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Gender: Male
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Member since: 2002
Number of posts: 28,208

Journal Archives

Beneath an Evening Sky.

(Sorry about the graphics, but the music is wonderful.)

A wonderful place to consider the interface of RNA catalysis and enzyme catalysis.

Sometimes I like to drift around in the scientific literature and learn about things about which I know little, or about which I haven't thought for a long time.

Many years ago - quite a long time ago - I used to play around with amino acid chemistry making some lovely messes of things as well as some very beautiful and interesting compounds that actually went commercial on a large industrial scale.

Anyway, back in the late 1980's Thomas Cech and Sidney Altman were awarded the Nobel Prize in chemistry for their discovery of the catalytic properties of RNA, which lead to much speculation about a prebiotic (or neobiotic) "RNA world" wherein life arose not as suggested in the famous Miller experiment, but rather from RNA. (It is known that the basic constituents of RNA, purines and pyrimidines, as well as some simple sugars not all that far from ribose are found in interstellar clouds.)

Over the years, I've been intrigued by origin of life and the related issue of the origin of chirality.

In my stumbles today, I came across an interesting recent review of something which I was unaware, the role of amino acid acylated tRNA in the synthesis of certain natural products with very complex structures and a wide array of precisely ordered chiral centers. (Chirality is the property of something which cannot be superimposed on its mirror image, the most convenient example being two hands on a person.)

For example, here is the structure of the natural product ergotamine, from which one can obtain (by hydrolysis) lysergic acid, the precursor of the notorious drug LSD:

If one looks at this molecule with an organic chemist's eye and one is also familiar with the twenty proteinaceous amino acids, one can see that the part of the system (the four fused ring portion that is the core of lysergic acid) can be derived from the amino acid tryptophan by self acylation of the benzo ring, followed by conversion of a resulting keto function into a double bond as part of a cyclization process, a process that one can certainly engineer relatively easily in a lab. Similarly, one can identify in the three fused ring system in the ergotamine molecule a possibly phenylalanine derived portion, a proline portion and an alanine portion. (I actually have no idea about the actual biosynthesis of this molecule.)

We see some very complex natural products of extreme importance to humanity, the total synthesis of which remains even in these times synthetically inaccessible. Examples include the core of taxanes, an important class of cancer drugs, as well as many complex antibiotics like for instance, vancomycin, which clearly involves tyrosine and phenylalanine origins:

And so it I'm wandering through this very beautiful review, which examines the role that the catalytic activity of acyl RNA plays in the biosynthesis of these important molecules: Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis (Mireille Moutiez†, Pascal Belin†, and Muriel Gondry, Chem. Rev., 2017, 117 (8), pp 5578–5618).

The review article - which I've not finished reading yet - is very interesting, and although I don't see where it offers any speculations on the origin of life and the role of RNA in creating the protein carbohydrate world in which we now live, it thrills the imagination.

Some stuff from the introductory text:

...aa-tRNAs are ubiquitous molecules originally identified as the compounds responsible for delivering amino acids for the mRNA-guided synthesis of proteins at the ribosome. They function as adaptors between the mRNA codons and the growing polypeptide chain.1−3 They are composed of a tRNA of about 80 nucleotides in length attached to an aminoacyl moiety consisting of a single amino acid. Several bases constituting the tRNA undergo species-specific posttranscriptional modifications that are important for folding, stability, translational efficiency, and fidelity, and for diverse regulatory processes4, 5 (Figure 1a). The tRNA part of the molecule has a characteristic cloverleaf secondary structure that folds into an L-shaped tertiarystructure6−8 (Figure 1a, b). One end of the L-shaped molecule carries the trinucleotide anticodon that specifically interacts with mRNA codons by base pairing, whereas the other end bears the attachment site for the cognate amino acid. Amino acid attachment is catalyzed by specific aminoacyl-tRNA synthetases (aaRSs) in a two-step reaction.9...

...The enzymes of the glutamyl-tRNA reductase family reduce the aminoacyl moiety of Glu-tRNAGlu to form glutamate1-semialdehyde, the first precursor in the biosynthesis of tetrapyrroles such as hemes and chlorophylls.29−31 Enzymes from other families catalyze modification of the aminoacyl moiety of aa-tRNAs (i.e., while this moiety is still attached to tRNAs) to generate aa-tRNAs loaded with asparagine, glutamine, formylmethionine, cysteine, or selenocysteine.15,32 The past decade has seen the identification of new aa-tRNA-dependent enzyme families, all of which are involved in the biosynthesis of microbial secondary metabolites,33−40 referred to hereafter asNPs (Figure 2).

