Nature and the Process of Science

Nature and the Process of Science How do models bridge the observable and unobservable worlds? Models are tools that make sense of phenomenon in a manner that provides more insights that what is currently known How do scientists build and test hypotheses about processes that can’t be seen directly or indirectly? Unknown system  Gather inferences and observations  Build a model that’s consistent with observations and inferences  Develop test able hypothesis and preform them  Repeat; revise model and continue the process What are some key characteristics of models? Build explanations for natural phenomena that cannot be directly observed Provide more insights into phenomena that what is currently known Link observable and unobservable worlds How do models of biological phenomena differ from the “real world”? Models are build to represent observations and inferences regarding real world phenomena; they’re used to understand unobservable aspects of the real world Models tests hypothesis  these models may or not be correct Pattern: Observable, documented once or many times, what occurs Observations, Facts, and Laws Law: repeated patterns; rules Process: Unobservable, how or why it happens Inferences and Theories (explanations of patterns) Theory: how or why the rules happen; explanations *** Theories Don’t Become Laws!!!!! Conceptual Models They help visualize things we cannot see; metaphors and analogies o Examples: “Organisms like a machine”, Evolutionary tree, “Cells are like rooms in a building” They’re not “physical things” Physical Models Physical representation of something; helps better test hypothesis about the function of certain biological structures o Example: wind tunnel Organismal Model: living physical model  laboratory animal; they have specific characteristics that resemble human disease Mathematical Models Quantitative representations of a system using numerical representations o Examples: computer simulations, equations, or chemical formulas Set of variables and equations that establish relationships o Great importance in physics where laws are represented by mathematical equations and concepts Association Study: collects data that’s already there (relationships) Establishes associations between variables  these relationships can be high/low, positive/negative o Correlations: how strongly related two variables are o Weakness: associations are not evidence of causation Comparison Study: compares 2+ conditions Individuals, populations, ect… are compared that differ in 1 or more pre-existing conditions  no random reassignment or controls o Examples: seedlings grown under 2 conditions – high vs. low light o Weakness: significant differences are not evidence of causation Thought Experiment: in our heads Using our minds to tests hypothesis, using only pre-existing knowledge o Example: what would an eusocial mammal be like if it were to exist o Related to conceptual models Natural Experiment: natural change Nature manipulates a system that was being studied before the event took place; the best nature experiments are ones that repeat themselves in space or time. o Example: forest fire, volcanic eruption, hurricane o Strength: realistic o Weakness: no control; difficult to be sure that the event actually took place Causation Experiment: “true experiment” – compares 2 conditions and has a control Has random assignment of subjects, treatment groups and control groups The goal is to demonstrate that manipulation of the independent variable has a causal influence on the dependent variable o Weakness: many patterns in biology can’t be studied this way. Genetics I: DNA to Phenotype Meiosis: Two cell divisions  produces 4 haploid cells Cells produced are different from starting cell and each other Pairing of homologous chromosomes and recombination Only occurs in stem cells that give rise to germline cells Mitosis: One cell division  produces 2 diploid cells Cells produced are copies of the starting cell and identical to each other Pairing of homologous chromosomes and recombination DOES NOT occur One occurs in somatic cells DNA: Made of molecules called nucleotides (1 DNA molecule = 2 nucleotide sequences) and is organized into chromosomes (makes up the genes of the chromosome) Chromosome: DNA that is tightly packed into thread like structures Chromatid: One of the 2 identical half’s of a replicated chromosome during meiosis or mitosis 1 DNA Molecule 2 DNA Molecules DNA  transcription  mRNA  translation  Protein 1 DNA Molecule DNA carry the genetic code required to make proteins in cells. The first step is to copy DNA onto a molecule called mRNA. Then the mRNA interacts with ribosomes to read the sequence bases to create codons. The codon codes for an amino acid where tRNA assembles the protein 1 amino acid at a time. Transcription: genetic info encoded in DNA is copied into mRNA in the nucleus Translation: genetic info that is encoded on the mRNA is used to assemble a protein (ribosome) Mutations in Non-coding