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This chapter discusses fatty acids, the building blocks of lipids, which represent a significant fraction of the total lipid pool in aquatic organisms. It explores how chain length and levels of unsaturation (number of double bonds) have been shown to be correlated to decomposition, indicating a pre- and postdepositional selective loss of short-chain and polyunsaturated fatty acids. In contrast, saturated fatty acids are more stable and typically increase in relative proportion to total fatty acids with increasing sediment depth. Polyunsaturated fatty acids (PUFAs) are predominantly used as proxies for the presence of “fresh” algal sources, although some PUFAs also occur in vascular plants and deep-sea bacteria. Thus, these biomarkers represent a very diverse group of compounds present in aquatic systems. The numerous applications of fatty acid biomarkers to identifying the sources of organic matter in lakes, rivers, estuaries, and marine ecosystems are discussed.

Essential fatty acids are polyunsaturated fatty acids from the n-6 family (i.e., linoleic acid and arachidonic acid) present in vegetable oils, and of the n-3 family (i.e., eicosapentaenoic acid and docosahexaenoic acid) present in seafood. These fatty acids may protect against coronary atherosclerosis and thrombosis. It is hypothesized that a balanced intake of n-6 and n-3 fatty acids is of great importance in relation to prevention of coronary heart disease (CHD). Research on n-3 fatty acids, fish consumption, and CHD was stimulated by the pioneering studies among the Inuit (Eskimos) in Greenland. This chapter begins by summarizing the results of the studies among the Inuit. The results on fish consumption and CHD mortality are then reviewed at the population and individual levels. Both observational epidemiology and experimental studies show that a small amount of fish protects against fatal CHD and sudden cardiac death. It is, therefore, recommended to eat fish (preferably fatty fish) once or twice a week.

This chapter reviews the crystal structures of fatty acid esters of linear fatty alcohols, revealing that no complete structure exists for a symmetric chain ester. Chain branching influences on layer packing are shown. The binary phase diagrams of esters with n-paraffins are presented, revealing how symmetric esters prefer tilted chain layer packing that are incompatible with n-paraffins of the same chain length, whereas asymmetric esters may be co-soluble. The arrangement of ester chains in natural waxes, including those from insects, is discussed.

In choosing the order for discussion of phospholipids, it is not the intention to single out one particular group as the most important; rather, an initial premise would be that all phospholipids are critical to a cell’s structure and metabolism. Certainly, as has been emphasized before, phospholipids have been shown to have key roles in the process of cellular signal transduction, and it is debatable which of several types of phospholipids is the most important. There is no doubt that the mechanism of involvement of membrane phospholipids in these complex reactions has presented a major experimental challenge, and as such this has titillated the acute scientific senses of many researchers. It is equally true also that an important field of study is emerging in cell signaling, in which unusual cellular disorders have been noted. Certainly the latter will implicate alterations or aberrations in membrane phospholipid chemistry and metabolism in one way or another. This digression was made to show quite simply that it behooves one to understand the chemical/ biochemical characteristics of the phospholipids in order to best meet the challenges of this field (and, of course, other related ones as well). On the basis of undoubted faulty logic on the choice of the order of topics, one simply can retreat to the argument of personal preference. Thus, the first group of compounds will be the choline-containing phospholipids—that is, the choline phosphoglycerides and the choline sphingolipids. As it so happens, these are among the most ubiquitous phospholipids in nature and, at least in the early “chemical” years of investigations on the phospholipids, the best-studied group. It is assumed at this junction that a highly purified phospholipid has been obtained, usually through the use of chromatographic procedures. A frequently asked question is, How do I tell whether the sample is pure? It is a logical question, especially with compounds isolated from naturally occurring sources. In actual fact, there is no simple answer.

This chapter discusses mitochondrial fatty acid oxidation defects, including normal fatty acid oxidation, metabolic abnormalities, and sudden infant death. Factors to be considered in diagnosis and nutritional management are discussed, including avoidance of fasting, prevention of nighttime hypoglycemia, supplementation with L-carnitine, and dietary fat restriction. Essential fatty acids, fatty acid oxidation during exercise, B vitamin supplementation, and liver disease in pregnancy are specifically described.

