Module 1 notes .docx

Cog 1.4 How we know earth is warming? I earth really warming. - **Climate changes:** - Belief in climate change has more to do with politics than with science. - The data shows that temperature have become, on average, increasingly warmer during the last century. Why, then, do many...

Cog 1.4 How we know earth is warming? I earth really warming. - **Climate changes:** - Belief in climate change has more to do with politics than with science. - The data shows that temperature have become, on average, increasingly warmer during the last century. Why, then, do many people fail to recognize what they should feel with their own skin? The problem has to do with the day-to-day changes in temperature that lead to stochasticity -- a word that means unpredictable variation. - To see the long-term pattern, we must examine temperature measured over the years. But how many years? Typically, scientists use the average temperature for a prior of several decades to gauge whether the current decade is unusually warm. The weather is cold, but climate could be warming -- A/B/C/D - Global warming and climate changes - Objectives - Distinguish among datum, a mean, and a deviation - Use standard deviation to infer how climates have changes - Normal temperature: average over many years. tell us what to expect at each time of the year without changing. - Temperature= datum - Normal temperature= mean (average) - Temperature anomaly= deviation - Mean anomaly= standard deviation - Key point: when something varies over space and time, one must compare sufficient samples to quantify effects accurately. - When calculating a normal temperature, one should include as many years as possible? False. To many years will not give you a god pictures since its to many data. - Climatologists use 30-year window to look at the normal temperature. Climate change 101 - Cause by small variation in earth orbits. Abrupt increase I earth temperature. - Cause by human activity that's what scientist think - Ocean surface acidification- because of global warming/climate changes - Causes sea level to rise. - A long-term overall temperature with permanent ramification Why humans are so bad at thinking about climate change - A lot of animals are extinct because of climate changes - Many Americans continue to think of climate change as distant problem: distant in time, that the impact won't be felt for a generation or more; and distant in space, that this is about polar bears or maybe some developing country. - CFCs destroy the ozone layer How the Greenhouse effect works - Is a special structure that is designs to regulate the temperature and humidity of the environment inside. - Greenhouse effect: not all the energy can escape. It gets trap or absorbed Global temperature patterns: Solar energy and seasonality - Distribution of biomes - General patterns: - Tilt of the earth is what causes the seasons throughout the year. 23.5-degree tilt of the earth. Where the direct rays land changes as it revolves around the sun. - In the equator the energy is directly concentrated in the equator The electromagnetic spectrum - The sun emits an enormous amount of electromagnetic radiation (solar energy). - Humans can see only a fraction of this energy, which is referred to as visible light - X-rays and UV rays are dangerous to living things. - So why are they so dangerous to living things? The answer lies in the relationship between wavelength and energy - Wavelength- the manner in which solar energy travels can be describes and measures as waves. Scientist can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points in a series of waves, such as from crest or trough to through. - Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. - Electromagnetic spectrum is the range of all possible wavelengths of radiation. Each wavelength corresponds to a different amount of energy carried - The longer the wavelength the less energy is carried - The short tight waves carry the most energy. The greenhouse effect-heating of the atmosphere - The composition of the atmosphere is also critically important. The earth receives electromagnetic energy from the sun in visible spectrum. There are also small amounts of infrared and uv radiation in this incoming solar energy. Most of the radiation is *shortwave* radiation, and it passes easily through the atmosphere towards the earth\'s surface, with some being reflected before reaching the surface. At the surface, some of the energy is absorbed, and this heats up the earth\'s surface. But the situation is a little more complex than this. - A large amount of the sun\'s energy is re-radiated from the surface back into the atmosphere as **infrared** radiation, which is invisible. As this radiation passes through the atmosphere, some of it is absorbed by **greenhouse gases** such as carbon dioxide, water vapor, and methane. These gases are very important because they re-emit the energy back towards the surface. By doing this, they help to warm the lower layers of the atmosphere even further. It is this \"re-emission\" of heat by greenhouse gases, combined with surface heating and other processes (e.g. conduction and convection) that maintain temperatures at exactly the right level to support life. Without the presence of greenhouse gases, most of the sun\'s energy would be lost and the Earth would be a lot colder than it is! Impact of Human Activity on Global Warming - Greenhouse gases: - Water vapors - Carbon dioxide: traps heat in the atmosphere and keep the earth warm - Nitrous oxide - Methane - CFCs - Carbon dioxide levels have been increasing for the past 100 years. Why is this happening and what is it doing to the earth? - We are the ones enhancing the levels of CO2 in greenhouse. It's not natural. - Photosynthesis (CO2) Role of greenhouse - Human activities have greatly increased their concentration, and this has led to a lot of concern about the impact that this could have on global temperatures. This phenomenon is known as global warming. - Because the natural concentrations of these gases are low, even a small increase in their concentration as a result of human emissions could have a big effect on temperature. - Human gas emissions come from - Carbon dioxide (CO
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) Carbon dioxide enters the atmosphere through the burning of fossil fuels (oil, natural gas, and coal), solid waste, trees and wood products, and also as a result of other chemical reactions (e.g. the manufacture of cement). Carbon dioxide can also be removed from the atmosphere when it is absorbed by plants during photosynthesis. - Methane (CH
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) Methane is emitted when coal, natural gas, and oil are produced and transported. Methane emissions can also come from livestock and other agricultural practices and from the decay of organic waste. - Nitrous oxide (N
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O) Nitrous oxide is emitted by agriculture and industry, and when fossil fuels and solid waste are burned. - Fluorinated gases (e.g. hydrofluorocarbons, perfluorocarbons, and sulfur hexafluoride). These gases are all synthetic, in other words, they are man-made. They are emitted from a variety of industrial processes. Fluorinated gases are sometimes used in the place of other ozone-depleting substances (e.g. CFC\'s). These are very powerful greenhouse gases and are sometimes referred to as High Global Warming Potential gases (\"High GWP gases\"). Climate change and weather - Scientists use the term global climate change to describe the change in the weather on Earth, including a worldwide rise in temperature. This change became increasingly noticeable during the last 60 years. - Climate refers to the long-term, predictable atmospheric conditions in an area. The climate includes average temperature and annual precipitation. Climate does not address the unusually warm day in winter or the amount of rain that fell on Tuesday. Those events we call the weather. - Specifically, weather refers to conditions of the atmosphere during a short period of time. Weather forecasts are usually focused on a few days. Ten-day forecasts exist but are seldom reliable. However, average conditions over long periods are easier to predict. Think of climate as the average weather over a long period. Evidence of Global Climate - Climates change prompts two types of questions: - Which aspects of climate have changed (and by how much)? The answer might include radiation, temperature, humidity, precipitation, - What factor caused the observed changes? The answer to this could include human activities or other processes. - Scientists cannot go back in time, but they can estimate past climates from indirect evidence, such as gases trapped in ice cores. By drilling deep into the Antarctic ice, scientists can get an idea of what the atmospheric conditions were like in the ancient past. The deeper the sample, the earlier the time period. Bubbles of air inside the ice reveal the composition and temperature of the atmosphere when the ice formed. - Analyses of ice cores tell us that CO2 concentration and air temperature have cycled periodically during the past 400,000 years (see figure below). Before the late 1800s, Earth had been as much as 9°C cooler and about 3°C warmer at some times. Increases and decreases in temperature were associated with increases and decreases in CO2 concentration. - The Industrial Revolution, which began around 1750, greatly increased the production of CO2 by humans. Prior to this time, the atmosphere has always contained fewer than 300 ppm of CO2. Advances in agriculture increased the food supply, which improved the standard of living for people. New technologies provided cheaper goods and services powered by fossil fuels, especially coal. Burning fossil fuel releases carbon dioxide, which accounts for the unprecedented rise in CO2 concentration during the 1900s. Based on the historical record from ice cores (and other sources of evidence), scientists believe the recent increase in atmospheric CO2 accounts for the recent increase in average temperature. Climate change and recent global natural events - Glacier National Park in Montana is undergoing the retreat of many of its glaciers, a phenomenon known as glacier recession. In 1850, the area contained approximately 150 glaciers. By 2010, however, the park contained only about 24 glaciers greater than 25 acres in size. One of these glaciers is the Grinnell Glacier at Mount Gould. - Between 1966 and 2005, the size of Grinnell Glacier shrank by 40 percent. Similarly, the