Discovery in Biology
- Sustatyti biologijos žinojimo rūmus ir jų pagrindu apibrėžti gyvybę.
- Kuria prasme biologijoje yra įvairūs lygmenys, pavyzdžiui, organizmas, organai, audiniai, ląstelės. Organizmui augant ląstelės neauga didesnės, o daugėja.
- Can one type change into another type? And how?
- Two ingredients in combination yield a result that neither would by itself.
- Griffith's experiment Injecting mice with a combination of a nonvirulent strain and the remains of a heat-destroyed virulent strain killed the mice and yielded both the nonvirulent strain and the virulent strain. Thus the dead strain yet had a "transforming principle" that transformed the nonvirulent strain.
- Quellung reaction (Serological typing) Make distinctions in strains of bacteria visible. Antibodies bind to a bacterial capsule and make it opaque and visible under a microscope.
Classification by biologically evoked response
- Avery–MacLeod–McCarty experiment: Background "Pneumococcus is characterized by smooth colonies which have a polysaccharide capsule that induces antibody formation; the different types are classified according to their immunological specificity."
Growing a biological responder
- Avery–MacLeod–McCarty experiment: Background "With the development of serological typing, medical researchers were able to sort bacteria into different strains, or types. When a person or test animal (e.g., a mouse) is inoculated with a particular type, an immune response ensues, generating antibodies that react specifically with antigens on the bacteria. Blood serum containing the antibodies can then be extracted and applied to cultured bacteria. The antibodies will react with other bacteria of the same type as the original inoculation."
Algebra of distinctions
- Counterstain We make every cell distinguishable (with the counterstain) and then distinguish certain cells (which retain the primary stain).
- Gram stain Classify bacteria into two groups as to whether they have a thick layer of peptidoglycan in the cell wall that retains the primary stain, or whether they have a thinner wall for which the primary stain can be washed out, leaving only the counterstain which stains everything. Note here the use of the washing out.
Sequence of extractions
- Avery–MacLeod–McCarty experiment "The purification procedure Avery undertook consisted of first killing the bacteria with heat and extracting the saline-soluble components. Next, the protein was precipitated out using chloroform and the polysaccharide capsules were hydrolyzed with an enzyme. An immunological precipitation caused by type-specific antibodies was used to verify the complete destruction of the capsules. Then, the active portion was precipitated out by alcohol fractionation, resulting in fibrous strands that could be removed with a stirring rod."
Extracting a suspected agent
- Avery–MacLeod–McCarty experiment "The purification procedure Avery undertook consisted of first killing the bacteria with heat and extracting the saline-soluble components."
- Avery–MacLeod–McCarty experiment Then, the active portion was precipitated out by alcohol fractionation, resulting in fibrous strands that could be removed with a stirring rod.
Destroying candidate agents
Use causality to verify the presence or absence of a substance
- Avery–MacLeod–McCarty experiment "An immunological precipitation caused by type-specific antibodies was used to verify the complete destruction of the capsules."
- Avery–MacLeod–McCarty experiment Is the substance destroyed or not by the testing agents? "To show that it was DNA rather than some small amount of RNA, protein, or some other cell component that was responsible for transformation, Avery and his colleagues used a number of biochemical tests. They found that trypsin, chymotrypsin and ribonuclease (enzymes that break apart proteins or RNA) did not affect it, but an enzyme preparation of "deoxyribonucleodepolymerase" (a crude preparation, obtainable from a number of animal sources, that could break down DNA) destroyed the extract's transforming power."
Identify by consistent proportions of parts
- Avery–MacLeod–McCarty experiment Chemical analysis showed that the proportions of carbon, hydrogen, nitrogen, and phosphorus in this active portion were consistent with the chemical composition of DNA.
Isolate from surroundings
- In vitro "In glass". Study in glassware.
- "Examples of in vitro studies include: the isolation, growth and identification of cells derived from multicellular organisms (in cell or tissue culture); subcellular components (e.g. mitochondria or ribosomes); cellular or subcellular extracts (e.g. wheat germ or reticulocyte extracts); purified molecules (such as proteins, DNA, or RNA); and the commercial production of antibiotics and other pharmaceutical products."
