Biology

"Koji usually serves as the basis of secondary fermentation, in which its s help to (break down or digest or split) basic nutrients. ... ...digests carbohydrates ... breaks down proteins, and ... ...digests lipids (fats). Rice... barley... and soybean koji are used to make three different types of . Koji for Japanese is made from a mixture of roasted wheat and defatted soybean meal; this koji is dark-green in color. Whole soybean koji is used to make traditional Chinese soy sauce and fermented black soy beans (also known as... ...etc.). Rice koji is used to make Japanese ... and ... Koji is to sake as is to beer. Each saccharifies the starch... so that... sugars can be fermented to alcohol by yeasts."

", or “fermented soybean paste,”... is an all-purpose high-protein seasoning, which has no counterpart among Western foods or seasonings. Made from soybeans, rice or barley, and salt... [i]t comes in a wide range of warm, earthy colors... Each miso has its own distinctive flavor and aroma... Miso’s range of flavors and colors, textures and aromas, is at least as varied as that of the world’s fine wines or cheeses."

"The is simply mixed with cooked, dehulled soybeans; the continues its growth without the... spores. ...however, [it] generally has a lightly weaker mycelium and the incubation time is a little longer than... sporulated methods. And... there are always some unwanted bacteria in the original tempeh. If you are careless and/or the humidity is high, their numbers will increase with each generation until eventually they prevail, preventing the formation of good tempeh. However, by being clean and careful, we have had no trouble in keeping this starter going for more than 12 generations..."

"Koji is a culture prepared by growing... '... mold on cooked grains and/or soybeans in a warm, humid place. Koji serves as a source of enzymes that break down (or hydrolyze / digest / split) natural plant constituents into simpler compounds when making , , , , and other fermented foods. Its fragrant white... mycelium... has a delightful aroma resembling that of mushrooms. ...Koji is written with the exact same character in China and Japan. ...In China this character is romanized as qu... Koji was invented in China at least three centuries before the Christian era."

"[T]he French Academy of Sciences in 1779 had posted a prize of one kilogram of gold for a solution of the mystery of fermentation. Unfortunately, the offer had to be withdrawn in 1793... but Cagniard-Latour's inquisitive spirit was undaunted by the cancellation... He described the features of yeast cells, classified them as plants, observed the process of budding and noted the differences in shape between wine- and beer-yeasts. He also found the multiplication of the cells required nitrogenous material in addition to fermentable carbohydrate. ...Unfortunately, however, he reverted to his research interest in physics."

"Why don't more animals regenerate? Although it's useful, regeneration isn't the best survival strategy because healing wounds is a trade-off between speed and accuracy. Perfect repairs can take time, whereas immediately closing an open wound minimizes the risk of infection or bleeding to death, although it does leave scar tissue. Animals use a fibrous connective protein called collagen to holds cells together (one-third of the human body consists of collagen). It's arranged in a basketweave (criss-cross) pattern in regular tissue, while scar tissue fibres are aligned side-by-side. Regular tissue is like fabric material, whereas scars are stitches holding two pieces of fabric together. Stitching is faster than weaving, so it's better for rapid repair."

"Regeneration is the fountain; sanctification is the river (in deeper or shallower degree). Entire sanctification is the river in fullest flow."

"Evolutionary game theory originated as an application of the mathematical theory of games to biological contexts, arising from the realization that frequency dependent fitness introduces a strategic aspect to evolution. Recently, however, evolutionary game theory has become of increased interest to economists, sociologists, and anthropologists--and social scientists in general--as well as philosophers."

"Ever since Darwin read Malthus, the theory of evolution has benefited from the interaction of ecology with economics. Evolutionary game theory belongs to this tradition: it merges population ecology with game theory."

"Evolutionary game theory is one of the most active and rapidly growing areas of research in economics. Unlike traditional game theory models, which assume that all players are fully rational and have complete knowledge of details of the game, evolutionary models assume that people choose their strategies through a trial-and-error learning process in which they gradually discover that some strategies work better than others. In games that are repeated many times, low-payoff strategies tend to be weeded out, and an equilibrium may emerge."