Sequence: most have no effect, but some are deleterious. Mutation in a Coding Sequence: some can be advantageous; if they don’t change the amino acid sequence they’re silent mutations (mutation in the coding region but both code for the same amino acids) If they change the amino acid sequence they’re non-synonymous mutations (alters the amino acid sequence due to a frameshift mutation) that alter the structure and function of the protein Germline Mutation: (rare) mutation that arose in the gametes; every cell in the organisms carries that mutation  50% chance the mutation can be passed down to the offspring Somatic Mutation: (common) mutation arose in the somatic cells (during mitosis); errors in DNA replication during individual development and only some cells carry this mutation  not passed down to offspring Describe how the cells in the same organism can have the same DNA yet differentiate into different cell types and tissues. All cells in the body have the same DNA (except sex cells); cells in different tissues in the body transcribe different genes which in turn produces different proteins  gene regulatory sequences interact with regulatory proteins to turn genes on in some tissues and off in others. Genetics II: Inheritance Describe the relationship between DNA, nucleotides, genes and alleles. Genes are composed of nucleotides in a portion of the DNA strand. Alleles are alternate forms of a gene caused by different nucleotides. An allele can be represented by a genotype or by phenotype. o Most genes have different alleles that cause traits in a species  all individuals of the same species generally have the same genes but different alleles (traits) Describe misconceptions about Mendel’s Work. One gene codes for one trait  phenotypes are the result of more than 1 gene There are only two genetic variations (A or a)  there are many alleles of each gene Complete Dominance: an organism with alternate forms of a gene will express the dominate form: Incomplete Dominance: the heterozygote offspring has a phenotype that is intermediate between the 2 homozygote parents: Co-Dominance: the effects of both alleles can be seen in the heterozygote offspring: Independent Assortment: (chromosomes) describes how different genes independently separate from one another during meiosis. In this process, the orientation of each homologous chromosome creates different combinations of parental chromosomes in the gametes; in humans, there are 223 possible chromosome orientations. Law of Segregation: (alleles) phenotypic traits can be passed from generation to another generation through genes  alleles separate from each other in the formation of gametes; half of the gametes carry 1 allele and the other half carry the other allele. Recombination: occurs in meiosis during gamete formation and leads to new combinations of alleles in the resulting offspring *only occurs between chromosomes in a single triad* Evolution Natural Selection: process by which some individuals survive and reproduce more than others due to how well suited they are to the environment. Production: Recombination, independent assortment, and mutations  VARIATION Transmission: Mendel’s laws and genetics  HEREDITY Sorting: (Process) Differential survival  SELECTION Differential reproduction  CHANCE (Pattern) Change in distribution of genetic variation in a population Describe the aspects of natural selection in terms of randomness Random  mutations in DNA Non Random, inevitable, and unstoppable  the favoring of mutations that promote survival and reproduction and the elimination of variations that don’t. Fitness: Highest  lifetime reproductive success of an individual (survival and reproduction) Fitness Proxy: if fitness is difficult to measure then traits positively associated with reproductive success are used as fitness proxies  examples: survival, body size, egg count ect… Why is fitness meaningless outside the context of the environment in which the organism lives? Natural selection results in adaptations that lead to higher fitness in a specific environment. Adaptions that lead to a high fitness in one environment might not have the same fitness in another. Stabilizing Selection: variance decreases and mean stays the same Directional Selection: mean value of the character changes Disruptive Selection: variance increases and mean stays similar Natural Selection: process by which some individuals survive and reproduce more than others due to how well suited they are to the environment  you need variation in phenotype, inheritance and differential survival and reproduction based on phenotype??? Sexual Selection: results from differences in mating success among individuals in a population  can cause reduced survival Competition over mates and choice in mating partners  is a model to explain patterns of elaborate male characteristics and female preference to specific characters Genetic Drift: random variation in allele frequencies due to sampling error  stronger in small populations Bottleneck: pattern = low genetic variation in species; process = population decreases in size due to loss of genetic variation (large population  small) Founder: pattern = low genetic variation in remote populations of a species; process = new population is established by small number of individuals (small population  “founding another population”) Inbreeding: pattern = increased homozygosity Describe how genetic drift causes evolution in a population. The populations that occur after bottlenecks or the founder effect are different from previous generations due to loss of genetic variation  this is due to chance and not natural selection Neutral alleles: result from genetic drift of alleles that don’t effect fitness (doesn’t increase or decrease an individuals fitness) o May explain most genetic variation among individuals, species and populations. o Can become fixed (100% or 0%) in a population by chance Why is evolution both a pattern and a process? Differential survival and reproduction is a process that can be explained by natural selection and genetic drift. The pattern is the change in distribution of genetic variation in a population from 1 generation to the next Speciation: how one species evolves into two or more species Allopatric Speciation: geographic isolation reduces or stops gene flow between diverging populations  once gene flow is reduced natural selection and drift operates independently Sympatric Speciation: populations are within the same geographic range but may live in adjacent “microhabitats” (rare) **** Both result in different phenotypes and genotypes that may cause reproductive incompatibility Biological Species Concept: based on reproductive isolation; if two species cant interbreed then they are different species Reproductive Isolation: reduced gene flow in diverging species that live in distinct or overlapping geographic regions Pre-zygotic: temporal isolation, behavioral isolation and gamete incompatibility (post-mating) Post-zygotic: hybrid unviability, hybrid infertility/low fitness Adaptive Radiation: divergence of several species descended from a common ancestor into a variety of different adaptive forms Allopatric speciation Environment changes that makes new resources available, creates new challenges or opens new environmental niches Ecology Exponential Growth: r = b-d Based on birth and death rates; leads to high, low, zero or negative growth rates (n ≠ 0 ¿ Logistic Growth: k-n/k More realistic; incorporates k value (the environmental carrying capacity) As n approaches k the population growth slows down and eventually the population remains constant “R” (Growth) High intrinsic rate; rapid population growth, high reproductive output, low parental care, high dispersal ability, poor competitive ability with other species, unstable population size. Dominated by population growth rate “K” (Carrying Capacity) Slow population growth, low reproductive output, high parental care, low dispersal, good competitors, displace others, stable population size at carrying capacity Dominated by carrying capacity Competition: (-,-) both interacting species loose Mutualism: (+,+) both speicies benefit Commensalism: (+,0) one species benefits while the other one doesn’t Ammensalism: (-,0) one species loses, the other one is unaffected Antagonistic: (+,-) one species benefits while the other suffers Predation, herbivory and parasitism Ecological Niche: the role and position a species has in its environment  a total of a species abiotic (nonliving [climate]) and biotic (living[species interactions]) resources Fundamental Niche: defined by an organisms ability to live in a given abiotic environment o Biotic interactions can limit fundamental niche which can result in the partioning of resources Realized Niche: a subset of the fundamental niche; made only of biotic resources Niche Space: is the subset of resources or environmental conditions in which a species can live Competitive Exclusion Principal: species with similar niches cannot live together in the same place  this would result in the extinction of the species or evolution of a shift in phenotype Resource Partioning: the use of different resources to avoid competitors (fundamental niche)  species will develop different behaviors (such as feeding) in the presence of competition or develop different morphology (phenotypic plasticity) Short term; Takes advantage of pre-existing conditions Character Displacement: the evolution of morphological differences (natural selection of different phenotypes related to food; beak size) that resolves competition Long term; takes place over many generations Limited by standing genetic variation and new mutations Intraspecific: competition between individuals of the species Interference: one species directly affects the ability of the other to gain resources Exploitation: one species indirectly makes resources unavailable to the other (nocturnal vs. diurnal predators) Apparent: negative impact of one species on the population growth of another through a shared enemy