mass of the ice sheets in Greenland and the Antarctic is decreasing Greenland lost 150--250 km of ice per year between 2002 and 2006. In addition, the size and thickness of the Arctic Sea ice are decreasing. - This loss of ice is leading to increases in the global sea level. On average, the sea is rising at a rate of 1.8 mm per year. However, between 1993 and 2010, the rate of sea-level increase ranged between 2.9 and 3.4 mm per year. A variety of factors affect the volume of water in the ocean, including the temperature of the water (the density of water is related to its temperature), and the amount of water found in rivers, lakes, glaciers, polar ice caps, and sea ice. As glaciers and polar ice caps melt, there is a significant contribution of liquid water that was previously frozen. - In addition to some abiotic conditions changing in response to climate change, many organisms are also being affected by the changes in temperature. Temperature and precipitation play key roles in determining the geographic distribution and phenology of plants and animals. (Phenology is the study of the effects of climatic conditions on the timing of periodic lifecycle events, such as flowering in plants or migration in birds.) Researchers have shown that 385 plant species in Great Britain are flowering 4.5 days sooner than was recorded earlier during the previous 40 years. - In addition, insect-pollinated species were more likely to flower earlier than wind-pollinated species. The impact of changes in the flowering date would be mitigated if the insect pollinators emerged earlier. This mismatched timing of plants and pollinators could result in injurious ecosystem effects because, for continued survival, insect-pollinated plants must flower when their pollinators are present. Cog 1.5 How Darwin Almost went Extinct Blending inheritance - Evolution by natural selection occurs because organisms with unique phenotypes pass these phenotypes to their offspring. Thus, Darwin's model of evolution by natural selection requires some process of inheritance. If for any reason, parents could not pass their unique phenotypes to offspring, a population cannot evolve. - When Darwin lived, biologists had a very different idea about how offspring inherited their phenotypes than the modern theory of inheritance. They believed that phenotypes of the parents blended to produce the phenotypes of the offspring. For instance, a tall man and a short woman would produce offspring of intermediate height. Similarly, a dark-skinned man and a light-skinned woman would produce offspring with intermediate skin color. Because phenotypes blended during reproduction, this process was called blending inheritance. - Blending inheritance created a major problem for Darwin's model of evolution by natural selection. If phenotypes blended in each generation, no variation among individuals would be left after a few generations. If you cannot understand why, imagine a bowl filled with white paint and black paint. The longer you stir the contents of the bowl, the less variation in color will remain. Eventually, the streaks of black and white paint will combine to form gray paint. In a similar way, phenotypes of organisms would become homogeneous over many generations. - As odd as blending inheritance sounds, the idea was reasonable in Darwin's day. Many traits, including body height and skin color, appear to blend in offspring. Because Darwin conducted many breeding experiments, he recognized the concept of blending inheritance and the observations that supported it. Skeptics of Darwin's model continued to develop **alternative models** of evolution that could explain the appearance of new species by **mutation**, despite blending inheritance within species. - By the end of the 19th century, Darwin's model of evolution by natural selection had lost its popularity among biologists. The only way to regain popularity was to wait for evidence that genetic variation could persist over many generations. Doubting Darwin - Some scientists didn't believe him it didn't seem to follow the evidence. - Natural selection - Phenotypic selection- some phenotypes reproduce more than others. - Genetic response- these phenotypes are at least partially heritable - There has to be a difference in phenotypes. How organisms look, and that has to relate to how much they reproduce and then the other half, though, the other requirement is it has to be some heritability of that phenotype. So, you could have a difference in how phenotypes reproduce but if these phenotypes are not at least partially heritable, meaning some component of that difference can be passed on to the offspring, then there isn't going to be any change in the population over time. - Objectives - Predict the pattern of phenotypic variation with a model of blending inheritance - Explain why Darwin's theory of natural selection conflicted with blending inheritance. - Variations: a different or distinct form or version of something - Model of blending: Blending 2 parents like Barak Obama parents. - Model of blending: a theory that offspring have a blend, or mix, of the characteristics of their parents - Blending inheritance: a theory that states that offsprings inherit a characteristic as the average of their parents' values for that characteristic - Key point: Biologists were wary to embrace Darwin's theory because it seemed to conflict with evidence. - Hugo De Vries: talk about mutation. Think evolution was driven by mutation. Blending inheritance - Evolution by natural selection occurs because organisms with unique phenotypes pass these phenotypes to their offspring. Thus, Darwin's model of evolution by natural selection requires some process of inheritance. If for any reason, parents could not pass their unique phenotypes to offspring, a population cannot evolve. - When Darwin lived, biologists had a very different idea about how offspring inherited their phenotypes than the modern theory of inheritance. They believed that phenotypes of the parents blended to produce the phenotypes of the offspring. For instance, a tall man and a short woman would produce offspring of intermediate height. Similarly, a dark-skinned man and a light-skinned woman would produce offspring with intermediate skin color. Because phenotypes blended during reproduction, this process was called blending inheritance. - Blending inheritance created a major problem for Darwin's model of evolution by natural selection. If phenotypes blended in each generation, no variation among individuals would be left after a few generations. If you cannot understand why, imagine a bowl filled with white paint and black paint. The longer you stir the contents of the bowl, the less variation in color will remain. Eventually, the streaks of black and white paint will combine to form gray paint. In a similar way, phenotypes of organisms would become homogeneous over many generations. - As odd as blending inheritance sounds, the idea was reasonable in Darwin's day. Many traits, including body height and skin color, appear to blend in offspring. Because Darwin conducted many breeding experiments, he recognized the concept of blending inheritance and the observations that supported it. Skeptics of Darwin's model continued to develop alternative models of evolution that could explain the appearance of new species by mutation, despite blending inheritance within species. - By the end of the 19th century, Darwin's model of evolution by natural selection had lost its popularity among biologists. The only way to regain popularity was to wait for evidence that genetic variation could persist over many generations.\\ Lamarckian inheritance - Jean Baptist Lamar had a theory that an animal could pass on to its offspring traits it acquires through its lifetime, but Lamarckian evolution was either ignored or ridiculed for its violation of basic heredity principle. - Modern principles state that traits are passed on through molecules of heredity, out DNA things you learn during your lifetime do not get written in your DNA and do not get passed on to your offspring, but Lamar believed information gained in one's lifetime could be transmitted biologically to the next generation. - A common example given is the giraffe's neck Lamar figured as they were reaching for taller branches their neck stretched then when they had babies the babies were somehow owed with this longer neck. - It's true giraffe necks have evolved that way but acquired information can be passed to the next generation the information isn't encoded in DNA but rather in molecules that are involved in decoding the DNA message epigenetics as it's called looks at how DNA is acted on by other molecules and these molecules can differently depending on the experience of an individual. Cog 2.1 How the Church Saved Darwin's theory Mendel's Peas-A/B - How do offspring inherit phenotypes? - Objective - Predict phenotypes using a mendelian model of inheritance - Explain how Mendelian inheritance preserves genetic variation - Mendel - Mathematically savvy - Mendel study peas - Discrete differences between traits. That's what he was studying. - True or false: According to the theory of blending inheritance, a mating between a plant that produces round peas and a plant that produces wrinkled peas would result in offspring that produce slightly wrinkled peas. The answer is - Mendel cross one round pea and one wrinkled pea and he got an offspring of round peas (the second generation of parents) - He breeds F1 with F1 and he finds that he gets 3 to 1 ratio. So, 2 round and 1 wrinkled, F2 generation. - Key point: Genetic variation depends on particles that segregate but do not blend during reproduction. Mendel's Model A/B - He came up with actual mathematic when you make this cross. He came up with little letter and big letter. - True or false: if some plants with round peas were heterozygotes, then these plants should produce offspring with wrinkled peas when mated to plants with wrinkled peas. The answer is True. - Discrete traits: a phenotype that manifests as clear and separable differences in a population. Why some Alleles are dominant- A/B - Objectives - Predict whether an allele will be dominant or recessive, given information about the protein for which it codes. - What determines which one is dominant or recessive - It relates to a concept called enzymes. The enzyme will break down for dominant and for recessive will not break down (protein that doesn't function properly) - Pheide oxygenase (PAD) enzyme - True or False? If a heterozygote (Aa) makes enough enzymes to catalyze as many reactions as a