"Traditionally, game theory has been seen as a theory of how rational actors behave. Ironically, game theory... has shown... the limited capacity of the concept of rationality alone to predict human behavior. ...Evolutionary game theory deploys the Darwinian notion that good strategies diffuse across populations of players rather than being learned by rational agents. ...[A]gents choose best responses, and otherwise behave as good citizens of game theory society. But they may be pigs, dung beetles, birds, spiders, or even... s and s. How do they accomplish these feats with their small minds and alien mentalities? ...the agent is displaced by the strategy as the dynamic game-theoretic unit. ...[W]e provide agent-based computer simulations of games, showing that really stupid critters can evolve toward the solution of games previously thought to require "rationality" and high-level information processing capacity."

"Evolutionary game theory is a way of thinking about evolution at the phenotypic level when the fitnesses of particular phenotypes depend on their frequencies in the population."

"Current evolutionary game theory — where ideas from evolutionary biology and rationalistic economics meet — emphasizing the links between static and dynamic approaches and noncooperative game theory."

"Oscillatory reactions of the epigenetic type are also well known. They occur as a consequence of regulatory processes at the cellular level. Proteins are generally stable molecules, whereas catalysis is a very fast process. Thus, it is not unusual for the protein level in a cell to be too high, in which case other bodily substances act to suppress the synthesis of macromolecules. Such feedback gives rise to oscillations and has been studied in detail in, for example, the regulation of the lactose operon in the bacterium Escherichia coli."

"The natural balance produced by the Rock, Paper, Scissors scenario is not confined to lizards. Researchers from Stanford and Yale have discovered that the same scenario is responsible for preserving biodiversity in bacterial neighborhoods. The bacteria concerned are Escherichia coli—the type that are found in all of our digestive systems. The researchers mixed three natural populations together in a petri dish. One population produced a natural antibiotic called “colicin” but was immune to its effects, as snakes are immune to poisoning by their own venom. A second population was sensitive to the colicin but could grow faster than the third population, which was resistant to colicin. The net result was that each established its own territory in the petri dish. The colicin producers could kill off any nearby bacteria that were sensitive to the colicin, the colicin-sensitive bacteria could use their faster growth rate to displace the colicin-resistant bacteria, and the resistant bacteria could in turn use their immunity to displace the colicin producers!"

"Bacteria, the study of which has formed a great part of the foundation of genetics and molecular biology, are the organisms which, because of their huge numbers, produce the most mutants. This is why they gave rise to an infinite variety of species, called strains, which can be revealed by breeding or tests. Like Erophila verna, bacteria, despite their great production of intraspecific varieties, exhibit a great fidelity to their species. The bacillus Escherichia coli, whose mutants have been studied very carefully, is the best example. The reader will agree that it is surprising, to say the least, to want to prove evolution and to discover its mechanisms and then to choose as a material for this study a being which practically stabilized a billion years ago!"

"The equivalent fundamental unit in DNA is the nucleotide base. Since there are 4 possible bases, the information content of each base is equivalent to 2 bits. The common gut bacterium Escherichia coli has a genome of 4 mega-bases or 8 megabits. The crested newt, Triturus cristatus, has 40,000 megabits. The 5,000-fold ratio between crested newt and bacterium is about the same as that between my present computer and my first one. We humans have 5,000 mega-bases or 6,000 megabits. This is 750 times as great as the bacterium (which satisfies our vanity), but what are we to make of the newt trumping us sixfold? We'd like to think that genome size is not strictly proportional to what it does: presumably quite a lot of that newt DNA isn't doing anything. This is certainly true. It is also true of most of our DNA."

"Without their threatening presence, there is no need for gene recombination or sexual (versus asexual) reproduction. We wouldn’t have to keep up with the Joneses, or in this case the Escherichia coli or the Entamoeba histolytica, which are constantly mutating to get better at attacking us so they can reproduce and survive. Disgust is the emotion that protects purity. Haidt suggests that the emotion of disgust arose when hominids became meat eaters. It appears to be a uniquely human emotion."

