just how much work has been done on the “silicon cycle” to see how it controls the carbon cycle via diatoms… a google of ‘life “silicon cycle”‘ gave about 5700 articles and a lot of them are ‘misses’ where the terms are there but the topic is different. I think the diatom and silicate guys are missing out on the AGW Gravy Train here. Someone needs to send them the memo… ).

How important? Per the wiki “They are especially important in oceans, where they are estimated to contribute up to 45% of the total oceanic primary production.” So about half of what’s being made in the ocean. I’d say that matters. But wait, there’s more…

There is a battle between differing ocean critters over who gets to control the ‘silicon cycle’. This is thought to be related to the evolution of grasses (that also use silicon and, I presume, provide a more bio-available form of it in runoff to the oceans, but that’s just a guess). So given all that we’ve done to change the pattern of grasses on land and what lives in the oceans (think of all the various filter feeders AND things that prey on them which we’ve hauled out of the ocean and eaten to the point where they are at very low levels); do you think that could be doing something to the pattern of life in the ‘silicon cycle’ that could then impact carbon recycle? And what happens when Nature has a hissy fit and a load of volcanoes unload. They dump silicate ash in the oceans too… and have a big impact on things like sunlight.

What we don’t know here is huge.

From: http://en.wikipedia.org/wiki/Diatom

Although the diatoms may have existed since the Triassic, the timing of their ascendancy and “take-over” of the silicon cycle is more recent. Prior to the Phanerozoic (before 544 Ma), it is believed that microbial or inorganic processes weakly regulated the ocean’s silicon cycle.[23][24][25] Subsequently, the cycle appears dominated (and more strongly regulated) by the radiolarians and siliceous sponges, the former as zooplankton, the latter as sedentary filter feeders primarily on the continental shelves.[26] Within the last 100 My, it is thought that the silicon cycle has come under even tighter control, and that this derives from the ecological ascendancy of the diatoms.

However, the precise timing of the “take-over” is unclear, and different authors have conflicting interpretations of the fossil record. Some evidence, such as the displacement of siliceous sponges from the shelves,[27] suggests that this takeover began in the Cretaceous (146 Ma to 65 Ma), while evidence from radiolarians suggests “take-over” did not begin until the Cenozoic (65 Ma to present).[28] The expansion of grassland biomes and the evolutionary radiation of grasses during the Miocene is believed to have increased the flux of soluble silicon to the oceans, and it has been argued that this has promoted the diatoms during the Cenozoic era.[29][30] However, work on the variation of diatom diversity during the Cenozoic suggests instead that diatom success is decoupled from the evolution of grasses, and that diatoms were most diverse prior to the diversification of grasses.[31] Nevertheless, regardless of the details of the “take-over” timing, it is clear that this most recent revolution has installed much tighter biological control over the biogeochemical cycle of silicon.

Ok, and we get to find out what “siliceous sponges” have been doing lately too if we want to understand the actual controls in the “carbon cycle” (via the silicon cycle controlling the diatoms as major primary production…)

In this article:

http://wattsupwiththat.com/2008/01/28/spencer-pt2-more-co2-peculiarities-the-c13c12-isotope-ratio/

Dr. Roy W. Spencer lays out that C13 and C12 both vary with the same profile over the seasonal changes, so the change in the C12 / c13 ratio is a residual of that process. So he thinks the oceans could control CO2 levels.

I would add that since many plants have a different preference for one isotope over the other, changes in their rate of production and destruction can also influence the C12 C13 ratio directly. And we’ve done a lot of producing and destroying. So exactly what ARE the diatom levels in the ocean and what HAVE they done over the last 100 years as agricultural wastes have run into the ocean all over the planet? And how has that impacted CO2 levels and C12 C13 ratios? Then after you answer that, tell me what trawling has done to the siliceous sponges …

From the “slide show” here: http://www.geo.wvu.edu/~kammer/g231/MassExtinctions.pdf

we have a slide about the C12 C13 ratio that shows a great dilution of the C13 and notes

Dilution of C13 in biosphere carbon reservoir by rapid influx of C12 caused by methane release and mass dying at the end of the Permian. Organisms concentrate C12, which is released when they die.

Has the great dying of masses of life that the conservationists constantly wail about resulted in their C12 being “released when they die” and diluting things? And how do the diatoms figure into all of this?

So has the NATURAL warming of the planet increased the methane release from shallow clathrates such that a natural process could be diluting the C12 / C13 ratio? We don’t know as we don’t monitor the ocean bottoms.