homozygote (AA) can, these genotypes would have the same phenotype. The answer is True. - Key point: dominance results from biochemical processes involving enzymes associated with the gene. - True or False? If a heterozygote (Aa) makes some enzymes, but not enough to catalyze as many reactions as a homozygote (AA) can, all genotypes would have the same phenotype (AA = Aa = aa). The answer is False - Incomplete dominance: genetic phenomenon in which the distinct gene product forms the two codominant alleles in a heterozygote blend to form a phenotype intermediate between those of the two homozygotes. - Codominance: a genetic phenomenon that occurs when two different versions of a gene, or alleles, are expressed simultaneously in an organism, resulting in a combination of both traits. Mendel's experiment: inherited traits - Heredity - What genetic principles best explain the passing on of traits from parents to offspring? - H1: one explanation is a blending hypothesis- the idea that genetic material contributed by two parents mixes in a manner like mixing blue and yellow paints to blend and make green. - H2: and alternative explanation is the particulate hypothesis of inheritance: the gene idea- parents pass on discrete heritable units, genes. - Genes: provide the instruction of all human traits, including physical features and how body parts function. Unit of heritable information on chromosome and consisting of a sequence of DNA - Each person inherits a particular mix of maternal and paternal genes - Character: a heritable feature, such as flower color - trait: a variant of a character such as purple or white purple - Each trait carries two copies of a gene, one inherited from the mother and the other the father Mendel's Crosses- Studying inheritance - Mendel's seminal experiments focused on pea plants to study inheritance. This species naturally self-fertilizes, meaning that pollen released by a flower will fertilize ova within the same flower. The flower petals remain sealed throughout pollination to prevent reproduction with other plants. Therefore, these plants always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected phenotypes. - Mendel disrupted the normal process of self-fertilization, by manually transferring pollen from one plant to the flowers of another plant. In this way, he hybridized plants with different phenotypes. - Plants used in first-generation crosses were called the P generation, which stands for parental generation. Mendel collected the seeds produced by these plants and allowed them to grow and develop in the following season. These offspring were called the F1 generation, which stands for a first filial generation (filial means daughter or son). - Once Mendel examined the plants in the F1 generation, he allowed them to self-fertilize naturally. The resulting seeds became the F2 generation, or second filial generation. Mendel's experiments extended to more generations, but the results of the first few generations intrigued him the most. These results inspired his model of inheritance. Genomic DNA - Prokaryotes - In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is called a nucleoid. - Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth. - Eukaryotes - In eukaryotes, the genome comprises several double-stranded, linear DNA molecules bound with proteins to form complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells. - Human body cells (somatic cells) have 46 chromosomes. However, it may be better to think of these as 23 pairs of chromosomes, one of each pair from your mother and one from your father. - In fact, it may be better to think of your genome as having 22 pairs of chromosomes plus one further pair, the X and Y sex chromosomes as these are, in many ways, different from the other 22. - The matched pairs of chromosomes your cells possess are called homologous chromosomes, which means that both chromosomes in a pair have the same genes. The position of a gene along a chromosome is called a locus (plural is loci). - Haploid vs Diploid - In humans, each cell of the body contains pairs of homologous chromosomes. To designate that each cell has two copies of each chromosome, we refer to the cells as being diploid or 2n. In humans, the number of unique chromosomes is 23, but the diploid number is twice that, or 2n = 46. - Cells that only contain only one copy of each chromosome are called haploid. For example, gametes such as sperm and eggs must fuse during sexual reproduction to produce a new, diploid organism. Prior to fusing each gamete has the haploid number of chromosomes, or n = 23. Meiosis - Undergo two round of cell division. The net results are that one diploid cell (2N) becomes four haploid cells (1N) - Stages in meiosis - To achieve the reduction in chromosome number, meiosis consists of: - one round of chromosome duplication - two rounds of nuclear division - The two rounds of division, are designated with a "I" or "II" where: - Meiosis I is the first round -- it reduces the number of chromosomes sets from two to one - Meiosis II is the second round which takes place in a way that is similar to mitosis - Crossing over/recombination - Meiosis is also crucial in creating variation in the population by generating new combinations of genetic material that differ from the combinations found in either parent. - Early in Meiosis I, the nuclear envelope begins to break down and the proteins associated with homologous chromosomes bring the pair close to each other. The tight pairing of the homologous chromosomes is called synapsis. - In synapsis, the genes on the chromatids of the homologous chromosomes are precisely aligned with each other. Then, an exchange of chromosome segments between non-sister homologous chromatids occurs. This is called crossing over or recombination. - In short, the paternal and maternal chromosomes exchange genes. - Now, when that sister chromatid is moved into a gamete during Meiosis II, it will carry some DNA from one parent of the individual and some DNA from the other parent. - So, each gamete has a combination of maternal and paternal genes that did not exist before the crossover. Basic of heredity- Dominant and recessive traits Garden pea characteristics revealed the basis of heredity - In his 1865 publication, Mendel reported the results of his breeding experiments with pea plants. These experiments focused on seven traits, defined genetically determined characteristics. Each trait could take on one or two phenotypes, which is a fancy word for how the trait looks. For example, a trait that Mendel called seed shape could have a round phenotype or a wrinkled phenotype. The figure below depicts the seven traits and their phenotypes. What determines the phenotypes? - To understand what Mendel discovered, let\'s consider the experiment in which he recorded flower color, which was scored as purple or white. Mendel bred plants to generate many offspring and grand offspring, which he called the F1 and F2 generations, respectively. In total, he generated thousands of plants in each generation. - Mendel controlled the phenotypes of the parents by applying pollen from a plant with purple flowers to fertilize a plant with white flowers. After allowing the offspring to grow, he found that all of them (100%) were had purple flowers. Thus, the phenotype of plants in the F1 generation resembled the phenotype of one parent. - Mendel\'s observation refuted a model of blending inheritance, suggesting that a more complex model was needed. If phenotypes of parents blended, the offspring should have produced flowers with an intermediate color, such as pale violet. Instead, the white phenotype completely disappeared in the F1 generation. - Importantly, Mendel did not stop there. Next, he allowed plants in the F1 generation to self-fertilize, in other words, pollen from each flower fertilized ova inside the same flower. This process resulted in an F2 generation, in which each offspring received all of its genetic material from a single parent. When the plants in this F2 generation matured, Mendel observed a surprising pattern: 705 plants had purple flowers and 224 had white flowers. The ratio was 3.15 violet flowers to 1 white flower, or approximately 3:1. - Based on this result, and similar results for the other six traits, Mendel categorized the phenotypes according to which was expressed, and which suppressed in the F1 generation. He named these categories dominant and recessive, respectively: - Dominant phenotypes pass to offspring unchanged (e.g., purple flowers). - Recessive phenotypes disappear when one of the parents has the dominant phenotype (e.g., white flowers). - But don\'t forget: the white phenotype reappeared in the F2 generation, meaning that the capacity to produce this recessive phenotype was still somewhere inside their parents with purple flowers. How inheritance works - Being an excellent student of mathematics, Mendel formulated a model that could explain the observed ratio of phenotypes. This model relied on the action of genetic factors that remained intact between generations, resulting in discrete phenotypes rather than blended phenotypes. Today, we refer to these genetic factors as alleles. - For example, consider the observations of flower color. If the F1 generation comprised plants with purple flowers, these plants must have carried allele purple flowers. However, these same plants must have also carried an allele for white flowers, because they produced some offspring with white flowers. Based on this reasoning, Mendel concluded, the F1 generation also had a genetic factor for making white flowers. He reasoned that allele for white flowers and alleles for purple flowers passed separately from parents to offspring, rather than blending together. - Mendel proposed that each plant possessed two alleles for each trait. Basically, he chose the minimum number of alleles that could produce two phenotypes. In his model, each parent contributed one of their two alleles to each offspring, such that offspring acquired a mixture of parental alleles without doubling their number of alleles. A dominant phenotype results when an offspring receives either one or two alleles for this phenotype. A recessive phenotype, however, resulted only when an offspring received two alleles for this phenotype. Genes and chromosomes - Mendel\'s insights were remarkable considering that biologists knew nothing about genes or meiosis at the time. Today, we know that the allele for white flowers and the allele for purple flowers are different forms of the same gene. We have two copies of each gene because we inherit one