A fascinating read...

Esoteric I know, but of interest certainly to chemists and biochemists.

I love this preface to a "Brief" on Tensor Analysis.

I sent my youngest boy off to college this week and of course, it brought back my own youth, even as I find myself living vicariously in his.

Recently I collected some books on Tensor Analysis to give him to read in his spare time - ha! as if he'll have any - and I just loved to death these opening lines from the Preface:

When I was an undergraduate, working as a co-op student at North American Aviation, I tried to learn something about tensors. In the Aeronautical Engineering Department at MIT, I had just finished an introductory course in classical mechanics that so impressed me that to this day I cannot watch plane in flight-especially in a turn-without imaging it bristling with vectors. Near the end of the course the professor showed that, if an airplane is treated as a rigid body, there arises a mysterious collection of rather simple looking integrals called the components of the moment of inertia tensor. Tensor-what power those two syllables seemed to resonate. I had heard the word once before, in an aside by a graduate instructor to the cognoscenti in the front row of a course in strength of materials. "What the book calls stresses is actually a tensor..."

With my interest twice piqued and with time off from fighting the brush fires of a demanding curriculum, I was ready for my first serious effort at self-instruction. In Los Angeles, after several tries, I found a store with a book on tensor analysis. In my mind I had rehearsed the scene in which a graduate student or professor, spying me there, would shout, "You're an undergraduate. What are you doing looking at a book on tensors?" But luck was mine: the book had a plain brown dust jacket. Alone in my room, I turned immediately to the definition of a tensor: "A 2nd order tensor is a collection of n2 objects that transform according to the rule... “and thence followed an inscrutable collection of superscripts, subscripts, over bars, and partial derivatives. A pedagogical disaster! Where was the connection with those beautiful, simple, boldfaced symbols, those arrows that I could visualize so well? I was not to find out until after graduate school. But it is my hope that, with this book, you, as an undergraduate, may sail beyond that bar on which I once foundered…

Been there, done that.

I wish my boy the same.

James G. Simmons: A Brief on Tensor Analysis


A Nice Paper Analyzing Heat Exchange Networks for the Utilization of Waste Heat for Desalination.

Despite much nonsensical wishful and often delusional thinking about the ersatz "triumph" so called "renewable energy," as of 2017 - as was the case in 2007, 1997, 1987, 1977...and so on - almost all of the world's energy is supplied by heat engines of various types, The fastest growing form of energy (as opposed to peak capacity on a sunny or windy day) is the dangerous fossil fuel natural gas which is, so far as power plants and vehicles is concerned, is utilized in heat engines.

The failed and expensive so called "renewable energy" industry - which is neither sustainable or, in fact, renewable, is nothing more than lipstick on the natural gas pig, as is readily seen simply by looking at the rate at which the dangerous fossil fuel waste carbon dioxide is accumulating in the atmosphere, currently the fastest rate ever observed, roughly 3.00 ppm per year.

The second law of thermodynamics, which cannot be repealed by any governmental organization or by scientifically illiterate claptrap put out by say, Greenpeace (or any other NGO), requires that heat engines must waste some energy as heat. The total amount of exergy - useful work - extracted by a heat engine can never equal the heat generated in the combustion of dangerous fossil fuels or dangerous biomass combustion. The ratio of the exergy to the heat output of the fuel is termed the "efficiency" of a system.

In 2004, a famous paper by Socolow and Pacala, two scientists at Princeton University, postulated that the "switch" from coal to high efficiency natural gas would stabilize the climate. Events, the concentration of carbon dioxide in the atmosphere, has shown that this hypothesis was not borne out by experiment, since the overwhelmingly largest source of new electrical energy generation on this planet is natural gas. Experiment, um - excuse the word - trumps theory.

Nevertheless, in general, the most efficient heat engines on the planet are, in fact, dangerous natural gas plants (along with some pilot demonstrator coal plants) known as "combined cycle" power plants, which have a brayton cycle (very high temperature) gas turbine in which the rejected heat is used to boil water to drive a steam turbine (rankine cycle). These plants can operate in excess of 50% thermal efficiency - even close to 60% - in the generation of electricity.

The higher the temperature at which a system can operate, the greater the efficiency it can realize. Combined cycle plants are only now possible because of developments in materials science, in particular the development of "super alloys" and thermal barrier coatings - generally ceramics - with which these alloys can be coated.

It is worth noting that combined cycles need not be limited to Brayton systems coupled to Rankine systems: It is possible to couple them to a third type of device, a high temperature thermal reformer which provides chemical energy. (Ideally such systems would be driven by nuclear heat.)