All completely speculative, of course, … or IS it?…

From this link:

http://austhrutime.com/mass_extinctions.htm

A decrease of the C13/C12 isotope ratio of 10 PPT has been found from end-Permian carbonate rocks around the world. This was the first and largest and most rapid of a series of changes of the isotope ratio that continued to occur until the Middle Triassic, when the ratio stabilised abruptly. It was only after the stabilisation of the C13/C12 ratio that organisms that form calcium carbonate structures like shells began to recover from the extinction event.

Oh. So we’ve had the ratio change before SUVs…. It’s a natural event and happens without us. Who knew?…

A similar situation to that during the closing Permian might be happening at the present. Scientists have been recording rising temperatures in the Arctic for some time. In 2008 a Russian research expedition vessel was measuring dissolved methane levels in the Arctic Ocean when they observed large patches of ocean where methane was bubbling to the surface along the north coast of Siberia. A British expedition also observed this phenomena in the seas closer to Britain. This indicates that the submarine permafrost is melting as well as the terrestrial permafrost, both of which are adding large amounts of methane to the atmosphere. Because of the low temperature of Arctic Ocean water the deposits of methane hydrates exist much closer to the surface of the ocean floor than they are elsewhere, where they can be several thousand metres below the sea bed.

On land melting permafrost has led to Arctic lakes, as in Siberia, becoming much larger, and with methane bubbling out of them.

So a load of old dead life from permafrost and old methane from under the arctic can be released / is being released, and all just from our present NATURAL warming cycle that’s been in place for several hundred years out of the bottom of the Little Ice Age and 1500 years before that in the Migration Era Pessimum / Dark Ages Cold Period when there was ice at Constantinople.

And now I’m left wondering what that has done to the diatoms and if they might be “contributing” anything?

In a couple of hours of search I was not able to find what the preferences were for C12 vs C13 in diatoms. This may be because I had poor choice of search terms or it may be because it changes:

This article behind a paywall

Abstract

The photosynthetic fractionation of carbon isotopes by blue-green algae in laboratory culture is dependent in a non-linear fashion on the CO2 concentration in the feed gas. For the three species tested, the minimum fractionation occurred at a CO2 concentration of 0.2% in air and was approximately zero for the two marine species tested. Enrichment of C12 in the reduced carbon is not an inevitable result of photosynthetic carbon fixation. Temperature and pH had no detectable effect on fractionation. The maximum fractionation observed in the laboratory cultures or in recent blue-green algal mats was 18‰. Differences in the isotope ratio of coexisting oxidized and reduced carbon in Precambrian stromatolites are as great as 31‰. Present carbon isotopic evidence is not consistent with the idea that blue-green algae were major contributors to the organic matter in Precambrian sediments.

Oh Great.

So now I get to go study “blue-green aglae” for a year or three… Maybe I can talk some Algae Specialist into getting a grant to study C12 / C13 ratios in algae fixation and it’s relationship to Global Warming and hiring me as a lab rat….

Meanwhile, back at the CO2…

Now I found this rather startling. It says that at 0.2% CO2 there is almost no fractionation in one species and it varies with changed concentration of CO2. One species had an 18% concentration observed. So, as different species flourish, we get differential impacts on the C12 / C13 ratio. (Or so it looks from the abstract. Being behind a paywall I could not check this against the details in the article.) And one is left to wonder if diatoms have the same differential fractionation with concentration. AND as the concentration in the air changes, the fixation fractionation changes. Gee, wonder if that might impact the C13 / C12 ratio…

OK, enough down that path. It’s “ploughed enough” for others to know it’s got a big “Dig Here!” sign on the C12 / C13 ratio question. Now we can get back to silicon life… Though in abbreviated form. I’ll need to push most of that into some future article.

Grasses

Oddly, an article about making pulp for paper and pulp products has an instructive chart about the relative presence of silicon in different plants. From:

http://www.tappsa.co.za/archive2/Journal_papers/Bamboo_pulping/bamboo_pulping.html

we find this chart:

Species  SiO2%
Pine     trace
Birch    trace
Bagasse  1.5-2%
Kenaf    3-4%
Bamboo   1.5-2%

It clearly shows how silicon usage is highest in the grasses and nearly none in the trees. This matters for things like Giraffes in the zoos as folks often feed them grass hay when they naturally eat “browse” from trees in the wild:

Giraffes Brouse Trees

Giraffes Brouse Trees

Original Image

http://www.ncbi.nlm.nih.gov/pubmed/17939353

Tooth wear in captive giraffes (Giraffa camelopardalis): mesowear analysis classifies free-ranging specimens as browsers but captive ones as grazers.

Clauss M, Franz-Odendaal TA, Brasch J, Castell JC, Kaiser T.