from each parent. In fact, we actually inherit chromosomes, but the same gene occurs on a chromosome from the father and a chromosome from the mother. During meiosis, these chromosomes separate into haploid gametes. - This separation, or segregation, of the homologous chromosomes, means also that only one of the copies of the gene moves into a gamete. The offspring form when that gamete unites with a gamete from another parent, giving the offspring two copies of each gene (diploid zygote). - Although Mendel\'s peas carried only two alleles, one for white flowers and one for purple flowers, a population of organisms can have many alleles for the same gene. We might imagine a pea plant that carries an allele for yellow flowers, which could be dominant or recessive to the alleles for white or purple flowers. Fortunately for Mendel, each of the phenotypes that he studied was determined by one gene with only two alleles. Mendel's experiments: phenotypes and genotypes - Opposing or alternative traits: two different traits - Phenotype: observable characteristics of an organism - Genotype: pair of alleles present in an individual - Homozygous: two alleles of trait are the same (YY or yy) - Heterozygous: two alleles of trait are different. (Yy) - Capitalized traits: dominant phenotypes (PP or Pp) - Lowercase traits: recessive phenotypes (pp) Phenotypes and Genotypes- Observed properties and genetic identity - Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. - An organism's underlying genetic makeup, consisting of both the physically visible and the non-expressed alleles, is called its genotype. - Difference between phenotype and genotype - Johan Gregor Mendel's hybridization experiments demonstrate the difference between phenotype and genotype. For example, the phenotypes that Mendel observed in his crosses between pea plants with differing traits are connected to the diploid genotypes of the plants in the P, F1, and F2 generations. - We will use a second trait that Mendel investigated, seed color, as an example. Seed color is governed by a single gene with two alleles: - the yellow-seed allele is dominant - the green-seed allele is recessive - When true-breeding plants were cross-fertilized, in which one parent had yellow seeds and one had green seeds, all of the F1 hybrid offspring had yellow seeds. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow seeds. - However, we know that the allele donated by the parent with green seeds was not simply lost because it reappeared in some of the F2 offspring. Therefore, the F1 plants must have been genotypically different from the parent with yellow seeds. - The P plants that Mendel used in his experiments were each homozygous for the trait he was studying. - Homozygous and homozygous - Diploid organisms that are homozygous for a gene have two identical alleles, one on each of their homologous chromosomes. The genotype is often written as YY or yy, for which each letter represents one of the two alleles in the genotype. The dominant allele is capitalized, and the recessive allele is lower case. The letter used for the gene (seed color in this case) is usually related to the dominant trait (yellow allele, in this case, or "Y"). - Phenotypes are physical expressions of traits that are transmitted by alleles. Capital letters represent dominant alleles and lowercase letters represent recessive alleles. The phenotypic ratios are the ratios of visible characteristics. The genotypic ratios are the ratios of gene combinations in the offspring, and these are not always distinguishable in the phenotypes. Pleiotropic: a biological phenomenon that occurs when a single gene or mutation affects multiple traits simultaneously Cog 2.2 How to predict Phenotypes Probability and outcome - A probability describes our certainty about an outcome or event. Because we never have enough knowledge to predict events with absolute certainty, we have to consider probabilities. - Let\'s consider the example of a coin landing on one side. Coin tosses are infamous for making decisions randomly, such which team will take offense or defense at the start of a football game. In reality, the outcome of a coin toss depends on the starting position of the coin, the speed, and angle of the toss, the direction of the wind, and the surface of the ground. If one knew all of these features, one could predict how the coin would land with 100% certainty. In practice, however, we say that a coin has a 50% chance of landing on a particular side. - In science, we use mathematical abbreviations to express probabilities. For example, P(A) means the probability of observing event A. These probabilities lie between zero and one. Consider how to interpret these probabilities: - P(A) = 0 \...\...\...\..... Event A never happens. - P(A) = 1 \...\...\...\..... Event A always happens. - P(A) = 0.5 \...\...\..... Event A is equally likely to happen or not. - A typical coin has a 50% probability of landing on one side, or P(A) = 0.5. - Of course, if you flip a coin once, you will get a particular side---heads or tails for an American coin. But what happens when you toss a coin 100 times or even 1000 times? - The more times you toss a coin, the closer the outcome should come to 50%. Toss a coin a hundred times and you will likely get one side 48% to 52% of the time. Toss a coin a thousand times and you will likely get an outcome between 49.5% and 50.5%. Toss it a million times and you will get 50.0%, plus or minus 0.01%! - For this reason, scientists prefer to use many observations when estimating the probability of an event. Two basic rules of probability - When calculating the probability of multiple events, we usually assume that events occur independently. For independent events, the knowledge that one event has occurred has no effect on the chance that the other event will occur. Therefore, one can simply add or multiply the probabilities of each event to determine a probability involving multiple events. Probability that multiple events will occur - Imagine two events, such as winning a lottery and getting struck by lightning. Each event seems unlikely, so both events happening to one person should be extremely rare. But how rare? - To answer this question, we have to calculate the probability that both events occur or joint probability. In other words, we want to know the probability of event B happening, given that event A already happened. - To calculate the joint probability, we must multiply the probability of event B by the probability of event A: - P(A and B) = P(A) · P(B). - Example 1 - The probability of winning a lottery is small. To simplify the problem, let\'s say it\'s a 1-in-a-million chance (10\^-6). The probability of getting struck by lightning is also small. We can say 1-in-a-million as well (10\^-6). Therefore, the joint probability becomes - P(A and B) = 10\^-6 · 10\^-6 = 10\^-12 - So, both events will happen only 1-in-a-trillion times. Pretty rare indeed! - Example 2 - A box contains 6 red balls and 4 black balls. Two balls are drawn, without returning the first ball in between draws. What is the probability that both of the balls are black? - Let A represent the event that the first ball is black, and B represents the event that the second ball is black. Given that the box contains 10 balls, 4 of which are black, the probability of P(A) = 4/10. - After drawing one black ball, only 9 balls remain in the box, 3 of which are black. Therefore, P(B) = 3/9. - By multiplying these probabilities, we find the joint probability of events A and B: - P(A and B) = (4/10) · (3/9) = 12/90 = 2/15 Probability that one of the multiple events will occur - Now, imagine two possible events, such as winning a lottery and getting struck by lightning. Both events seem unlikely, but how can we know whether one of these will happen? - We have to calculate the probability that either event occurs. - If a lottery win and a lightning strike are designated as events A and B, the probability of either event becomes: - P(A OR B) = P(A) + P(B) - P(A AND B). - Example - The probability of winning a lottery is small. To simplify the problem, let\'s say it\'s a 1-in-a-million chance. The probability of getting struck by lightning is also small. We can say 1-in-a-million as well. - So, what is the probability of a lottery win or a lightning strike? - Solution - Based on the addition rule, the probability of either event would be - Thus, the probability of either happening is approximately 2-in-a-million. Not very for sure! - In some cases, only one of the events can happen, or P(A and B) = 0. In those cases, the probability becomes P(A OR B) = P(A) + P(B) - So, if getting struck by lightning meant that you couldn\'t play the lottery, the probability of either event occurring becomes exactly 2-in-a-million. Independent events: Joint probability: The monohybrid cross and Punnett squares - Mendel hybridized plants with different phenotypes for a single trait (called a monohybrid cross). He made 7 monohybrid crosses, each involving a trait such as seed shape or flower color. - In each experiment, he got the following results: - the F1 offspring had the phenotype of one parent - the F1 offspring, when self-fertilized, produced offspring with a 3:1 ratio of phenotypes - On the basis of these results, Mendel postulated the following rules of inheritance - each parent in the monohybrid cross contributed one of two alleles to each offspring - every combination of alleles was equally likely. - The results of Mendel's research can be explained in terms of probabilities, which are mathematical measures of likelihood. - The probability of an event is calculated by the number of times the event occurs, divided by the total number of opportunities for the event to occur. A probability of one (100%) indicates that an event always occurs, whereas a probability of zero (0%) indicates that an event never occurs. A probability of 0.5 (50%) means an event has an equal chance of occurring or not occurring. Probability in Mendel's experiments - Consider the case of true-breeding pea plants with either yellow or green seeds. The dominant seed color is yellow; therefore, the parental genotypes with yellow seeds are YY and those with green seeds are yy. What is the probability that offspring will be one of these genotypes? - A British geneticist, Reginald Punnett, developed an easy way to visualize the probability of each genotype among offspring, which became known as a Punnett square. This diagram predicts all possible outcomes of all possible random fertilization, as well as their expected frequencies. - The figure below shows