The problem with waste heat is that is has to go somewhere, and that "somewhere" is often a body of water. This is a big problem whenever the water in question is fresh water, since it is evaporated in the process, leaving the water unavailable for other uses, such as irrigation or residential or commercial water supplies.

However, since waste heat drives the evaporation of water, it can also be utilized to purify water, in particular, seawater. This process as described is just "distillation" but distillation is actually only one of the ways that waste heat can be utilized to desalinate water. There are a large number of processes other than simple distillation that can be utilized, for example flash distillation at low pressure, reverse osmosis driven by pressure gradients resulting from water expansion (or electrical power), multiple-effect distillation in which a linked series of heat exchangers evaporate and condense water in series with each distillation unit driven partially be waste heat from the previous system.

These types of systems are not new, and they are not exotic. The Diablo Canyon Nuclear Plant in California for instance, uses fresh water for cooling, and has always utilized fresh water for cooling, and all of the fresh water - some of the purest in the State of California has been obtained by desalination of seawater at this plant. Originally this desalination was performed by flash distillation using reduced pressure and waste heat, although materials science at the time of the building of the plant was relatively primitive, and corrosion in the heat exchangers lead to the replacement of the flash system with reverse osmosis systems. (There were plans to expand the water desalination capacity at the plant, but the decision was made to kill people by shutting the plant because of appeals to stupidity: Nuclear power plants save lives.)

Prevented Mortality and Greenhouse Gas Emissions from Historical and Projected Nuclear Power (Environ. Sci. Technol., 2013, 47 (9), pp 4889–4895)

Thus the desalination capacity will not be expanded.

In any case, advances in materials science have allowed new technologies for desalination to be realized and a very nice paper in one of my favorite scientific journals, Industrial & Engineering Chemistry Research evaluates the economics of utilizing waste heat to desalinate water, regrettably focusing on dangerous fossil fuel plants, dangerous biomass plants and useless and expensive solar thermal plants - which in every single case morph into dangerous natural gas plants when their economics belie the wasteful hype that caused them to be built is exposed as flawed. Despite this flaw in evaluating these types of plants, there is no reason that the same evaluation could not be applied to more sustainable, if unpopular, nuclear plants.

The paper is here: Optimal Design of Water Desalination Systems Involving Waste Heat Recovery (Ramón González-Bravo†, José María Ponce-Ortega*† , and Mahmoud M. El-Halwagi, Ind. Eng. Chem. Res., 2017, 56 (7), pp 1834–1847) If you are able to access the paper in a good scientific library you will see a lot of math directed at calculating the economics of various approaches for model systems operating in the State of Sonora in Mexico, analyzing the profit from power generation and water sales.

Water in that region is fossil water. The dire situation is described in the paper's text:

In this paper, the problem of overexploitation of water in the region of Costa de Hermosillo (CH) in the state of Sonora in Mexico was selected as a case study. The CH is one of the most overexploited aquifers of Mexico; the volume of water extracted is used mainly for crops with high water consumption.23 The volume of water is mainly used for agricultural purposes in the irrigation district “051 Costa de Hermosillo” (ID051). TheID051 has an annual water extraction of 461 hm3, an estimated natural recharge between 250 and 320 hm3 per year, and an annual seawater recharge of 98.4 hm3, which has caused serious salt pollution of the water.24 The energy sector in this regionals represents a challenge because it is located near to the Sonoran Desert, where the energy consumption increases in the warmer months due to the use of cooling systems.

In any case, for the model system, the most profitable network is found to be a multiple effect distillation system (described above) coupled to a thermal membrane distillation system, which would generate about 154M USD of power, 26M USD of water while generating a profit of roughly 110 USD while creating over 1000 jobs. For the system described about 8.7 million tons of the dangerous fossil fuel waste carbon dioxide would be released into the atmosphere. (See table 3 in the original paper, page 1844).

Were the plant nuclear powered, there would be very little carbon dioxide involved at all.