"Snake: I thought using genetically modified soldiers was prohibited by international law."

"Hannah Devlin: In 2015, you called for a moratorium on the clinical use of gene editing. Where do you stand on using Crispr to edit embryos these days?"

"Hannah Devlin: In your book you describe a nightmare you had involving Hitler wearing a pig mask, asking to learn more about your “amazing technology”. Do you still have anxiety dreams about where Crispr might leave the human race?"

"The genetic material for modification may be either derived from natural organisms using standard recombinant DNA techniques, or produced by DNA synthesis, the latter being much less labor intensive. In recent work, DNA sequences on the order of 1 million base-pairs have been synthesized entirely from digitized genome sequence information, and the resulting organisms were phenotypical and capable of self-replication."

"Development of novel (i.e., not known to be naturally-occurring) GMOs exhibiting unique designer characteristics requires substantially greater knowledge and capability. Many industrialized nations have laboratories capable of analyzing which immune response modifier genes in humans and livestock, when inserted into an organism together with pathogenicity (e.g., adherence and invasive) factor, will yield highly infectious pathogenic organisms."

"Since its first pragmatic elucidation in 1953, DNA structure and genetic engineering has extended its reach into agriculture, animal husbandry, medicine, and even organic materials."

"Evaluating the potential threat posed by advances in biotechnology, especially genetically modified organisms (GMOs), and synthetic biology remains a contentious issue. The rapid development of the tools of molecular biology and metabolic engineering has enabled the development of chimeric organisms which possess characteristics which are not native to the wild variant. This is commonplace in the area of biomanufacturing, where genes are introduced into organisms such as E coli and products manufactured via large-scale fermentation. More recently, entire metabolic pathways, albeit of limited complexity, have been engineered into organisms, for example, for the production of artemisinin in yeast. In addition to such metabolic engineering projects, whole genomes are being sequenced, leading to the possibility of creating organisms de novo. Numerous lectures, briefings and articles have argued that the dual use nature of biotechnology, the training of foreign students in American universities, and the easy availability of information on the internet have given potential adversaries access to biological weapons of unimagined which pose an existential threat. Some believe that, inevitably, these advances will lead to a catastrophic biological attack. Others have argued the opposite that making all information publicly available will enable a more universal “white biotechnology” which will ultimately monitor the field and provide the means to defeat any threat developed by adversaries. It has been argued that, despite these advances, the scientific and technical requirements, as well as the fundamental laws of natural selection, will prevent such an attack."

"Since the early 1990’s genetically engineered plants have been commercially available. So called “first generation” transgenic plants have been engineered for characteristics that enhance the agricultural yield and marketing. Such characteristics include resistance to pests, herbicides and extreme climates, as well as improved product shelf life. For example, since their first commercial cultivation in 1996, plants have been genetically modified for tolerance to the herbicides glufosinate and glyphosate. A “second generation” of transgenic plants, now in research and development, is aimed at enhancing consumer satisfaction by enhancing taste, texture, or appearance of produce. To date, no second generation transgenic plants are on the market."

"When we wrote Ecofeminism we raised the issue of reductionist, mechanistic science and the attitude of mastery over and conquest of nature as an expression of capitalist patriarchy. Today the contest between an ecological and feminist world-view and a worldview shaped by capitalist patriarchy is more intense than ever. This contest is particularly intense in the area of food. GMOs embody the vision of capitalist patriarchy. They perpetuate the idea of ‘master molecules’and mechanistic reductionism long after the life sciences have gone beyond reductionism, and patents on life reflect the capitalist patriarchal illusion of creation. There is no science in viewing DNA as a ‘master molecule’ and genetic engineering as a game of Lego, in which genes are moved around without any impact on the organism or the environment. This is a new pseudo-science that has taken on the status of a religion. Science cannot justify patents on life and seed. Shuffling genes is not making life; living organisms make themselves. Patents on seed mean denying the contributions of millions of years of evolution and thousands of years of farmers’ breeding. One could say that a new religion, a new cosmology, a new creation myth is being put in place, where biotechnology corporations like Monsanto replace Creation as ‘creators’. GMO means ‘God move over’. Stewart Brand has actually said ‘We are as gods and we had better get used to it.’"