Most enzymes discussed in the preceding chapters consist of single proteins that catalyze single biochemical reactions. Many of them contain one type of polypeptide chain, although most exist as oligomers of a polypeptide, and some consist of different polypeptides that cooperate to catalyze one reaction. Increasing attention is being focused on enzymes that catalyze more complex processes and are composed of more than one enzyme or enzymatic domain, each of which catalyzes or facilitates a specific biochemical process. These complex enzymes are the subjects of this chapter. Complex enzymes are so numerous and the processes they catalyze so complex that a complete discussion would fill a book. We therefore limit this discussion to a few examples. The first complex enzymes to be discovered were the multienzyme complexes. They included the four terminal electron transport complexes of the respiratory chain: complex I, known as NADH dehydrogenase (formerly DPNH dehydrogenase); complex II, known as succinate dehydrogenase; complex III, known as cytochrome c reductase; and complex IV, known as cytochrome c oxidase. Other multienzyme complexes discovered at about the same time were the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase complexes, the fatty acid synthase complexes, and the glycine reductase complex and the anthranilate synthase complex. Later, the multimodular polyketide synthases and nonribosomal polypeptide synthetases were characterized. The ATP synthases are multiprotein complexes that function as molecular motors in catalyzing a complex reaction, the condensation of ADP with Pi driven by proton translocation to form ATP. The ribosome catalyzes the polymerization of amino acids in defined sequences specified by the nucleotide sequences in species of mRNA, and nitrogenase catalyzes the ATP-dependent reduction of molecular nitrogen to ammonia. Some of the actions of complex enzymes link together common biochemical reactions of the types discussed in preceding chapters. Others catalyze difficult reactions through mechanistic coupling to energy-producing processes that provide driving force for otherwise unfavorable transformations. We present examples of each type. Catalysis by an α-ketoacid dehydrogenase complex is carried out by three physically associated enzymes, a TPP-dependent α-ketoacid dehydrogenase (E1), a dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase (E3).

Though the biomarker saga began with attempts to understand the ancient provenance of petroleum and with the concept of “fossil molecules” and search for early forms of life, the explorations of the past 50 years have led organic geochemists far afield of these first endeavors. As Geoff and Max Blumer recognized back in the 1960s, and as microbiologists began to realize in the early 1980s, the usefulness of the biomarker concept is not restricted to geologic time. Most organic geochemists have, at one time or another, applied their techniques and expertise to the resolution of environmental problems, or found a way to address some archaeological mystery. One of the Bristol group’s most vibrant research programs now has its chemists brushing shoulders not with geologists and oceanographers, but with archaeologists and anthropologists concerned with the evolution of human civilizations and societies. Much of the impetus for the application of biomarker concepts to archaeologists’ questions in the 1970s and 1980s came from petroleum geochemists, not least from Arie Nissenbaum, a geochemist at Israel’s Weizmann Institute of Science who developed a keen interest in the role that geological events and circumstance might have played in the history of civilizations in the Fertile Crescent region. Nissenbaum was fascinated by the bizarre geology and chemistry of the Dead Sea Basin area, where oil seeps and impressive raftlike chunks of asphalt floating on the surface of the lake had long tempted oil prospectors to no avail. Renewed interest in the area’s oil potential in the early 1980s attracted a wave of geochemical studies, and Israeli geochemists scrambled for laboratory resources and funding from abroad. Jürgen, still with Dietrich Welte’s group, did a detailed biomarker study at the behest of an Israeli colleague, and when Nissenbaum saw the results he suggested to Jürgen that they apply Jülich’s considerable GC-MS capability to solving an entirely different sort of mystery. Excavations of archaeological sites in the vicinity of the Dead Sea had turned up solid chunks of black, sticky material that was used as early as 3000 B.C., either in materials used for construction or as a glue to attach tool heads to wooden handles.