Thermal membrane distillation systems are described in an earlier paper in the same journal, this one: Integration Design of Heat Exchanger Networks into Membrane Distillation Systems to Save Energy (Yanyue Lu†‡ and Junghui Chen†* Ind. Eng. Chem. Res., 2012, 51 (19), pp 6798–6810)

Text from that paper describes the technology:

Membrane distillation is a thermal-driven process. The transmembrane vapor pressure difference, which is generated because of the temperature difference between the hot feed stream and the coolant stream, is the driving force of vapor through the microporous membrane. For this reason, the high thermal energy consumption becomes one of the main barriers of MD to realize common commercial application. In the field of pure water production, the comparison of several desalination technologies shows that the cost of pure water produced by reverse osmosis (RO) is the least; however, if the low grade energy sources, such as the waste heat and the solar energy, are used in the MD process, the expected cost for the MD process will become more competitive than RO.12

It should be noted that no desalination system, even a nuclear powered system, is entirely environmentally benign, chiefly because there is a need to dispose of the brine resulting from the recovery of water. Depending on the ecosystem into which the brine is discharged, the consequences can have fairly severe effects. (cf Brine Discharge: One Size Does Not Fit All Environ. Sci. Technol. Lett., 2017, 4 (7), pp 256–257)

Nonetheless, like many other resources, fresh water, as is the case in the Mexican State of Sonora, is a stressed resource, and there is no ideal solution to this very challenging problem.

It is not the case that in our desire to resist Trump that we forget the basic problems that need to be addressed and which he and is enablers are incompetent to address and, frankly too ignorant to address.

Have a nice week.

Bull, John Danforth: Trump IS a Republican, the logical extension of Republican policy for decades.

Ex-Senator John Danforth, a lifelong Republican is trying to claim that Trump isn't a Republican:

Many have said that President Trump isn’t a Republican. They are correct, but for a reason more fundamental than those usually given. Some focus on Trump’s differences from mainstream GOP policies, but the party is broad enough to embrace different views, and Trump agrees with most Republicans on many issues. Others point to the insults he regularly directs at party members and leaders, but Trump is not the first to promote self above party. The fundamental reason Trump isn’t a Republican is far bigger than words or policies. He stands in opposition to the founding principle of our party — that of a united country.


John Danforth: Trump is Exactly What Republicans Are Not

Trump is the logical extension of Nixon's "Southern Strategy," Reagan's fantasy "Welfare Queens," George H. Bush's obscene gesture of digging up Clarence Thomas to "replace" Thurgood Marshall, the racist refusal of by Mitch McConnell to spit on the graves of John Adams, Thomas Jefferson and John Marshall by refusing to consider a Supreme Court Justice appointed by an African American President etc, etc, etc.

Trump is the culmination of 50 years of what used to be subtle appeals to racism, now written publicly for all the world to see.

You built it; you displayed it; you voted for it; you own it, Danforth.

Ion imprinted polymers for metal separations from seawater, selecting uranium over vanadium.

There is growing consternation among scientists about the depletion of critical elements of the periodic table, many of which are integral to the so called "renewable energy" industry, which despite unjustified worldwide popularity is not sustainable, not safe, and not effective at doing anything at all about the most serious environmental issue ever to come before humanity, climate change.

This periodic table from the Royal Chemical Society (UK) shows the elements of concern:

The importance of elemental sustainability and critical element recovery

Note that among the actinides, uranium is included. Why Neptunium is even mentioned is something of a mystery to me. It's a synthetic element. Despite the minor criticisms and objections I may have, these papers point to an important issue before humanity, we in this generation are depleting the chemical elements that also should belong to all future generations.

There are many such periodic tables available in the scientific literature and while they all focus on important issues in sustainability, they all rely on certain assumptions and can and do vary considerably. Most rely on assumptions about the technology of element recovery, assuming that the practices of the 20th and 21st century are the only technologies that can be applied to resources.

Most of us who have been concerned with environmental sustainability will be familiar with the "peak oil" arguments that were fashionable a few years back; regrettably and at great cost to the future of humanity what were once "unconventional sources" of oil and gas, for example horizontal fracturing ("fracking" ) and oil sands were developed at great cost to and with great contempt for all future generations. Peak oil has, regrettably, not come to pass, at least not yet

Critics of the nuclear industry, which I personally regard as the only safe, sustainable, and economically feasible source of energy available to the greater bulk of humanity, the only source of energy that can eliminate human poverty without destroying the environment, often speak of "peak uranium."

I have calculated elsewhere that humanity could in fact double the energy available to the average citizen of the world - which can be expressed as a continuous average watt-year - by converting just roughly 13,000 tons of uranium to plutonium and fissioning it. Current Energy Demand; Ethical Energy Demand; Depleted Uranium and the Centuries to Come The current figure for the average continuous power per year for the average citizen of the world is 2500W, roughly 1/4 the demand of the average American. By contrast, billions of tons of carbon dioxide are dumped with no restriction into the planetary atmosphere each year, and the rate of such dumping is increasing, not decreasing, as a result of the pixilated faith in so called "renewable energy" which has not worked, is not working and will not work, despite the squandering of trillions of dollars on it in the last decade alone.