a Punnett square for a cross between a plant with yellow peas and one with green peas. All possible combinations of the parental alleles are determined to see the genotypes of the gametes. The top of the square lists the possible alleles contributed by one parent, while the side of the square lists the possible alleles contributed by the other parent. These alleles are combined in each box to determine the four possible genotypes. - Each box represents the diploid genotype of a zygote. Because each possibility is equally likely, genotypic ratios are determined by summing the genotype for all four boxes of the Punnett square. If one knows which allele is dominant, one can determine the phenotypic ratios as well. - For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible in the F1 offspring. All offspring are Yy and have yellow seeds. - When the F1 offspring are crossed with each other, each has an equal probability of contributing either a Y or a y to the F2 offspring, which results in - 25% probability of both parents contributing a Y, resulting in an offspring with a yellow phenotype - 25% probability of parent A contributing a Y and parent B a y, resulting in offspring with a yellow phenotype - 25% probability of parent A contributing a y and parent B a Y, also resulting in a yellow phenotype - 25% probability of both parents contributing a y, resulting in a green phenotype - When summing all possible outcomes, we find that 75% of offsprings (3/4) should have the yellow phenotype, while the remaining offspring (25% or ¼) should have the green phenotype. - This Punnett square explains why Mendel's observed a 3:1 ratio of phenotypes in the F2 generation. For a large number or crosses, Mendel was able to calculate probabilities, found that they fit the model of inheritance, and used the patterns infer a model of inheritance. What are the odds of that? -- A/B/C - Why do experiments? - Replicate observations-increase reliability - Control conditions- isolates effects of certain factors - Randomize subjects- decrease bias from uncontrolled factors - Sampling error- if we don't replicate our sampling enough - Objective - Calculate the probability of a set of observation given a model - P value= the probability of the observed, deviation or a greater deviation, when the model is correct. - Chi-square test statistic. - Degrees of freedom is the sum of phenotypes minus one. For example, if you have 2 phenotypes like albino and wild, that add up to 2 and you will subtract 1 and you will have 1 degree of freedom. - True o false: Given a P value less than 0.01, out model of genetic probably fails to explain the observed phenotypes. The answer is true. - Key point: a statistical test estimates the probability of obtaining a certain deviation from predictions based on sampling error. Cog 2.3 Most Traits Don't follow Mendel's Model Beyond Mendel's Simple Model of Inheritance - Mendel proposed a model of inheritance that worked for some traits, but many other traits failed to follow his model. - Many traits vary continuously, such as human height. For example, the height of a human female average is 165 cm but ranges from less than 60 cm to more than 200 cm. Although some women will have an average height, most women will be shorter or taller than the average. - If we consider only three women---the shortest woman, an average woman, and the tallest woman---we could force Mendel's model to fit the data. We might conclude that the average woman was a heterozygote for alleles possessed by the shortest woman and the tallest woman. But how can we explain all of the women who deviate from these three heights? - The simple answer is that we cannot use Mendel's model alone to explain variation in continuous traits, such as height. Mendel's model applies only to discrete traits, which have only two or three phenotypes (e.g., round or wrinkled peas; or red, pink, and white flowers). Unfortunately, the majority of traits vary continuously rather than discretely. As the proponents of blending, inheritance recognized, these continuous traits need a special explanation. - Fortunately, that explanation came within 20 years of rediscovering Mendel's model of inheritance. A statistician and biologist by the name of Ronald Fisher showed that Mendel's model could be extended to generate continuous variation. Fisher argued that many genes could influence a trait at once. The net effect of these genes depended on the alleles for each gene and the sum of their effects on the phenotype. Because many combinations of alleles were possible for the set of genes, many different heights could be produced. - Fisher's revised model of inheritance started the field of quantitative genetics, which focuses on continuous traits. Eventually, Fisher and others combined this new view of genetics with Darwin's model of natural selection. The resulting theory of evolution grew during a period known as the Modern Synthesis, which lasted from 1920-1940. - In Fisher's model of inheritance, the effects of alleles sum to yield a phenotype. Independent assortment leads to a greater chance of inheriting an intermediate phenotype than an extreme phenotype. The Punnett square on the left depicts the summed effects of alleles that contribute to large and small phenotypic values (A/B/C and a/b/c, respectively). The histogram on the right depicts the chance of inheriting each phenotype. How Mendelian trait Blend- A/B/C - Traits don't blend. Traits are the combination of genes - Objective - Explain how parental phenotypes blend despite being controlled by discrete particles (alleles) - Ronald Fisher- he took mendelian and Darwin theory and put them together. - Additive model of genetics- he came up with this - True or false: A genotype with many alleles that contribute to height will be taller than a genotype with many alleles that detract from height. The answer is true - Quantifying heritability. Mean trait value and the mean height of the offspring. - Heritability: % of phenotypic variation determined by the additive effects of alleles - True or False? A trait with a heritability of 25% can evolve more rapidly than a trait with a heritability of 50%. The answer is - Key point: effects of many alleles sum to cause continuous heritable variation - Modern Synthetism A screenshot of a cell division Description automatically generated Inheritance can be sexy- A - Objective - Apply the concepts of mendelian inheritance and dominance to predict phenotype controlled by a gene on a sex chromosome - True or false: If male carries a recessive allele for white eyes, he could have either white eyes or red eyes. The answer is False - Key point: when the female has recessive alleles and the male has a dominant allele, only female offspring will have the dominant phenotype. - True or false: A mutation on a sex chromosome is more likely to create a novel phenotype in a male than in a female. The answer is true Some Traits depend on the sex of an organism - For many species, including humans, the sex of an individual depends on the presence of special chromosomes, called sex chromosomes. - These chromosomes look different than autosomal chromosomes (or autosomes), which have no influence on sex. Although sex chromosomes also come in a pair, the two sex chromosomes differ in length and in genes. Autosomes, by contrast, are the same length and contain the same genes. - Take a human, for example, which has 22 pairs of autosomal chromosomes and 1 pair of sex chromosomes. One possible sex chromosome, called the X chromosome, resembles a typical chromosome in length. The other, called the Y chromosome, has a shorter length and contains fewer genes. - The genes on the sex chromosomes determine the sex of an individual. A human with two X chromosomes develops as a female, whereas a human with one X chromosome and one Y chromosome develops as a male. Because of a man and woman mate, offspring can never have more than one Y chromosome. Thus, the genetic information needed to build a male phenotype must occur on the Y chromosome. - When a gene on a sex chromosome determines the phenotype, we refer to the trait as sex-linked. We must modify Mendel\'s model to predict the inheritance of a sex-linked trait. A model of sex-linked inheritance - Thomas Hunt Morgan was the first biologist to describe a sex-linked trait. He noticed that the eye color of a fruit fly (Drosophila melanogaster) depended on sex chromosomes. As in humans, flies become develop as males if they have an X chromosome and a Y chromosome; females have two X chromosomes. Flies with red eyes (XW) and it is dominant to white eye color (Xw). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. - Males are said to be hemizygous because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw. - In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P1 generation. With regard to Drosophila eye color, when the P1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F1 generation exhibit red eyes (Figure). The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P1 female and their Y chromosome from the P1 male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). - Now, consider a cross between a homozygous, white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous, red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw), and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY), and half would be white-eyed (XwY). - Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father\'s Y chromosome. In humans, the alleles for certain conditions (some forms of color blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, recessive X-linked traits appear more frequently in males than females. - In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous. Cog 2.4 Where alleles come from Mutation and proofreading when copying DNA - When a cell prepares to divide, it must copy its DNA such that each daughter cells ends up with all of the necessary genetic material. Biologists call this process DNA replication. - Cells replicate DNA very accurately, but some mistakes can occur. Sometimes the enzyme that copies DNA (called DNA polymerase) will insert the wrong nucleotide. Other times, this enzyme might skip one of the nucleotides or add an extra one. These errors are called mutations. - Mutations can have serious consequences for an organism. For this reason, a cell proofreads a copy of DNA and corrects mistakes. In rare cases, however, a mistake goes uncorrected. The mutation then passes to the daughter cell, resulting in a new allele. How cells correct mutations - Most of the mistakes during DNA replication are corrected by DNA polymerase (see figure below). This enzyme proofreads the newly added nucleotide before adding the next one. If the added nucleotide matches the one on the template strand of DNA, the enzyme moves to the next nucleotide. If the added nucleotide differs, the enzyme breaks the phosphodiester bond and releases the wrong nucleotide. Once the incorrect nucleotide has been removed, the correct one can be added. - Some errors are not corrected until after replication, in a process called mismatch repair (see figure below). Enzymes recognize the incorrect nucleotide, cut it out, and put the correct nucleotide in its place. In mismatch repair, the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base. - Sometimes, a mutation is corrected by an enzyme that cuts both the 3\' and 5\' ends of the incorrect base (see figure below). The DNA polymerase then removes the incorrect segment and puts the correct one in its place. Once the correct nucleotides have been added, the gap is sealed by an enzyme, DNA ligase. This repair mechanism when UV light damages DNA. Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced. Recognize the difference between the template and the copy - How do enzymes recognize which of the two bases is the incorrect one? This process differs between prokaryotic and eukaryotic cells that have been studied. - In prokaryotes, such as E. coli, the nitrogenous base adenine acquires a methyl group after replication. Thus, the template strand of DNA will have methyl groups attached, whereas the new strand will not. Enzymes such as DNA polymerase recognize the newly synthesized strand of DNA by the absence of methyl groups. - In eukaryotes, the mechanism is not very well understood but may rely on markers in the new strand, as well as a physical attraction between proofreading enzymes and a new strand that continues beyond replication. Where alleles come from- A/B/C - Where do alleles come from? - Objectives - Explain how mutations generate new alleles - Predict mutation rates given information about the environment - Mistake made by the DNA and passing it to the daughter. - Codons- 3 letters from the DNA. a sequence of three nucleotides in a DNA or RNA molecule that codes for a specific amino acid or signals the end of protein synthesis - Point mutation: it occurs specifically in a part of the DNA. - Insertion mutation - Deletion mutation - Mutations create new alleles that are good and some that are bad - True or False? Natural selection should minimize the chance of mutation. The answer is false - Mutation rate/selective pressure - Deleterious mutation- a change in a gene\'s DNA sequence that can increase the risk of developing a disease or disorder or cause one to have it. - Beneficial mutation- a mutation that has a positive effect on an organism, increasing its chances of survival and reproduction. - Cost of accuracy- - Key point: mutation rates evolve according to the benefit of variation and the cost of tinkering with proteins - True or False? In a rapidly changing environment, a population would likely benefit from more frequent mutation. The answer is true - Mutations might be random-mutation rate is adaptive  One in a Million- A/B/C - Objective - Identify properties of the genetic code that minimize deleterious effects of mutation - The bigger the effect of a mutation that is the bigger the magnitude of some change in your phenotype, the lower the chance - Random changes are bad - A change in DNA can cause a big change in phenotype - True or False? An amino acid with a nonpolar R-group is more likely to end up on the inside of a protein after folding. The answer is true - Nonpolar molecules will be found in the inside of a protein. They are trying to be away from the water - Polar molecules- attracted to water. Always on the outside. - Missense mutation- would be really bad if it changes the kind of polarity it gets. a genetic alteration that changes a DNA sequence in a gene, resulting in the replacement of a protein building block (amino acid) with a different one - Silent mutation: a DNA mutation that doesn\'t have a noticeable effect on an organism\'s phenotype. - True or False? A point mutation in the third position of a codon is more likely to change the structure of the protein synthesized from the gene. The answer is false. Because is a silent mutation. It doesn't cause any changes - Minimizes the chance of a bad mutation to happen. Polar with polar or nonpolar with nonpolar - Bad genetic code: every time you have a change it will go to a polar to a nonpolar or vise verse. - Key point: the genetic code evolved to minimize the effect of each mutation on the phenotype Cell division and DNA Replication - When a cell divides, it is important that each daughter cell receives an identical copy of the DNA. This is accomplished by the process of DNA replication. - The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell enters mitosis or meiosis. How the two strands of the helix relate to each other - The structure of DNA, referred to as a double helix, provided a hint as to how the molecule is copied. Recall that certain nucleotides pair with one another; adenine pairs with thymine, and cytosine pairs with guanine. Therefore, the two strands are complementary to each other. - For example, a strand of DNA with a nucleotide sequence of AGTCATGA will have a complementary strand with the sequence TCAGTACT (see Figure a). - Because of the complementarity of the strands, having one strand means that a cell can recreate the other strand. - This model for replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. - During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or "old" strand. - Each new double strand consists of one parental strand and one new daughter strand, also known as semiconservative replication. - When two DNA copies are formed, they have an identical sequence of nucleotides, which are divided equally between the two daughter cells (see Figure b). Cell Division - Mitosis- produce two identical daughter cells that are exact replicas of the parental cell - Most body cells are somatic cells (non-reproductive), usually with chromosomes present in pair the number of chromosomes is the diploid number (2n) - The haploid chromosomes number includes one of each chromosome pair (n) Reproductive cells - Gametes- are produced from ger line, or reproductive cells - Meiosis- produces gametes that have half the number of chromosomes as the original cell - The gametes are not identical to one another Cell cycle - G1 phase- cell growth - S phase- DNA replication. The cell copies its DNA, creating identical pairs of DNA molecules called sister chromatids - G2 phase- the cell prepares for mitosis by growing rapidly and synthesizing proteins. The cell also checks for DNA damage of the G2 checkpoint - Mitosis (M phase)- the cell divides Substage of M phase - M phase is divided into - interphase - Prophase - Metaphase - Anaphase - Telophase: cytokinesis - M phase accomplishes karyokinesis, partitioning of DNA into daughter cell nuclei and cytokinesis, the partitioning of the cytoplasm After replication, chromosomes exist as dyads - Each dyad consists of two identical sister chromatids - The chromatids are joined at their centromere specialized regions of DNA Homologous chromosomes vs sister chromatids - Sister chromatids- two copies of the same chromosome. They are identical, copy of each other. - Homologous- one that came from your father and one from mother. The smallest unit of a living organism - A cell is the smallest unit of a living thing. A living thing, like you, are called an organism. Thus, cells are the basic building blocks of all organisms. - In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example, stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems functioning together form an organism (such as an elephant, for example). Unified cell theory - In a 1665 publication, called microphage, experimental scientist, Robert Hooke, coined the term \'cell\' (from the Latin cella meaning \'small room\') for the box-like structures he observed when viewing cork tissue through a lens. - 1670s Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses, discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see different components inside cells. - By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that: - All living things are composed of one or more cells - The cell is the basic unit of life - All new cells arise from existing cells - This principle still stands today Types of cells - The are many types of cells, but all are groups into one of two broad categories - Prokaryotic (pro- = before; -karyon- = nucleus) These are predominantly single-celled organisms of the domains Bacteria and Archaea - Eukaryotic (eu- = true; karyon- = nucleus) Animal cells, plant cells, fungal cells, and protist cells are classified as eukaryotic Common components of all cells - All cells share four common components which include - a plasma membrane, an outer covering that separates the cell's interior from its surrounding environment - cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are found - DNA, the genetic material of the cell - ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways Cog 1.1 Biology's unifying principles - How many species live in the planet? We don't know. there are many out there. Bacteria, viruses, etc. Reasonable estimate is 3-5 million species. Surviving enough to reproduce. - Why is life so incredibly diverse yet so strangely similar? Evolution. - Diversity: size, structure, move about the way they are active (water, air, earth), the way they get their energy, common structures. - Even the most disparate organisms share come features, suggesting that a single, nonrandom process generated diversity. - True or false: Biodiversity in earth will likely decrease in the near future: True. Because there are species that are dying that doesn't exist anymore. Increasing rate of extinction - Decrease in biodiversity: spread of invasive species (competing and killing other species), rapid change in the global climate (affecting precipitation, temperature, surfaces, air, stream events like floating), and habitat destruction (building new structure that will have a control climate) Why Americans don't believe in evolution - Objectives - Contrast three worldwide that influence public perception of biology - Describe reasons why biologists accept evolutionary theory Worldview - Natural evolution: evolution by natural process (15% of people will choose this) (scientist 55%) - Theistic evolution: evolution guided by a god (32% of people