The endocannabinoid system was only discovered about 25 years ago, but it is now known to be a major modulator of synaptic activity throughout the brain. CB₁ receptors are located on presynaptic terminals of neurons that release other neurotransmitters and the action of agonists of these receptors is to turn-off neurotransmitter release. These receptors are ubiquitously located, indeed they are the most widely distributed receptor system in the brain. Administration of THC by use of marijuana activates all CB₁ receptors, producing global activation. On the other hand, endocannabinoids (anandamide and 2-AG) are produced where and when they are needed from depolarized post-synaptic neurons, serving as retrograde messengers to act on nearby presynaptic neurons. The fine-tuned regulation of synaptic activity is the primary function of this neuromodulatory system that plays a major role in protection of neurons. The duration of action of these “on demand” endocannabinoids is brief because they are hydrolysed enzymatically by Fatty Acid Amide Hydrolase (FAAH) and monoacylglycerol lipase (MAGL). Newly developed FAAH and MAGL inhibitors provide a therapeutic opportunity to boost the action of AEA and 2-AG respectively for up to 24 hr, where and when they are produced naturally. Preclinical evidence indicates that FAAH and MAGL inhibitors have therapeutic potential in relief of pain, anxiety, depression and nausea, in the absence of psychoactive side effects of global activation of CB₁ receptors produced by marijuana.

For many of us who studied and came of age in the last two decades of the twentieth century, there was nothing more prosaic, lacking in romance, and less worthy of our scientific curiosity than petroleum. The basic questions about its composition and origin had been answered, and it was no longer one of Nature’s secrets luring us to discovery, but rather the dull stuff of industry and business, money and technology. Some of us even imagined, naively, that we would witness the end of the age of fossil fuels: they were the bane of modern man, the source of pollution, environmental disaster, and climate change that threatened to disrupt ecosystems and civilizations around the entire globe. Finding new reserves, we reasoned, would only forestall the inevitable, or exacerbate the havoc. But when Jürgen joined Germany’s government-funded Institute of Petroleum and Organic Geochemistry in 1975, there was still a sense of mission in finding new reserves. The energy crisis of the early 1970s had created a heightened awareness of the value of fossil fuels and the need for conservation, but the accepted wisdom remained that oil was the key to the future and well-being of civilization. And the chemistry, it seems, was anything but banal—it was, in fact, leading not just to a better success rate in finding new reserves of oil, but also to a new understanding of life that no one had foreseen. Certainly for Geoff and the generations of organic chemists that came before him, the oils that occasionally seeped out of a crack in a rock, or came spouting out of the earth if one drilled a hole in the right place, were as intriguing as the life some said they came from. Liquid from a solid, organic from mineral, black or brown or dark red, it was as if blood were oozing from stone, an enigma that inspired inquiry from scientists long before it found its place among man’s most coveted commodities.

Anaerobic methanotrophs are not the only ecologically important archaea to surprise microbiologists in the last decade. And their isoprenoid ethers are not the only useful lipids—and certainly not the strangest—to have joined the lexicon of microbial biomarkers. Though much of that lexicon is still too generic to be of much use in understanding geologic history, some of these structures have allowed geochemists to transcend biological complexity and garner clues to past climates and environments. In the 1990s, when Stefan Schouten first started finding ring-containing biphytanyl ethers in his sediment samples, he was still working on his doctorate at NIOZ. Like everyone else at the time, he assumed that they derived from the lipids of methanogenic archaea and that it was only a matter of time before ring-containing biphytanyl tetraethers would be identified among the lipids of some newly isolated culture of methanogens, as Guy Ourisson had predicted. Schouten was studying oxygen- and sulfur-bound biomarkers, which meant he treated his sediment extracts chemically to cleave the ether and sulfur bonds, and the treatments often turned up biphytanes. But then, he says, he and another student started finding the ring-containing compounds in some really unlikely places, such as the oxic surface layer of marine sediments where neither methanogens nor extreme thermophilic and halophilic archaea were likely to make a home. The only thing they could think of at the time was that the tetraethers had come from methanogens that lived in the oxygen minimum zone, the layer of water beneath the photic zone where heterotrophic bacteria are active, sometimes to the point of using up all of the oxygen. When Schouten presented these ideas at the 1995 organic geochemistry meeting, Stuart Wakeham immediately piped up with the suggestion that they look for the lipids in the water column—and offered the perfect samples for the enterprise. He had collected particulate matter at different depths in the Black Sea and Cariaco Basin, just the sort of anoxic environments where one might expect to find methanogens in the water column. . . .