But what about peak uranium?

Actually the supply of uranium is infinite in the sense that humanity would never under any circumstances ever be able to succeed in consuming all of it that is available. This is because there are over 5 billion tons of it naturally in the earth's oceans, and any effort to remove it would be defeated by the recharge from crustal and mantle sources. (I elaborated on this at some length elsewhere: Sustaining the Wind: Is Uranium Exhaustible?

Many thousands of papers, maybe tens of thousands of papers have been published on the recovery of uranium from seawater over the last 50 or 60 years, and they are becoming more and more sophisticated and interesting. This approach is economically viable because of the extremely high energy to mass ratio of plutonium synthesized from uranium in comparison to all other forms of energy. Slightly less than 100 grams of plutonium could supply the entire lifetime needs of an individual who lived to be a hundred years old while consuming on an average continuous basis 5000 watts of power.

In my general reading in one of my favorite journals, Industrial Engineering Chemistry Research I came across an interesting one, referring to an issue in "chemical imprinting," this one: Surface Ion-Imprinted Polypropylene Nonwoven Fabric for Potential Uranium Seawater Extraction with High Selectivity over Vanadium. (Lixia Zhang†, Sen Yang†, Jun Qian†, and Daoben Hua, Ind. Eng. Chem. Res., 2017, 56 (7), pp 1860–1867)

Whenever seawater is processed to cover uranium, the element vanadium is also recovered, thus reducing the efficiency of uranium recovery. These scientists have utilized a technique that I really love, again, chemical imprinting, in which a polymer (or other extracting agent) is formed in the presence of the element (or molecule) that it is designed to separate. These scientists formed polymers in the presence of uranium so that little (nanoscale) pockets would form it that precisely fit uranium.

Some text from the paper describes this approach:

Several reports 7, 26,27 focused on separation of uranium and vanadium by elution: uranium could be easily eluted, but vanadium tended to be adsorbed firmly onto the sorbents, thus occupying the binding site of synthesized materials and reducing the recycle efficiency. Therefore, it is still crucial to develop a new approach to tackle this challenge. A surface ion-imprinting technique can be considered to solve the problem of selectivity between uranium and vanadium. This method is based on the cross-linking and copolymerization of some monomers with the existence of template ions.28 The recognition is introduced by template molecules during the polymerization based on the affinity of ligand and the size of generated cavities,28,29 which provides the advantages of fast sorption kinetics and highly selective bindingsite.29,30

A surface ion-imprinting technique has been successfully used to remove uranium with high selectivity from aqueous solution.31−35 For instance, Preetha et al.31reported uranyl ion imprinted polymer particles for uranium removal from nuclear power reactor effluents, and Qian et al.33prepared a magnetic surface ion-imprinted microsphere through locating polymerization for selective and rapid uranium separation from aqueous solution of pH 5.0. However, there are few reports on surface ion-imprinted materials for uranium extraction from seawater until now...

In this paper, a polypropylene is functionalized by a glycidyl (epoxide) ester of methyl methacrylate using γ radiation, and further elaborated with the actual uranium recognition species, a quartenary imidazole copolymer (from a vinyl imidizaole monomer) with vinyl benzyl chloride - similar to those found in ionic liquids - with the imprinted and supporting polymers linked via a thiocarbonate functionalized intermediate.

The resulting polymer can be eluted (for uranium) with EDTA, and the reported recovery of uranium was 133.3 mg/g of the woven polymer, quite good for these kinds of polymers. The polymer showed high selectivity not only for vanadium, but also copper, zinc, iron and cobalt.

Esoteric, I know, but interesting.

Cause we've ended as lovers...

Pediatricians say Florida hurt sick kids to help big GOP donors

I don't know if this has been covered here, but if not, here it is.

Pediatricians say Florida hurt sick kids to help big GOP donors

Unsurprising, of course. Besides being traitors and racists, Republicans hate poor people, especially if it interferes with their selfish desire to leave nothing left standing after they die of excess.

My youngest starts college next week. I'm going to spend the day with him writing a program to...

...solve the Peng Robinson equation using Matlab.

There are internet calculators to do it, but there's nothing better to understand the equation than to write a program to do it.

I hate him going away, but tomorrow will be a very beautiful day in our last weekend of his life at home with us.

I'm very proud of him - I hope he will prove to be a wonderful engineer - but I'll miss him terribly. I've loved talking science with him.

The big guy has lived with us during college, but the little guy got a big time scholarship and will be going away. It's my first experience with one of my boys moving out.
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