will choose this) (scientist 40%) - Creation: species created by God (oldest one) (46% of people will choose) (scientist 5%) - True or false: Scientist believe in evolution even though they currently leach evidence for the theory. It is False. Evolutionary theory based on known mechanism that causes evolution: - natural selection: (Darwin made famous) - Mutation - Genetic drift Why biologist believes in evolution Make accurately predictions: - Mathematical models of evolution have been tested, refined and retested for more than a century. To make accurate predictions. Conduct experiments to be able to prove your hypothesis. Simplifies our worldview - Explains diverse patterns at level of organization ranging from molecules to continents - Key point: Biologists accept evolutionary theory because its predictions match observations, Predictions are possible. "We believe in evolution because the evidence supports it, and we would abandon it overnight if new evidence arose to disprove it." Evidence is what matters. Evidence of evolution abounds - Darwin dedicated a large portion of his book, on the origin of species, to identify patterns in nature that reflected evolution. Since Darwin's time, our understanding has become clearer and broader. - Today, evidence comes from many sources, including paleontology, anatomy, embryology, and biochemistry, and biogeography Paleontologist have uncovered a fossil record - Fossil record reveals profession of evolution from small to large or simple to complex, and sometimes in reverse. Scientist data these progressions by estimating the age of fossils from all over the world. - Horses represent transitional species, which possess intermediate anatomy to earlier and later species. The fossil of horses extends back to a dog like ancestor that lived 55 million ago. Shared anatomy reveals a common ancestry - Evidence of similar structures in organisms with different lifestyles. For example, the limb of a human, a dig, a bird, and a whale all share the same form: one large bone at the base connected to more, smaller bones at the tip. This similarly results from a skeletal design that evolved in a common ancestor. Over time, the shapes and sizes of these bones evolved, but the number and organization remained roughly the same. - Vestigial traits: structure that have lost their function over time due to changes in an organism's environment or behavior patterns. - Many species with unique anatomies possess similar anatomies as embryos. - Mutations that altered embryonic development amplified differences in adult anatomy, without changing the anatomy of earlier stages. Unity of molecular structures and biochemical processes underlies biodiversity - Ancient evolutionary events led to deep divisions among three domains of life (bacteria, plants, animals). These divisions are marked by key variations on an otherwise conservative theme, such as the structure of ribosomes and membranes. - One can infer the relatedness of species by comparing their DNA. The more similar the structure of DNA between two species, the more they relate they shared a common ancestor. The study of DNA also sheds light on the mechanisms of evolution. Distribution of species reflect evolution in a shifting landscape - The distribution of species on earth follows patterns explained by the movement of tectonic plates during evolution. About 200 million years ago, all terrestrial species occupied a single, massive continent called Pangaea. - Groups of species that evolved after the breakup of Pangaea occur only in one region of the Planet. - endemic species: species found nowhere else. Australia has many of this. Misconceptions about evolution - Many people have misconceptions about the theory of evolution that led them to reject it as an explanation for the diversity of life. Evolution is just a theory - Theory refers to a set of models that have been extensively tested and supported over time. For example, scientists developed a theory of atomic particles, a theory of gravity, and a theory of electricity. In the same way, the theory of evolution describes and predicts the processes by which populations evolve - In building a theory, scientists subject their model to many tests designed to support or reject the models. - When critics of evolution say evolution is just a theory, they presume that little evidence supports current models of evolution. - Mathematical models of evolution have been tested in thousands of experiments and have found their way into fields such as medicine and engineering. Organisms evolve - An organism lives and dies, but it does not evolve. Evolution depends on a change in the genes present in a population. An organism holds one set of genes, which remain virtually constant throughout life. Therefore, organisms do not evolve as they age. An organism does change throughout its life, but such change involves the selective use of genes over time - a process called development. - Evolution is the change in the genetic composition of a group of organisms usually called a population. Such changes occur over several generations when some organisms reproduce more offspring than others. The organisms that reproduce the most will cause their genetic material to be overrepresented in the population in future generations. - When thinking about evolution, it is best to think about the change in the average value of a trait in a population. For example, when we say that the size of a bird's beak has evolved, we do not mean that the beak f a single bird has changed. We mean that the average size of the beaks of birds in a particular population has changed over generations. Evolution explains the origin of life - People often assume that the theory of evolution explains how life on earth originated. However, biologist have not designed the theory of evolution to explain the origin of life. - The theory explains the origin of species, not life itself. - Th early stages of life included the formation of organic molecules such as carbohydrates, amino acids, or nucleotides. - so, also evolution does not currently spin the origin of life, the theory may one day tell us how reproducing systems made of inorganic chemicals could evolve to form reproducing systems made of organic chemicals. After all, leaving things are merely reproducing systems of organic chemicals, no matter how complex they may seem. Species evolved on purpose - Evolution is blind to its outcome. A change in an environment, causes some organisms in a population to reproduce more than others. Consequently, genetic composition of the population may change. Organisms need no knowledge of this process to play their role. - Genetic factor behind the resistance, will become more frequent in the population. - Evolution does not proceed toward a goal. Species only become "better" overtime in the sense that they reproduce better in a particular environment. - Evolution has no goal of making a faster, bigger, more complex, or even smarter species. Also common in popular literature, this kind of languish generates a misconception that extant species, including we, represent the pinnacle of evil evolution, or were perfected by evolution. - Evolution will never produce a perfect species. Evolution is controversial among scientists - Biologist still debated whether evolution proceeded exactly as Darwin proposed or whether other mechanisms were more important. - Religious leaders and conservative politicians still promote the misconception that evolution remains a controversial idea. - Divine creation: Other theories should be taught - Intelligent design: - Religious leaders and conservative politicians have argued that alternative theories about the origin off biodiversity should be taught along with the theory of evolution. - Consider 2 reasons why we should not teach non-scientific ideas about the origin of life - Non-scientific ideas cannot predict the result of experiments: Experiments cannot test supernatural explanations for natural phenomena. Thus, teaching these ideas as science in public distracts our focus on testable ideas. - The United States prohibits Cog 1.2 How science works The Nature of Science - Biology is a science, but what exactly is science? And what features does the biology share with other scientific disciplines? - Science meandering knowledge, being derived from the Latin word scientia. Biology is the pursuit of knowledge about our world, more specific, about life. - Discoveries emerge using standardized methods. Standardized methods are processes that establish a streamlined system for performing tasks and operations - Scientists use the following methods: - Careful observation - Record keeping - Mathematical reasoning - Experimental tests - Revie by peers - Communication to the public Theories, models and hypotheses - Scientific method: consists of steps that combine reasoning and observations. One of its major features is a model or a hypothesis. - Hypothesis: is a suggested explanation for an event which can be tested through observations. Hypothesis takes the simple form of "X causes Y because of Z", the first part "x causes y" defines hypothetical relationship between two variables. The second part "because of Z", identifies hypothetical mechanism for the relationship. Wen a hypothesis takes this form, one can also refer to it as theoretical model. - Scientific theory: when scientists have a collection of models that address a common phenomenon or problem. - Well tested theories are the foundation of knowledge. - The most general of theories (those that apply to virtually all circumstances) are sometimes called scientific laws. Self-assess: - Can you describe what we mean by science? - What are some of the key features of science? Designing a Sound Experiment - Experiment means something to most people. The power of an experiment comes from its ability to establish cause and effect by breaking correlation. - Earliest medical experiments: Dr. Muhammad al-Razi conducted an experiment to establish treatment for meningitis. He suspected that meningitis could be eliminated by bloodletting. After his treatment, the patient displayed no symptoms of meningitis. One would be tempted to conclude that the treatment was a success, but the patient might have never developed meningitis or might have recovered for another reason. For this reason, the result should be viewed as a correlation rather than evidence that bloodletting cures meningitis. - To establish a cause-and-effect Razi divided patients into two groups. - The group treated by bloodletting - Untreated group - Razi reports that patients in the first