Division of Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 260, 8057 Zurich, Switzerland. mclauss@vetclinics.unizh.ch

Abstract

Captive giraffe (Giraffa camelopardalis) mostly do not attain the longevity possible for this species and frequently have problems associated with low energy intake and fat storage mobilization. Abnormal tooth wear has been among the causes suggested as an underlying problem. This study utilizes a tooth wear scoring method (“mesowear”) primarily used in paleobiology. This scoring method was applied to museum specimens of free-ranging (n=20) and captive (n=41) giraffes. The scoring system allows for the differentiation between attrition–(typical for browsers, as browse contains little abrasive silica) and abrasion–(typical for grazers, as grass contains abrasive silica) dominated tooth wear. The dental wear pattern of the free-ranging population is dominated by attrition, resembles that previously published for free-ranging giraffe, and clusters within browsing herbivores in comparative analysis. In contrast, the wear pattern of the captive population is dominated by abrasion and clusters among grazing herbivores in comparative analyses. A potential explanation for this difference in tooth wear is likely related to the content of abrasive elements in zoo diets. Silica content (measured as acid insoluble ash) is low in browse and alfalfa. However, grass hay and the majority of pelleted compound feeds contain higher amounts of silica. It can be speculated that the abnormal wear pattern in captivity compromises tooth function in captive giraffe, with deleterious long-term consequences.

So feed your Giraffe alfalfa, OK? (The things you learn growing up in farm country… I always loved it when alfalfa was being harvested. Alfalfa hay has a wonderful smell to it.)

Humans and Lab Rats

I’m going to quote from a site pushing “supplements”. But it looks like a decent article and it’s neither paywalled nor does it have the copy function broken (like the academic articles I found).

http://www.eidon.com/silica_article.html

Silica: A Little Known Element Comes of Age

by Rick Wagner

Silica’s importance in overall optimal bodily function has been recognized for quite some time. As early as 1878, Louis Pasteur predicted that silica would be found to be an important therapeutic substance for many diseases and would play a significant role in human health and consequently nutrition.
Silica Research

During the 20th century, progress was made by pioneering researchers and scientists such as Carlisle, Butenandt, Iler, Bergna, Kervran, and Schwartz. Edith Carlisle’s work in the 70’s through the 90’s at the UCLA School of Public Health, perhaps more than any other, demonstrated the necessity of having silica in the body for proper growth and development. As a result of her research, we know that silica is absolutely essential for the body to create and maintain collagen. What was dramatically shown through Carlisle’s research was that when silica is withheld from normal nutrition, gross abnormalities develop and normal growth does not take place. While Carlisle’s work was done with chickens and mice, humans have also been experimenting with silica.

This more scholarly article abstract says:

http://onlinelibrary.wiley.com/doi/10.1111/j.1753-4887.1975.tb05106.x/abstract

The highest levels of silicon are found in the epidermis and it’s appendages and in connective tissues in general.

So make sure you eat your bamboo shoots and grasses…

In Conslusion

The point behind all this?

We already HAVE silicon life. Just not silicon BASED life. It would not be a great leap to increase the use of silicon in biological systems and I could even see the potential of having enzyme systems that built silicone like protein like structures. All purely the stuff of Sci-Fi; but not much to prevent it. Given that grasses evolved about 6 million years ago and the history of diatoms above indicates that they started using silicon after the fact; perhaps were simply on the first rung of that particular evolutionary ladder…

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About E.M.Smith

A technical managerial sort interested in things from Stonehenge to computer science. My present "hot buttons' are the mythology of Climate Change and ancient metrology; but things change...
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20 Responses to Silicon in Life

  1. Adrian Vance says:

    This C12, C13 issue sounds like more snake oil to me.

    Chemistry happens in the orbitals, not the nucleii. The addition of one neutron in the nucleus will have no effect on what is happening at the perimeter of an atom where bonding happens.

    If you scale up a nucleus to the size of a softball the electrons are a quarter of a mile away! Please, grant grabber parasites do not insult our intelligence with more myths. Eventually the taxpayers who support this nonsense are going to get tired of it say, “No more whitecoats!”

    For more conservative thought, science and humor check out The Two Minute Conservative at: http://adrianvance.blogspot.com We can arm you to piss off every liberal within earshot.

  2. j ferguson says:

    Adrian,
    I like the idea of conservative thought and humor, but science?

    I had hoped that there was no POV to science.

    E.M. Ah, imagine life without silicone. Not to be found in the Valley.

    Yah, i know, it’s the “E”

  3. E.M.Smith says:

    @Adrian Vance: There is differential chemistry with isotopes. Especially in living systems. Drink too much heavy water you die as the reaction RATE is lower and for some critical systems it gets so low you expire. That’s often the factor that gives the separation. The added mass slows down some reaction so you end up with the other preferentially being used.