Advocates of practical though controversial lifestyle approaches have always found a sympathetic ear in the United States since the time folk practitioner Sylvester Graham’s principles of health, nutrition, and fitness (in addition to inventing the Graham cracker) achieved cult status in the 1840s. Heroic, misguided therapies were administered by allopathic (mainstream) physicians throughout the nineteenth century. This created fertile ground for promoters of patent medicines and nostrums to those escaping organized medicine’s use of leeches, cupping, phlebotomy (blood drawing) knives, and brutal laxative regimens. During the Progressive Era, medicine started to improve with the establishment of postgraduate training programs at Johns Hopkins University just before the turn of the century and the regulation of medicines as part of the Pure Food and Drug Act of 1906. The final revolution occurred when two-thirds of the medical schools in the United States closed following revelations of their inadequacies by the investigative Flexner Report funded by the Carnegie Foundation in 1910. Despite these changes, however, the appeal of alternative therapies to the American public continues unabated. The previous two chapters have described how mainstream, organized, conventional medicine approaches fibromyalgia. Even though their therapies usually provide significant relief of symptoms and signs, traditional physicians to some extent must regard themselves as failures. In the United States, one person in three has consulted a complementary medicine practitioner. These individuals spend $23 billion a year on this approach, $13 billion of which is out-of-pocket and not reimbursed by insurance. This exceeds all expenditures on hospital care in the United States. A 1996 Canadian study found that of several hundred fibromyalgia patients, 70 percent purchased unproven over-the-counter rubs, creams, vitamins, or herbs; 40 percent sought help from alternative medicine practitioners such as chiropractors, massage therapists, homeopaths, reflexologists, or acupuncturists; and 26 percent went on special diets. Since it is logical to believe that people who are tired and hurt want to get better, it follows that some fibromyalgia patients will try anything that is not harmful to improve their medical condition. This chapter is dedicated to patients who wish to “look before they leap” into nontraditional therapies.

In this chapter we demonstrate the feasibility of digital computation in cells by building several operational in vivo digital logic circuits, each composed of three gates that have been optimized by genetic process engineering. We have built and characterized an initial cellular gate library with biochemical gates that implement the NOT, IMPLIES, andANDlogic functions in E. coli cells. The logic gates perform computation using DNA-binding proteins, small molecules that interact with these proteins, and segments of DNA that regulate the expression of the proteins. We also demonstrate engineered intercellular communications with programmed enzymatic activity and chemical diffusions to carry messages, using DNA from the Vibrio fischeri lux operon. The programmed communications is essential for obtaining coordinated behavior from cell aggregates. This chapter is structured as follows: the first section describes experimental measurements of the device physics of in vivo logic gates, as well as genetic process engineering to modify gates until they have the desired behavior. The second section presents experimental results of programmed intercellular communications, including time–response measurements and sensitivity to variations in message concentrations. Potentially the most important element of biocircuit design is matching gate characteristics. Experimental results in this section demonstrate that circuits with mismatched gates are likely to malfunction. In generating biology’s complex genetic regulatory networks, natural forces of selection have resulted in finely tuned interconnections between the different regulatory components. Nature has optimized and matched the kinetic characteristics of these elements so that they cooperatively achieve the desired regulatory behavior. In building de novo biocircuits, we frequently combine regulatory elements that do not interact in their wild-type settings. Therefore, naive coupling of these elements will likely produce systems that do not have the desired behavior. In genetic process engineering, the biocircuit designer first determines the behavioral characteristics of the regulatory components and then modifies the elements until the desired behavior is attained. Below, we show experimental results of using this process to convert a nonfunctional circuit with mismatched gates into a circuit that achieves the correct response.