- "Viruses, which only replicate in living cells, are studied in the laboratory in cell or tissue culture, and many animal virologists refer to such work as being in vitro to distinguish it from in vivo work in whole animals."
- "Polymerase chain reaction is a method for selective replication of specific DNA and RNA sequences in the test tube."
- "Protein purification involves the isolation of a specific protein of interest from a complex mixture of proteins, often obtained from homogenized cells or tissues."
- "In vitro fertilization is used to allow spermatozoa to fertilize eggs in a culture dish before implanting the resulting embryo or embryos into the uterus of the prospective mother."
- "In vitro diagnostics refers to a wide range of medical and veterinary laboratory tests that are used to diagnose diseases and monitor the clinical status of patients using samples of blood, cells, or other tissues obtained from a patient."
- "In vitro testing has been used to characterize specific adsorption, distribution, metabolism, and excretion processes of drugs or general chemicals inside a living organism; for example, Caco-2 cell experiments can be performed to estimate the absorption of compounds through the lining of the gastrointestinal tract; The partitioning of the compounds between organs can be determined to study distribution mechanisms; Suspension or plated cultures of primary hepatocytes or hepatocyte-like cell lines (HepG2, HepaRG) can be used to study and quantify metabolism of chemicals. These ADME process parameters can then be integrated into so called "physiologically based pharmacokinetic models" or PBPK."
Study within surroundings
Moving from in vivo to in vitro
- Tagging of Pacific Predators The tagging of 22 marine species belonging to 2,000 animals. Tags may be surgically implanted and archive various parameters. Tags may be removed later. Or tags may self-release and transmits data to a satellite. Air-breathing marine animals may carry an antenna. Tags can record information on pressure, light, internal and external body temperature, speed of travel. Tags provide information on migration routes and ecosystems.
Extinction and nonextinction in contrived environment
- Huffaker's mite experiment Contrived world with one species of prey mites and one species of predatory mites. Variation of potential for dispersion in a contrived environment leads to a variation of population dynamics for predator and prey. An optimal environment yields oscillations in populations and a nonoptimal environment yields extinctions.
- Free-air concentration enrichment Releasing CO2 in a natural competitive environment, thus maintaining high levels of CO2, and then measuring percentage increased growth compared to control group.
- Chronosequence Comparing similar ecological sites that represent different ages in a process of change such as in ecological succession, for example, after fires. As a glacier retreats, the distance from the nose of the glacier can be used as a proxy for age.
Examining the capabilities for self-sustainability of a closed system
- Bioregenerative life support system
- Yuegong-1 is a Chinese research facility for developing a moonbase that recycled oxygen, water, food, waste, etc. Yellow mealworms were grown for protein but were met with resistance by Western astronauts.
- Ecosphere Freshwater closed systems are often attempted by nature hobbyists and as experimental projects or demonstrations for biology classes. These require nothing more than a large glass jar with an airtight lid, a few cups of lake or river water, and mud or other substrate from the same body of water. Kept indoors at room temperatures, with exposure to sunlight from a window, such systems have been found to contain living organisms even after several decades. The original level of diversity always falls drastically, sometimes exhibiting interesting patterns of population flux and extinction. Multicellular organisms fare poorly. Eventually an equilibrium of micro-organisms is established.
Simulation of an environment
- Daisyworld A computer simulation of a hypothetical world which mimics elements of the Earth-Sun system to show the plausibility of the Gaia hypothesis. Daisyworld has two varieties of daisies, one which reflects light and one which absorbs light. The combination maintains an almost constant temperature despite changes in the power of the sun's rays.
Selected introduction of species
- Australian Dung Beetle Project Dung accumulated upon introduction of cattle. Various species of dung beetles were therefore selected and introduced in Australia, studying their effects on soil quality, fly control, worm control. Also, researchers in South Africa, where there are hundreds of species of dung beetle, worked to identify species that would match 8 selection criteria. Beetle collection surveys were undertaken to understand the environmental conditions preferred by different species. Habitat specifity matching proved important in achieving success.
Need to sort