    Clearly this effect is largest with the lightest elements as the mass difference percent is higher (with H vs D it’s doubling of mass…) and that’s why it doesn’t work as well for things like U235 vs U238.

    So it has nothing to do with the number of electrons nor the distance from the nucleus. It has a great deal to do with the change of shape of the reaction rate curve due to the changed mass of the species.

    @j ferguson:

    Yes, California, the land of the Two Valleys. Up north it’s Silicon valley and down south where they make pictures is Silicone Valley ;-)

    Yes, it’s an old “valley joke”…

  4. Adrian Vance says:

    “Differential chemistry?” That must have happened since I got my degree. I was a Chem major undergrad, but did most of my grad work in biology and education.

    In this case the mass difference is 1 part in 13 or 0.076 and I do not think that is going to change anything happening in the orbitals. And, this is a very rare species that you cannot compare to using pure D2O, but even there I would doubt there would be and difference in terms of the chemistry. Please give a citation. I am aware of none other than a short paper many years ago of a lady seeking an issue who grew some plants in deuterium rich sample of water and reported no difference.

    Please…

  5. E.M.Smith says:

    @Adrian Vance:

    The term “differential chemistry” is descriptive, not a term of art. You get differences in the chemistry of different isotopes. That’s all it says. Not a lot of difference, especially in bulk inorganic chemistry, but enough.

    From the wiki: http://en.wikipedia.org/wiki/Heavy_water

    Heavy water is water that was highly enriched in deuterium, up to as much as 100% D2O. The isotopic substitution with deuterium alters the bond energy of the water’s hydrogen-oxygen bond, altering the physical, chemical, and, especially, the biological properties of the pure, or highly-enriched, substance to a degree greater than is found in most isotope-substituted chemical compounds. Pure heavy water is not radioactive. It is about 11% denser than water, but otherwise, is physically very similar to water.

    Heavy water exhibits dose and species-dependent chemical toxicity. The adult human body naturally contains deuterium equivalent to that in five grams of heavy water, which is thought to be harmless. Comparable laboratory doses are used as non-radioactive tracers in human and animal metabolic experimentation. However, larger concentrations of heavy water are toxic in eukaryotic organisms, when heavy water replaces about 25% to 50% of the body’s water. At these levels, the substance interferes with cellular mitotic apparatus, preventing cell-division. Single-celled prokaryotic organisms such as bacteria, which do not have a mitotic apparatus, may survive and grow slowly in heavy water. However, eukaryotic organisms as simple as single-celled protozoa, and including all higher (multi-cellular) organisms, if given only heavy water, soon stop dividing and growing. For example, plant seeds will not germinate in heavy water. Mammals given heavy water fall ill from lack of needed blood-cell and intestinal-cell replacement, and die when about 50% of their body-water has been replaced with heavy water.

    Yeah, it’s the wiki, but D2O toxicity is not a political subject and is pretty well attested. There are references in the article. A google of “deuterium toxicity” gives:

    About 156,000 results (0.07 seconds)

    and that’s a bit much for me to wade through…

    This one is typical:

    http://www.ncbi.nlm.nih.gov/pubmed/4024121

    you get a lot of those kinds of detailed things (interactions of a particular drug with D2O in a species and such) which is why I quoted the wiki (as it gives a decent overview).

    Per C, it’s not the percentage difference that matters, it is that there is ANY difference. Enzyme systems are very sensitive to minor variations in the size and shape of molecules, so a CO2 with a heavier C will be a slightly different size, shape, and mass, so give slightly different results. Enough to have variation in percent utilization.

    A Google of “Isotope chemistry” gives

    About 6,430,000 results (0.17 seconds)

    So you’ve got a lot of available material. Typical is this Brookhaven National Laboratory page that gives an overview:

    http://www.bnl.gov/chemistry/History/IsotopeChemistry.asp

    Isotope Chemistry

    One of the most important scientific discoveries of the twentieth century was the discovery of isotopes: variants of elements that differ only in the number of neutrons contained in their nuclei, and therefore have different masses. This seemingly subtle variation has profound effects that can be exploited in numerous ways. Some isotopes may be unstable and can fission, leading to radioactivity and nuclear reactions. Isotopic substitution in specific locations in molecules can also have profound effects. Absorption and emission spectra may be altered: the wavelengths of features may shift. Reaction rates and equilibrium concentrations may change. Some properties may change dramatically: the effects of changing the number of particles in a nucleus can cause population of some atomic or molecular energy states to appear or disappear altogether. Nonzero nuclear spin in some isotopes (and not in others) open molecules to study by new methods, such as Nuclear Magnetic Resonance (NMR). All these effects can be exploited in order to obtain a window into detailed reaction mechanisms, reaction rates, and to effect chemical separations otherwise impossible.

