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Andrius Kulikauskas

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Gyvybė, Life, Biology Fresh Air

生物学

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.
  • Collect examples of ways of figuring things out in biology from related episodes of Fresh Air.

Sources


Main ideas

Natural and artificial. Biology is the inverse of physics. In physics we isolate and study a subsystem. In biology, we study nature, the living system. We make sure to include the living spirit from the system into our subsystem. We study that living spirit which is present in the natural but not in the artificial. Although ultimately there is no escaping the natural, it is all around us.

Pre-systemic

Biopsies

Post-systemic

Study within surroundings


Document an environment

Comprehensively document an environment

  • Bioblitz An intense period of biological surveying in an attempt to record all the living species within a designated area. Groups of scientists, naturalists and volunteers conduct an intensive field study over a continuous time period (e.g., usually 24 hours). There is a public component to many BioBlitzes, with the goal of getting the public interested in biodiversity. To encourage more public participation, these BioBlitzes are often held in urban parks or nature reserves close to cities.

Compare similar environments that are at different stages of development

  • Chronosequence A common assumption in establishing chronosequences is that no other variable besides age (such as various abiotic components and biotic components) has changed between sites of interest. Because this assumption cannot always be tested for environmental study sites, the use of chronosequences in field successional studies has recently been debated. Since many processes in forest ecology take a long time (decades or centuries) to develop, chronosequence methods are used to represent and study the time-dependent development of a forest. Field data from a forest chronosequence can be collected in a short period of several months. Chronosequences are often used to study the changes in plant communities during succession. A classic example of using chronosequences to study ecological succession is in the study of plant and microbial succession in recently deglaciated zones. For example, a study from 2005 used the distance from the nose of a glacier as a proxy for site age.

Modify an organism

Breeding

  • Breed back Selective breed domestic animals in an attempt to achieve an animal breed with a phenotype that resembles a wild type ancestor. The extinct wild type ancestors of a given species are known only through skeletons and, in some cases, historical descriptions. In order to test genetic closeness, DNA (both mitochondrial and nuclear) of the breeding animals must be compared against that of the extinct animal. Humans have selected animals only for superficial traits, and as a rule did not intentionally change less-observable traits, such as metabolic biochemistry. Natural selection might serve as an additional tool in creating "authentic" robustness, "authentic" behaviour, and perhaps, the original phenotype as well. In some cases, a sufficient predator population would be necessary to enable such a selection process; in today's Europe, where many breeding-back attempts take place, this predator population is largely absent.

How organisms affect environments (analysis)

Contrasting similar natural environments, determining stages in evolution, characterizing robustness

Comparing ecosystems

  • 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.

Monitoring ecosystems

  • Collecting data over decades allows the understanding of the progression of causes and effects of ecological changes. Data may include soil samples, surveying, photographing landscapes from airplanes, tagging salmon, as in the Arctic.

Introduce natural ingredient that transforms the whole

Transformative ingredient

  • 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.

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 specificity matching proved important in achieving success.

Reconstructing an environment

  • Pleistocene Park Sergey Zimov and Nikita Zimovn are attempting to re-create the northern subarctic steppe grassland ecosystem that flourished in the area during the last glacial period. They are reintroducing large herbivores and monitoring their effect on local fauna, studying the conversion of ecologically low-grade tundra biome to a productive grassland biome.

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."

Restrict the natural ingredient

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

Destroying candidate agents

Classify agents by responses

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."

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."

Analyze the natural ingredient

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.

Interrelated species

Interrelated population dynamics

  • Wolves and moose on Isle Royale Moose came to Isle Royale in the early 1900s, later followed by wolves. The populations have been studied since 1958. They are stressed because the moose overbrowse and the wolves are inbred. The populations fluctuate dramatically and have yet to settle down.

How environments affect organisms (algebra)

Center: Alter environment to make visible distinctions in organisms

Distinction

  • 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.

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.

Tagging animals

  • 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.