Throughout the 1980s, while the molecule collectors were busy exploring the ocean sediments, tracking their finds into the past, and learning to read the messages hidden in the carbon skeletons, one analytical chemist cum geochemist at Indiana University was finding that important elements of the lexicon lay not only in the molecular structures, stereochemistry, and distributions of the carbon skeletons, but in the carbon atoms themselves. John Hayes had done his graduate work at MIT in the mid-1960s under Klaus Biemann, one of the doyens of mass spectrometry who, like Carl Djerassi, was interested in natural products with biomedical applications. When Hayes told Biemann he wanted to do his doctoral thesis on the organic constituents in meteorites, Biemann was uninterested, to say the least. Forty years later, Hayes can still quote the eminent scientist’s response to his proposal, replete with thick Austrian accent: “Don’t talk to me about zat junk.” Biemann walked away from the discussion without another word, and Hayes was so mortified by his own foolishness that he couldn’t bring himself to tell his wife about the incident. When he went into the lab the next day, he was convinced that his graduate career was over—but Biemann had done some homework and had a change of heart. “It seems we can get lots of money for zat junk!” he exclaimed as soon as he saw Hayes. NASA was, at the time, offering generous funding for such projects. For all his skepticism, Biemann was eventually seduced by the extraterrestrial “junk” and even ended up designing the mass spectrometer for the Viking Mars mission. Hayes remembers him commenting, a couple of years into the meteorite project, that it was actually “much more interesting than the thousandth alkaloid in the thousandth tree,” though Hayes himself says his doctoral thesis was unexceptional, completed before the Murchison meteorite fell and things really got interesting.

What does a political campaign have to do with tetrahedrane, a beautiful yet unstable hydrocarbon with four CH groups at the corners of a tetrahedron? Just look and listen (you’ll have a hard time not doing so) to the onslaught of masterfully crafted oversimplifications thrown at you in any campaign, by all the parties. And think about why people—no, not you, of course—succumb to it. It has something to do with the reasons why we lust for the elegantly simple molecule in the shape of a Platonic solid or the beautiful (and preferably, soluble) equation. I want to think about what gives us satisfaction in science when simplicity fails us, as it must, in a real world. If one can make any generalization about the human mind, it is that it craves simple answers. The ideology of the simple reigns in science, as it does in politics. So we have the romantic dreams of theoreticians (for example, Dirac) preferring simple and/or beautiful equations. And the moment Richard Smalley, Harold Kroto, Robert Curl and their coworkers intuited that the C60 peak in their laser-ablated carbon mass spectrum came from a molecule that should grace the flag of Brazil, I believed it. It could not be otherwise. And they were right. Simplicity, symmetry, and order ride a straight ray into our souls. I wonder why? Perhaps (this is far out) we have evolved a psychobiological predilection for the qualities of the world that rationalize our existence as locally contraentropic creatures that build molecules and poems. And I am a little unfair to the creative force implicit in the psychological imperative for the simple. The cult of mathematical simplicity as beauty is a reaching for essences that parallels the compact truthtelling of poetry. This is what Dalton, Dirac, and Einstein aspired to. And this perspective has led to “the majesty, subtlety, and grace of science, and her deepest insights and discoveries,” as Michael Fisher so aptly put it. But what if the world is determined by us, by scientific us, to be complex, unsymmetrical, and moderately chaotic? How do we find satisfaction, and I do mean psychological satisfaction, in such a world? I think the answer is simple (I’m smiling).

This chapter reviews and briefly discusses a set of computational methods that can assist biologists when seeking to model interactions between components in spatially heterogeneous and changing environments. The approach can be applied to many scales of biological organization, and the illustrations we have selected apply to networks of interaction among proteins. Biological populations, whether ecological or molecular, homogeneous or heterogeneous, moving or stationary, can be modeled at different scales of organization. Some models can be constructed that focus on factors or patterns that characterize the population as a whole such as population size, average mass or length, and so forth. Other models focus on values associated with individuals such as age, energy reserve, and spatial association with other individuals. A distinction can be made between population (p-state) and individual (i-state) variables and models. We seek to develop a general approach to modeling biosystems based on individuals. Individual-based models (IBMs) typically consist of an environment or framework in which interactions occur and a number of individuals defined in terms of their behaviors (such as procedural rules) and characteristic parameters. The actions of each individual can be tracked through time. IBMs represent heterogeneous systems as sets of nonidentical, discrete, interacting, autonomous, adaptive agents (e.g., Devine and Paton [5]). They have been used to model the dynamics of population interaction over time in ecological systems, but IBMs can equally be applied to biological systems at other levels of scale. The IBM approach can be used to simulate the emergence of global information processing from individual, local interactions in a population of agents. When it is sensible and appropriate, we seek to incorporate an ecological and social view of inter-agent interactions to all scales of the biological hierarch. In this case we distinguish among individual “devices” (agents), networks (societies or communities), and networks in habitats (ecologies). In that they are able to interact with other molecules in subtle and varied ways, we may say that many proteins have social abilities . This social dimension to protein agency also presupposes that proteins have an underlying ecology in that they interact with other molecules including substrates, products, regulators, cytoskeleton, membranes, water, and local electric fields.