    The recognition of the great utility of isotopic substitution in the last three-quarters of a century has also spurred much theoretical work seeking to understand the effects of isotopic substitution and to predict new effects that can be exploited for chemical studies.

    This one looked interesting, but I’m not sure exactly how to use it for anything:

    http://www.pnas.org/content/93/18/9393.abstract

    Abstract

    The temperature coefficient of equilibrium isotope fractionation in the heavy elements is shown to be larger at high temperatures than that expected from the well-studied vibrational isotope effects. The difference in the isotopic behavior of the heavy elements as compared with the light elements is due to the large nuclear isotope field shifts in the heavy elements. The field shifts introduce new mechanisms for maxima, minima, crossovers, and large mass-independent isotope effects in the isotope chemistry of the heavy elements. The generalizations are illustrated by the temperature dependence of the isotopic fractionation in the redox reaction between U(VI) and U(IV) ions.

    I found this one particularly fascinating as it involves a spin difference artifact:

    http://www.pnas.org/content/102/31/10793.full

    Abstract

    Phosphoglycerate kinase (PGK) is found to be controlled by a 25Mg2+-related magnetic isotope effect. Mg2+ nuclear spin selectivity manifests itself in PGK-directed ADP phosphorylation, which has been clearly proven by comparison of ATP synthesis rates estimated in reaction mixtures with different Mg isotopy parameters. Both pure 25Mg2+ (nuclear spin 5/2, magnetic moment +0.85) and 24Mg2+ (spinless, nonmagnetic nucleus) species as well as their mixtures were used in experiments. In the presence of 25Mg2+, ATP production is 2.6 times higher compared with the yield of ATP reached in 24Mg2+-containing PGK-based catalytic systems. The chemical mechanism of this phenomenon is discussed. A key element of the mechanism proposed is a nonradical pair formation in which 25Mg+ radical cation and phosphate oxyradical are involved.

    I hope that’s enough citations to prove the point. Isotopes do matter, and with increased sensitivity in biological systems.

    BTW, that last one was found with a google of “isotope enzyme selectivity” that gave
    About 771,000 results (0.22 seconds)

    so again, a lot available for reading.

  6. Adrian Vance says:

    “Isotopic chemistry” has much more to do with the transmutation of elements once in a compound and not any affect a different nucleus will have on what is happening to the electrons in the orbitals. That is where the chemistry is happening. And again…

    In the prototype atom if the nucleus were scaled up to the size of a softball the electrons would be the same size and a quarter mile away! Get serious. You are giving us a lot of armchair bullshit and obfuscation. You should be working for Jim Hansen. He could use your chutzpah.

  7. Adrian Vance says:

    In a footnote: You have clearly misunderstood everything you have read.

  8. P.G. Sharrow says:

    Vance; you have really cut your stature down with me. pg

  9. tallbloke says:

    E.M.

    Check out Julian Flood’s comments on diatoms on Judith Curry’s blog from here:
    http://judithcurry.com/2010/11/26/skeptics-make-your-best-case/#comment-19914

    Seems diatoms may be flourishing and outcompeting other phytoplankton and altering the d13/d12 ratio.

  10. Adrian Vance says:

    Well P.G. that’s the way the cookie crumbles, but while you’re at it read some basic chemistry and you will learn that chemistry is what happens in the orbitals which are a long way away from the nucleus. Where the nucleus is 1/10,000 the size of the atom and the mass difference from C12 to C13 is 0.003 and K = m X v^2 a 0.3% change in mass for the entire atom is not going be detectable in a species that occurs once in many millions of atoms. Get serious.

    The “heavy water” written about in early nuclear engineering era never had more than 18% D2O and often much less. Much of what has been written about it is like Jim Hansen’s fantasies about CO2 telling water vapor when it can evaporate.

    When we’re dealing with atoms that are banging into one another five million times a second a room temperature it is the bumpers and fenders that are important, not the sack of oranges in the back seat you’re taking to Grandma’s house over the river and through the woods.

  11. BlueIce2HotSea says:

    @Adrian Vance

    “the mass difference from C12 to C13 is 0.003”

    You must mean 0.083, no?

    Also here is a nice wiki article explaining the kinetic isotope effect.

  12. Adrian Vance says:

    Oops! My calculator is dying and gave me a 0.003 instead of a 0.083 as the LCD display is malfunctioning. I should have known that number was wrong having just done 1/13, etc.

    Anyway: deuterium is 156 ppm in water and is far below significant in any way in water, much less its’ chemistry. I continue to maintain that discussions of isotopes having different chemistry from their atomic litter mates is ridiculous.