Balance: Noting the natural balance, the base state

  • Functional equilibrium, balanced growth hypothesis, optimal partitioning theory. Analysis of the relative proportion of plant biomass present in the various organs of a plant. Similarly, analysis of the biomass in a plant community. The balance may change depending on environmental conditions, thus reflecting them. See: Biomass allocation
  • C-budget.(Carbon-budget) A way to determine sugar allocation in a plant to its various organs. Measurements are made of uptake of carbon (dioxide) through photosynthesis, and the losses of carbon through roots and shoots by way of respiration. See: Biomass allocation
  • Growth allocation measure the increase in the total biomass of a plant and its various parts. See: Biomass allocation
  • Biomass allocation can involve a measurement of the total allocation of growth over the years, discounting yearly turnover in leaves and fine roots.

Set: Cataloguing the variety of natural solutions along with their norms and variations. (The norms and deviations within the norms and deviations.)

  • Statistical shape analysis An analysis of the geometrical properties of some given set of shapes by statistical methods. For instance, it could be used to quantify differences between male and female gorilla skull shapes, normal and pathological bone shapes, leaf outlines with and without herbivory by insects, etc. Important aspects of shape analysis are to obtain a measure of distance between shapes, to estimate mean shapes from (possibly random) samples, to estimate shape variability within samples, to perform clustering and to test for differences between shapes. One of the main methods used is principal component analysis (PCA).
  • Cataloguing a divergence of solutions.

List: Analyzing versions of an organism's structure to note how they are optimized for different natural environments

Observation and proposed explanation of deviations from norms

  • Observation of trade-offs with regard to environments. In the Arctic, trees reduce the risk of freezing by having risk-diffuse wood with narrower pores which, however, are less efficient for transporting water.
  • Observation of adaptations to extreme environments. In the snowy Arctic, large feet in proportion to body weight act like snowshoes; larger size reduces the ratio of surface area to body volume; layers of plumage, fat and fur retain body warmth; digestive adaptations to better digest woody plants with or without the aid of microbial organisms; animals hibernate or migrate.
  • Interspecific allometry Compare related species (for example, insects) to see how total body size is related to the size of various body parts.
  • Evolutionary allometry Over the course of the evolution of a species, consider how total body size is related to the size of various body parts.
  • Ontogenetic allometry In the growth of an organism, consider whether the growth is isometric or allometric, that is, consider whether the size of various body parts changes, proportionately, as total body size increases.
  • Allometry Given a species, consider the distribution of organisms in terms of body size, and see whether the size of various body parts changes.
  • Allometry Given differences in the relationship between total body size and the size of various parts, consider whether, how and why behavior changes.
  • Allometry Note deviations from isometry during growth as evidence of physiological factors forcing allometric growth.
  • Allometry Plot an animal's basal metabolic rate against their body mass, obtain a power-law dependence, Kleiber's law. Thus body mass can explain much of the variation in basal metabolic rate.
  • Phylogenetic comparative methods Infer the evolutionary history of some characteristic (phenotypic or genetic) across a phylogeny.
  • Phylogenetic comparative methods Infer the process of evolutionary branching itself (diversification rates).
  • Confirming the optimum, as with Lack's principle. The clutch size of birds is observed along with the number of birds that are then successfully fed and raised. The average is confirmed to be the optimum, in accordance with the expectations of natural selection. The point here is that the assumption of conservatism and optimality facilitates the analysis and identification of relevant characteristics.