That the evolution of organisms depends in large part on the evolution of their environment is something paleontologists have been noting since the early nineteenth century, and indeed, it is so inherent in Darwinian theory as to seem almost banal. That this dependency might have been two-way—that the earth’s minerals, atmosphere, oceans, and climate have been in large measure determined by the evolution of different life-forms—was somewhat harder to document and accept, partly because the most dramatic evidence was hidden, at the molecular level, in the elusive Precambrian rocks. The concept of the coevolution of Earth and life saw its first cohesive and most provocative expression when James Lovelock presented his Gaia hypothesis in the early 1970s, but not until the end of the twentieth century were the basic tenets of the hypothesis accepted as a valid theory. Lovelock began conceiving the Gaia hypothesis when he was designing instruments for NASA’s first extraterrestrial explorations and it occurred to him that, unlike the moon and Mars, the earth had an atmosphere composed of gases that couldn’t and wouldn’t coexist without life’s intervention. At the same time, a handful of paleontologists and geochemists had been conceiving similar if less provocatively formulated hypotheses based on their studies of the earth’s most ancient rocks and sediments. In 1979, a decade after Geoff, Thomas Hoering, and Keith Kvenvolden had more or less given up on the prospect of garnering clues about early life-forms from the fossil molecules in Archean and early Proterozoic rocks, one of those paleontologists inadvertently inspired a certain Australian chemist to give it another go. Roger Summons met the paleontologist Preston Cloud when Cloud was on sabbatical at the Australian Institute of Marine Science. Summons was working in the biology department at Australian National University and had been assigned to play guide and chauffeur for Andrew Benson, a visiting American plant physiologist who was staying out at the marine institute. “There was a couple living in the guesthouse next to us,” Summons tells me. “And this guy was a jogger. He’d leave every morning at 5:00 A.M. and run past the house, clump clump clump clump, and I’d wake up.”

In search of a chemical conversation, we are on a farm in Uniow, a little Ukrainian village in Austro-Hungarian Galicia, just before the onset of World War I. In the farm yard we see a big, steaming, lead-lined iron pot. The men have mixed some potash in it (no, not the pure chemical with composition KOH from a chemical supply company, but the real ash from burning good poplar) and quicklime, to a thickness that an egg—plenty of eggs here, judging from the roaming chickens—floats on it. Elsewhere in the yard, women are straining kitchen grease, suet, pig bones, rancid butter, the poor parts skimmed off the goose fat (the best of which had been set to cool, cracklings and all). This mix doesn’t smell good; they would rather toss the kitchen leavings and bones into the great iron pot, but the fat must be free of meat, bones, and solids for the process to work. They are making soap. Not that we had to go that far, near where one of us was born, for soap was prepared in this way on farms from medieval times until the twentieth century. Fat was boiled up with lye (what the potash and quicklime made). The reaction was slow—days of heating and stirring until the lye was used up, and a chicken feather would no longer dissolve in the brew. One learned not to get the lye on one’s hands. The product of a simple chemical reaction was then left in the sun for a week, stirred until a paste formed. Then it was shaped into blocks and set out on wood to dry. And inside the steaming pot, deep inside, where the fat and the lye are reacting? There is the conversation we are after, a hellishly animated molecular conversation. The lye that formed was an alkaline mixture of KOH, Ca(OH)2, and NaOH. In the vat one had hydroxide (OH-) ions, and K+, Ca2+, Na+ all surrounded in dynamic array and disarray by water molecules. Contaminants aside, the fat molecules are compounds called esters, in which an organic base, glycerol, combines with three long-chain hydrocarbon chains.