    The amount of crap that gets published and patented today is unbelievable. Just because you see it print means nothing. Just read through 250 patents in an area where you have expertise, as have I on the way to obtaining my own recently, and you will see stuff that belongs in Star Trek and nowhere else.

  13. E.M.Smith says:

    @Adrian Vance:

    Did you even bother to read the citations?

    Look at the last one. It specifically lists two different isotopes of Mg and gives a differential reaction rate in a particular enzyme system.

    In the presence of 25Mg2+, ATP production is 2.6 times higher compared with the yield of ATP reached in 24Mg2+-containing PGK-based catalytic systems.

    Isotopes having chemical behaviours that are DIFFERENT from each other for the same element.

    It does not matter how much you wave about your theoretical argument. This is observed and measured.

    So take a short period of time to go do some reading on the subject. It’s not hard to find. I even gave you some sample search terms.

    Yes, some of the articles returned will be about things like radio tagging molecules for the determination of which reactant donated which product atom. Yes, some of the articles will be about making radioactive isotopes into medicinal compounds. Yes, some of them will be about making ‘markers’ for imaging in medicine.

    But no, I’ve not “clearly misunderstood everything”.

    So: you have some blinder on. You have a preconceived notion that you can not get past. And you have lost the joy of discovery of a new bit of nature. And replaced it with what? A simplified bit of dogma.

    I’m sorry, but I can’t help you past that hurdle. Only you can make that change in your self.

    Per “armchair bullshit” and “obfuscation”: I took the time to find example references that were from folks who are NOT doing anything “armchair” and that are fairly clear.

    National Institutes of Health
    Brookhaven National Laboratory
    Columbia University (Editor of the Mg article)

    and each of them has a load of equally good references in them.

    So I don’t know what’s so hard to see in a simple statement like:

    This seemingly subtle variation has profound effects that can be exploited in numerous ways. Some isotopes may be unstable and can fission, leading to radioactivity and nuclear reactions. Isotopic substitution in specific locations in molecules can also have profound effects. Absorption and emission spectra may be altered: the wavelengths of features may shift. Reaction rates and equilibrium concentrations may change.

    But it’s pretty clear you missed it.

    “Reaction rates can change”. So you can have two molecular species differing only in an isotopic substitution at one point, and the two species will have different reaction rates and different equilibrium concentrations.

    That alone will have one species preferentially turned into a product (say, cellulose) while the other is preferentially left behind.

    And there is no doubt at all that plant enzyme systems can sort C based on C12 vs C13. This is easily demonstrated with a comparison of C3 metabolism plants to C4. They have different enzyme systems so they have different isotope concentrating properties. It’s not hard at all to find a boatload of references to this. Folks who’ve done their lab work and found the reality.

    So you can choose to look. To see. To learn a new trick.

    Or you can choose to ignore the reality and wave theoreticals about.

    BUT name calling is not one of the options.

    So drop the attack tone (and comparisons to Hansen with words like “bullshit” is an attack tone) or head for the door.

    You want to assert that there is no difference at all in the chemistry of any atom. Fine. Then show where the existing body of literature has been overturned. With citations. NOT just waving your atomic sizes around and asserting “it isn’t so!!!” with ever greater vigor.

    Here’s a book reference (of a sort which exist in abundance) for the assertion that C3 vs C4 plants have different isotope responses:

    http://books.google.com/books?id=yRMgYc-8mTIC&pg=PA114&lpg=PA114&dq=c3+isotope+preference&source=bl&ots=OCO83Hv2MC&sig=2CZXnf8Al-Zv00J-I6dUqbQ_ZMg&hl=en&ei=CgAFTfuVDYK6sAOB7qTZDQ&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBUQ6AEwAA#v=onepage&q=c3%20isotope%20preference&f=false

    you can find a boatload more with the google search terms “c3 isotope preference” Try c4 and CAM as alternates and you will also get interesting results. (CAM plants can swap from C3 to C4 as desired. Often seen in desert plants that conserve water during part of the day.)

    And here’s another one showing differences in reaction rates for isotopes (and I’m assuming your a good enough chemist to understand that different reaction rates can be used to give different product concentrations)

    http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V66-4887S71-Y8&_user=10&_coverDate=10%2F31%2F1986&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1576394673&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c7a4fe8d92334496ea44b29a07208d69&searchtype=a

    Kinetic fractionation of stable nitrogen isotopes during amino acid transamination

    Stephen A. Macko1, a, Marilyn L.Fogel Estepa, Michael H. Engel2, a and P.E. Harea

    Geophysical Laboratory, Carnegie Institution of Washington, Washington, D.C. 20008, U.S.A.
    Received 19 September 1985; accepted 23 June 1986. Available online 31 March 2003.
    Abstract

    This study evaluates a kinetic isotope effect involving 15N, during the transamination reactions catalyzed by glutamic oxalacetic transaminase. During the transfer of amino nitrogen from glutamic acid to oxaloacetate to form aspartic acid, 14NH2 reacted 1.0083 times faster than 14NH2. In the reverse reaction transferring NH2 from aspartic acid to α-ketoglutarate, 14NH2 was incorporated 1.0017 times faster than 15NH2. Knowledge of the magnitude and sign of these isotope effects will be useful in the interpretation of the distribution of 15N in biological and geochemical systems.