"In principle, there's now nothing to stop intelligent moral agents "fixing" the [conditionally-activated level of] subjective physical distress undergone by members of entire free-living species by choosing and propagating benign alleles of SCN9A or its homologs via gene drives, i.e. engineering via CRISPR-mediated gene-editing not a currently utopian "no pain" biosphere ... but a “low pain” biosphere."

"I know it's a long shot and people would say it's 'too absurd'… but I'm doing this with hopes of making a Mickey Mouse some day."

"Everyone is scared of genetic DIY. It's crucial for artists to work with such technologies. It is important that we work between science and art."

"I went to Monsasnto, and I spent a lot of time with the scientists there, and I have revised my outlook, and I'm very excited about telling the world. When you’re in love, you want to tell the world."

"Genetic engineering crosses a fundamental threshold in the human manipulation of the planet, changing the nature of life itself."

"There is an expression out there that a failed gene therapy makes a good vaccine."

"Genetic engineering is to traditional crossbreeding what the nuclear bomb was to the sword."

"But if the same tests, the same foods are examined by an independent scientist, then it turns out that in almost every case there are quite serious harms done to the rats, the mice or the other poor unfortunate animals, particularly internal organs like liver and kidneys and things of that sort."

"So you did do it. You amalgamated one of Godzilla's cells together with the plant's cells. Are you proud of this? What kind science do you call this?"

"It is difficult to make a general judgement about genetic modification (GM), whether vegetable or animal, medical or agricultural, since these vary greatly among themselves and call for specific considerations. The risks involved are not always due to the techniques used, but rather to their improper or excessive application. Genetic mutations, in fact, have often been, and continue to be, caused by nature itself. Nor are mutations caused by human intervention a modern phenomenon. The domestication of animals, the crossbreeding of species and other older and universally accepted practices can be mentioned as examples. We need but recall that scientific developments in GM cereals began with the observation of natural bacteria which spontaneously modified plant genomes. In nature, however, this process is slow and cannot be compared to the fast pace induced by contemporary technological advances, even when the latter build upon several centuries of scientific progress. Although no conclusive proof exists that GM cereals may be harmful to human beings, and in some regions their use has brought about economic growth which has helped to resolve problems, there remain a number of significant difficulties which should not be underestimated."

"Animals tell us something. If the animals have suffered this way [from GMOs], potentially for us, let’s listen to what they’re telling us. Let’s take heed."

"I stand by my assertions that although you can know what happens to any individual species that you modify, you cannot be certain what will happen to the ecosystem. Also, we have a strange situation where we have malnourished fat [[people]. It’s not that we need more food. It’s that we need to manage our food system better. So when corporations seek government funding for genetic modification of food sources, I stroke my chin."

"In a more general sense, all the quarter-million plant species— in fact, all species of organisms—are potential donors of genes that can be transferred by genetic engineering into crop species in order to improve their performance. With the insertion of the right snippets of DNA, new strains can be created that are variously cold-hardy, pest-proofed, perennial, fast-growing, highly nutritious, multipurpose, water-conservative, and more easily sowed and harvested. And compared with traditional breeding techniques, genetic engineering is all but instantaneous."

"Gene therapy, involving the use of viruses as a vector for introducing generic material into cells, has had some success in treating genetic disorders such as severe combined immunodeficiency, and treatments are being developed for a range of other currently incurable diseases such as cystic fibrosis, sickle cell anemia, and muscular dystrophy. Genes introduced in this manner are not transmitted to the next generation. Gene therapy targeting the reproductive cells—so-called “Germ line Gene Therapy”—at present carries an unquantifiable risk associated with interfering with other genes, hence near-term development and commercialization of this technology is unlikely."

"Can genetic engineers restore a rapid worldwide rise in grainland productivity? This prospect is not promising simply because plant breeders using traditional techniques have largely exploited the genetic potential for increasing the share of photosynthate that goes into seed. Once this is pushed close to its limit, the remaining options tend to be relatively small, clustering around efforts to raise the plant’s tolerance of various stresses, such as drought or soil salinity. One major option left to scientists is to increase the efficiency of the process of photosynthesis itself—something that has thus far remained beyond their reach."