Creating deviations from norms and studying the effects

  • Allometric engineering Alter a body part with respect to the entire body to see its effect on performance. For example: Cropping or extending bird tail lengths to affect success in mating. Removing an ovary in cockroaches to reduce number of progeny, increase resource allocation to each offspring.
  • Determining primary and secondary factors. A comparative study shows that in explaining basal metabolic rates of mammals, body mass is of first importance, taxonomy is of second importance, and environment is of subsequent importance. (See: Allometry)
  • Distinguish features which depend on the size of an animal or not. Muscle tissue is the same across animals but larger animals have a greater number of muscle fibers and lower intrinsic speed.
  • Analysis of diversity among similarity. Analysis of features that affect movement and gaits of different species, making use of the similarities. Application of these models to form realistic hypotheses for extinct species.
  • Assemble patterns of dimensions into behavioral invariants. Allometry Alexander found that animals of different sizes and masses traveling with the same Froude number consistently exhibit similar gait patterns. Dynamically similar gaits are those between which there are constant coefficients that can relate linear dimensions, time intervals, and forces. Animals of different sizes tend to move in dynamically similar fashion whenever the ratio of their speed allows it. Duty factors—percentages of a stride during which a foot maintains contact with the ground—remain relatively constant for different animals moving with the same Froude number. Body mass has even more of an effect than speed on limb dynamics. Leg stiffness, peak force experienced, various other factors are proportional to mass to a power.
  • Model how a common form is diversely applied. Allometry Living organisms of all shapes and sizes utilize spring mechanisms in their locomotive systems, probably in order to minimize the energy cost of locomotion. The allometric study of these systems has fostered a better understanding of why spring mechanisms are so common, how limb compliance varies with body size and speed, and how these mechanisms affect general limb kinematics and dynamics.
  • Scaling with regard to a power of body mass of physiological effects of drugs and other substances. Allometry

Appreciating the factors in an organism's reproductive strategy

Identifying critical points

  • Constructing a theory by interpreting and associating manifest genetically based functionality with the propensity to reproduce the genes.

How artificial changes affect natural environments

Model: Variously modify an environment and compare resulting differences

  • Biological Dynamics of Forest Fragments Project Some rainforests on the outskirts of Manaus, Brazil were inventorized and studied before and after fragmentation. The continuous rainforest was fragmented into 11 regions the size of 1 hectare, 10 hectares and 100 hectares. This was in response to the SLOSS (single large or several small) reserve size debate. Three main questions were: What effect does fragment size have on the rate of species extinction? Would the local extinction rate eventually slow and halt, equalizing the number of species? How do species interactions and demography change as a result of reduced habitat? Edge effects, extinction rates, biotic and abiotic interactions, mortality factors and soil quality were studied over a 25 year period that started before the deforestation. Factors surveyed at edges include temperature, vapor pressure deficit (VPD), and soil moisture. Mark-recapture programs for birds reveal changes in species composition and activity level.

Alter nonliving parameter in living environment

  • 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.

Isolating from natural environment

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.[6] These ADME process parameters can then be integrated into so called "physiologically based pharmacokinetic models" or PBPK."

Moving from in vivo to in vitro

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.

Maintaining artificial environments

Examining the capabilities for self-sustainability of a closed system or controlled system

  • Controlled (or closed) ecological life-support systems (acronym CELSS) are a self-supporting life support system for space stations and colonies typically through controlled closed ecological systems, such as the BioHome, BIOS-3, Biosphere 2, Mars Desert Research Station, and Yuegong-1. These are life support systems for humans. The system includes air revitilization, food production, waste-water treatemnt.
  • 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.
  • BioHome was used for a variety of experiments. BioHome focused on alternative, non-chemical sewage treatment methods utilizing non-edible plants of aquatic disposition. The aquatic and semi-aquatic plants were chosen based on their previously known abilities for waste treatment. Another usage for the plants used in the wastewater treatment included its implementation as compost, which was feasible as the plants grew as more sewage was introduced. The processed water is subsequently used as toilet and plant water. Plants, or more accurately, the root systems of aquatic plants found to have a filtering effect include bulrush, reed, soft rush and water iris. Water suitable for human use was extracted from the condensate from three sources: dehumidifier units, air conditioning, and plant leaves. In fact, plant leaves proved to be a major, consistently reliable source of water vapors. The condensate was run through ultraviolet equipment to ensure its safety. The plants established and maintained indoor air quality.
  • Life support system The combination of equipment that allows survival in an environment or situation that would not support that life in its absence. It is generally applied to systems supporting human life in situations where the outside environment is hostile, like in space or underwater, or medical situations where the health of the person is compromised to the extent that the risk of death would be high without the function of the equipment.

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.

Need to sort

Search for determining factors

  • Allometry Factors that affect body mass include the type of physiological design (such as open or closed circulatory system), mechanical design (endoskeleton or exoskeleton), habitat (available land area, water vs. land)

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