    Pretty hard to misunderstand what that is saying, though I’m sure you will try.

    So don’t wave the measurements of the nuclear size around. That HYPOTHETICAL is not going to change the lab work done and published. DEMONSTRATE where that article is wrong and that there is no difference in the reaction rate of the two Nitrogen isotopes.

    And do it without impugning the character of the participants here, and without insulting me.

    Cute metaphors about Grandma’s oranges bouncing around are amusing, but not science (and not even very good rhetoric). So go do your homework, present a cogent set of references, or let it drop (and I’ll quietly ignore that you obstinately refuse to learn some chemistry from the nuclear age).

    And yes, in chemistry “nuclear size matters”.

  14. Adrian Vance says:

    Well that’s interesting: The heavier Mg isotope reacts faster than the heavier one! This is contrary to your fantasy!

    There is nothing to this for two reasons: (1) Chemistry happens in the orbitals and (2) isotopes are present in “trace” amounts and are by definition insignificant.

    You took a shot at me first. I hit back. If you don’t like it take your sandbox and go home.

  15. Adrian Vance says:

    That should be “lighter one” for the second Mg isotope.

  16. E.M.Smith says:

    @Adrian Vance: “took a shot”?

    Sorry, I don’t see it. I stated the science driving the effect as I understand it. Simply and directly. Nothing aimed at you personally at all. Then you asked for references, which I provided.

    Any emotion or attack you are reading into it are of your own making.

    The Mg rates have nothing to do with my “fantasy” as I have none. I’ve stated KNOWN and DEMONSTRATED laboratory results. Yes, for water vs D2O the heavy one goes slower. For Mg it’s a spin related impact on an enzyme system, not a mass effect. Again, a KNOWN and DEMONSTRATED laboratory result.

    You continue to issue simple denials of reality and wave about a hypothetical. I presume this means you are unwilling to read the citations or dismissive of anything contrary to your preconceived notions. So why waste my time chasing citations if you are just going to ignore them?

    Please take some time to do some background reading before bothering to post more of the same.

    I’ve got NO emotional load here. Just admiring an interesting bit of chemistry. It was barely mentioned when I had chemistry in the 1970’s; but it was mentioned as a new field. Since then a great deal has been learned. It’s a fascinating area that you really would enjoy, IMHO. If only you would take the blinders off long enough to look at it.

    Best wishes.

  17. Adrian Vance says:

    Much of what has been called “chemistry” in the last 50 years is not and more like what was written in the pre-Wohler days, before 1832.

    Molina and Roland were given a Nobel prize for a reaction that has never been documented in our atmosphere or done in the lab. Molina has been at MIT for a decade or two on our money trying to make it work, but with their fantasy destroyed Freon(tm) and let Dupont patent the same chemical that killed 400 people in the Copa Cabana fire in 1940 and now every refrigerator in America is full of that stuff and a potential time bomb.

    They have also postulated an “ozone shield” or layer that reflects energy to space and/or back to earth, but that too is a fantasy as gases cannot form reflective surfaces as can liquids and solids. The ozone in the atmosphere is made from hard UV interacting with oxygen all the way to the bottom hence, the smog of Los Angeles where the indigenous Indians called the LA basin “The Valley of the Smokes” for 9500 years before Cabrillo landed in Santa Barbara and got his foot stuck in tar on the beach from natural seepage.

    Jim Hansen’s chemistry only works if molecules have tiny pilots or there is Divine or Satanic intervention. So pardon me if I am dubious of “science” that says something barely detectable, i.e. with a 0.0156% presence and no chemical difference with H2O will kill my Marigolds, poison my cat and give me “the vapors.”

    Perhaps you did not insult me personally, but this entire issue offends the science I learned a long time ago and have seen nothing yet that would dash those principles. Given the price I have paid for trying to warn education and publishing of these fraudsters I reserve the right to be offended by the perpetrators of the myths.