"By using genetic engineering, biological researchers have already developed new weapons that are much more effective than their natural counterparts. Countless examples from the daily work of molecular biologists could be presented here, not least the introduction of antibiotic resistance into bacterial pathogens, which today is routine work in almost any microbiology laboratory. Indeed, many research projects in basic science show—sometimes unwillingly and unwittingly—how to overcome current scientific and technological limits in the military use of pathogenic agents. Furthermore, genetic engineering is not merely a theoretical possibility for future biowarfare: it has already been applied in past weapons programmes, particularly in the former Soviet Union. One example is the USSR's 'invisible anthrax', resulting from the introduction of an alien gene into Bacillus anthracis that altered its immunological properties (Pomerantsev et al., 1997). Existing vaccines proved to be ineffective against this new genetically engineered strain."

"Molecular biology and genetic engineering are still in their infancy, and more technical possibilities will arise in the years to come—for military abuse too (Fraser & Dando, 2001). More efficient classical biowarfare agents will probably have only a marginal role, even if the genetically engineered 'superbug' is still routinely featured in newspaper reports. More likely and more alarming are weapons for new types of conflicts and warfare scenarios, namely low-intensity warfare or secret operations, for economic warfare or for sabotage activities. To prevent the hostile exploitation of biology now and forever, a bundle of measures must be taken, from strengthening the Biological and Toxin Weapons Convention to building an awareness in the scientific community about the possibilities and dangers of abuse. Any kind of biotechnological or biomedical research, development or production must be performed in an internationally transparent and controlled manner. In cases in which military abuse seems to be imminent and likely, alternative ways to pursue the same research goal have to be developed. Furthermore, as we mentioned above with regard to the smallpox genome sequence, it might also be necessary to apply restrictions to certain research and/or publications."

"You can stop splitting the atom; you can stop visiting the moon; you can stop using aerosols; you may even decide not to kill entire populations by the use of a few bombs. But you cannot recall a new form of life."

"Transferring genes between utterly unrelated species takes us into the realms that belong to God, and to God alone."

"When scientists began creating adenoviral vectors in the 1980s, most worked with a particular kind of adenovirus called Ad5, which ubiquitously infects humans and causes the common cold. Researchers stripped Ad5 of the genes it needed to replicate and inserted those genes into genetically engineered cell lines. That ensured that the modified viruses could be grown only in these special cells in the lab. It also opened up space in the Ad5 genome for scientists to stitch in new genes of their choosing. Many scientists hoped to use Ad5 to deliver a human gene that could correct rare genetic mutations—an approach called gene therapy. Those efforts came to a grinding halt in 1999 when a teenage boy with a rare genetic liver disease died after receiving an injection of an Ad5-based gene therapy, which had been designed in James Wilson’s lab at the University of Pennsylvania. The large dose of 38 trillion viruses the patient was given sparked massive body-wide inflammation and sent his immune system into overdrive. After that, scientists mostly stopped using adenoviral vectors for gene therapy, in which the dose needs to be high to reach many cells of the body."

"Because we have to use numbers so much we tend to think of every process as if it must be like the numeral series, where every step, to all eternity, is the same kind of step as the one before. ... There are progressions in which the last step is sui generis—incommensurable with the others—and in which to go the whole way is to undo all the labour of your previous journey."

"According to the extent to which a spirit is sui generis, the limits of what is permitted—that is, beneficial to him—become more and more narrow."

"In the human race, also, the superior specimens, the happy cases of evolution, are the first to perish amid the fluctuations of chances. ... The short duration of beauty, of genius, of the Caesar, is sui generis: such things are not hereditary. The type is inherited, there is nothing extreme or particularly "happy" about a type. ... The higher type is an example of an incomparably greater degree of complexity—a greater sum of co-ordinated elements: but on this account disintegration becomes a thousand times more threatening. "Genius" is the sublimest machine in existence—hence it is the most fragile."