  18. BlueIce2HotSea says:

    International Atomic Energy Agency (IAEA):

    ABUNDANCE AND FRACTIONATION OF STABLE ISOTOPES
    In classical chemistry isotopes of an element are regarded as having equal chemical properties. In reality variations in isotopic abundances occur far exceeding measuring precision… (as is) the case with the modern mass spectrometers…

  19. E.M.Smith says:

    I ought to also put here a quote from another site that also had some discussion of slicon in life, and the impact of diatoms on C12 / C13 ratios.

    From:

    http://judithcurry.com/2010/11/26/skeptics-make-your-best-case/#comment-19914

    the following comment is copied (partly just so I don’t have to go looking for it at some future time…

    BEGIN QUOTE:

    Julian Flood | December 8, 2010 at 7:35 am | Reply

    Re Julian Flood | November 27, 2010 at 9:12 am

    Volcanic ash fuels anomalous plankton bloom in subarctic northeast Pacific
    Hamme, Roberta C.; Webley, Peter W.; Crawford, William R.; Whitney, Frank A.; DeGrandpre, Michael D.; Emerson, Steven R.; Eriksen, Charles C.; Giesbrecht, Karina E.; Gower, Jim F. R.; Kavanaugh, Maria T.; Peña, M. Angelica; Sabine, Christopher L.; Batten, Sonia D.; Coogan, Laurence A.; Grundle, Damian S.; Lockwood, Deirdre
    Geophysical Research Letters, Volume 37, Issue 19, CiteID L19604

    quote
    Using multiple lines of evidence, we demonstrate that volcanic ash deposition in August 2008 initiated one of the largest phytoplankton blooms observed in the subarctic North Pacific. Unusually widespread transport from a volcanic eruption in the Aleutian Islands, Alaska deposited ash over much of the subarctic NE Pacific, followed by large increases in satellite chlorophyll. Surface ocean pCO2, pH, and fluorescence reveal that the bloom started a few days after ashfall. Ship-based measurements showed increased dominance by diatoms. This evidence points toward fertilization of this normally iron-limited region by ash, a relatively new mechanism proposed for iron supply to the ocean. The observations do not support other possible mechanisms. Extrapolation of the pCO2 data to the area of the bloom suggests a modest ∼0.01 Pg carbon export from this event, implying that even large-scale iron fertilization at an optimum time of year is not very efficient at sequestering atmospheric CO2.
    unquote

    I would add ‘in a region not deficient or limited in dissolved silica’ to that last line. AFAIK the usual limit on diatoms is dissolved silica for their shells, and given enough silica, diatoms will out-compete calcareous phytos. It would be instructive to see if the silica-feeding leg of my case above stands up to reality.

    One thing is resolved: diatoms pump down unexpectedly small amounts of CO2. If they actually are replacing calcareous phytos because of our silica export from the land, then the export of 12C to the deep ocean will be reduced (assuming that calcareous phytos do not exhibit the same unexpectedly small pull-down) and a light carbon isotope signal will be left in the atmosphere — and, of course, the amount of atmospheric CO2 in total will rise. Light signal, more CO2, must be anthropogenic. Or not.

    Anyone know the pull-down over a bloom of Emiliania huxleyi?

    JF
    Who has been to Sorrento and, while the management exclaimed over the food, the views, the shops, took lots of pictures of the oil smooths on the Bay of Naples.
    tallbloke | December 8, 2010 at 7:54 am | Reply

    Julian,
    does this mean that the reduction in plankton may have skewed the normal carbon cycle by a significant amount over the last years? What period, and how much? Roughly?
    Julian Flood | December 8, 2010 at 3:33 pm | Reply

    I don’t see how we can tell, but if we’ve lost 40% of the plankton then there will certainly be some effect.

    Ferdinand Engelbeen has a graph of 12C/13C isotope change which he says shows the industrial revolution kicking in about 1850. So it does, but it shows the ratio beginning to change from about 1750. This latter inconvenient fact, he claims, is natural variation, but he didn’t mention how he knows the difference.

    Agriculture causes run-off, dust deposition, which, presumably leads to silica increase. Diatoms win in a competition with calcareous phytos as long as there is enough silica. The paper certainly shows that diatoms don’t cause much of a CO2 pull-down. Have we increased the diatom population as well as knocking back the other phytos by stratification nutrient depletion? I don’t know. It’s a nice economical explanation, light isotope signal and CO2 increase in one tidy package.

    We got better (better in the sense that we made a bigger impact) at agriculture before the good men of Ironbridge began to make the iron wheels hum, so one would expect something to show somewhere in the climate record. This paper hints at where to look.

    Handwave, handwave, I know. Does a calcareous phyto bloom pull down light carbon? Until we find that out it’s just handwave.

  20. Pingback: Of Silicon, Iron, and Volcanoes | Musings from the Chiefio

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