group were saved hale those in the second group developed meningitis. He concluded that bloodletting should be used to treat patients with symptoms of meningitis. - What makes his experiment more reliable is that he treated multiple patients identically to ensure that success was more than a coincidence. We refer to this practice as replication. In addition, he included a control group: patients who received no treatment. By comparing both outcomes he concluded more confidently that the treatment itself cured meningitis. - He randomly assigned his patients. randomization presents bias resulting from the patients' histories. Scientific must have faith - Many people believe that science depends only on data and requires no faith. This view ignores the reality that all knowledge requires some degree of faith - Observations and memories are flawed, because the nervous system evolved to be good enough, but not perfect. Moreover, false memories are an adaptation to handle adversity or deceive enemies. Therefore, any person who draws on observations to support a belief must have faith in the accuracy of those observations. To bolster this faith, a good scientist relies on other people or specialized instruments to validate personal observations whenever possible. - A scientist always re-evaluates his or her worldview with each new observation. - Faith in ones' senses and faith in universal rules are necessary feature of science. A good scientist recognizes when faith is justified by daily experience and bolstered by multiple observers. Induction? Experiment - Replicate observations: included many mice in the study to ensure that results represented a broad population - Control conditions: standardized flow and composition of air - Randomize experimental units: sampled mice randomly from a population and assigned to smoking treatments randomly Comparing Inductive and Deductive Reasoning - Inductive reasoning: is a process in which one relates several observations to arrive at a general conclusion. This type of reasoning commonly occurs in descriptive research. A person observes some phenomena and qualitatively or quantitatively summarizes the observations. The raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, one can form a general principle (or theoretical model) about how systems work - Inductive reasoning involves 2 activities - the analysis of a large amount of data - Formulating generalization inferred from careful observations - Studies of the human brain often rely on inductive reasoning. Researchers use machines to observe the brains of many people who perform a task. The part of the brain that becomes active in these people presumably controls a person's response to the task. Novel situation, assuming that the assumptions underlying the general principle remain valid. - For example, consider the following prediction. If the climate of a region warms the distribution of plants and animals should shift to a cooler region. Scientists have compared distributions in the past to those in the present, and the changes agree with these predictions. Finding the predicted changes in distributions supports the general principle that climate change affects where species can live. Self asses: Can you describe the difference between inductive and deductive reasoning? Role of replication - Replication of the study a scientist is doing to make sure the results are accurate. When scientist publish their study that allow other scientist to replicate the experiment to evaluate its quality. Randomized experiments - "The gold standard" for establishing causation - Treatments: the conditions we are comparing e.g. new drug, standard drug, control (no drug) - Treatment group: set of people/entities given the same treatment - Interventions: We manipulate who gets what treatment - Randomly choose who is to be each treatment group to achieve a fair test. On average this achieves balance on other factors Randomized Experiments: Casual inference bootcamps - no systematic difference between the groups - It produces balance - Three kinds of variables - outcome variable - Treatment or policy variable - Pre-treatment variables: happened before treatment. The groups are all the same because they haven't been randomly placed in as group - Because the two groups are similar in everything but treatment, any changes in the average outcomes are because of the treatment. - Treatment has a causal effect in outcomes - In order to make sure both treatment and control groups have the same average values for all variables, you need big populations in each. Causality? Designing a Fair test: Things to considerate - Comparing outcomes: To be confident in test results; it's generally important to have something to compare them to. For example, in your cookie test, you'd want to actually compare batches of cookies made with different brands of chocolate chips. You might also want to make a batch without anything chocolate chip at all --- just to make sure the chocolate chips are really making a difference in the cookies' taste., Making just one batch of cookies with one brand of chocolate and seeing how they taste wouldn't help answer your question. In experiments, whatever you are comparing your test results to is sometimes the control group or control treatment. - Controlling variables: In most test, we want to be confident in the relationship between cause and effect. Is it really the chocolate chip brand, and not the baking temperature, that makes one cookie taste better than another? To be able to make a strong statement about the cause and effect, you will need to control variable --- that is, try to keep everything about the test comparing the same, except for the variables you are interested in. So, in the cookie case, this would mean, for each batch standardizing the dough recipe, the method for mixing and baking the dough, and the procedure dough tasting and rating the cookies. The only element that should vary across batches is the one variable you are interested in: brand of chocolate - Avoiding bias: No matter how hard we humans try to be objective, bias can sneak into our observations and judgment. In a sense, bias occurs because it's very difficult to control variables associated with humans' judgement. For example, your cookie tasters might be hungry and so the first cookie they eat could seem tastier to them than the rest. To avoid this potential source of bias, you'd want to set up the test so that the different testers taste the cookies in different orders. And if testers knew which cookies were made with which brands of chocolate, they might be subconsciously biased towards more expensive chocolate brands. To avoid this, you could label your cookies batches with letters instead of brand names. It's even possible that you, the cookie baker, would give subtle clues to your tasters if you knew that cookie B was made with personal favorite brand of chocolate. So, you might want to arrange to stay out of the room while the e tasting is going on. - Distinguished chance form real differences: All sort of subtle things that your either don't or cannot an affect the outcome of a test. Some cookies in a batch might have wound up with a few less chocolate chips than others. The oven might have heated unevenly and burnt a few cookies. One taster might have been distracted during the test and not given careful rating. All of these random factors will affect the outcome of the test --- but in small ways. So how do you know if the difference between a cookie with an average rating of 4.1 and one with an average rating of 4.25 is due to random factors or real difference in chocolate brand? First, sample size is important. Cookies from each batch should be rated by many different people. The larger your sample size, the more likely it is that these random factors will cancel each other out and that real differences (if they exist) can be detected statically --- which leads to our second point: Statistics can be used to analyze your raw data. The purpose of conducting such statistical tests is to tell you how likely it is that a difference in rating like the one that you observed is actually due to random factors. Understating science: an overview - Science is knowledge but more importantly, is also a reliable process by which we learn about all that stuff in the universe. - Science relies on testing ideas with evidence gathered from natural world. - Science can lead to technological advances, as well as helping us learn about enormously important and useful topics, such as out health, the environment and natural hazards. Science is complex and multifaceted, but most important characteristics of science are straightforward: - Science is a way of learning about what is in the natural world., how the natural world works, and how natural world got to be the way it is. It is not simply a collection of facts; rather it is a path to understanding - Science focuses exclusively on the natural world and does not deal with supernatural explanations. - Although scientists work in many different ways, all science relies on testing ideas by figuring out what expectations are generated by an idea and making observations to find out whether those expectations hold true. - Accepted scientific ideas are reliable because they have been subjected to rigorous testing. But, as new evidence is acquired and new perspectives emerge, these ideas can be revised. - Science is a community endeavor. It relies on a system of checks and balances, which helps ensure that science moves in the direction of greater accuracy and understanding. This system is facilitated by diversity within the scientific community, which offers a broad range of perspectives on scientific ideas. To many sciences may seem like an arcane, ivory-towered institution --- but that impression is based on a misunderstanding of science. In fact: - science affect your life every day in all sorts of different ways - Science can be fun and is accessible to everyone - You are probably already using scientific thinking in your everyday life --- maybe without even knowing it - Anyone can do science by investigating questions scientifically Tactics for testing ideas - experiments are one way to test some sorts of ideas, but science doesn't live on experiments alone. There are many other ways to scientifically test ideas too - An experiment is a test that involves manipulating some factor in a system in order to see how that affects the outcome. Ideally, experiments also involve controlling as many other factors as possible in order to isolate the cause of the experimental results. Beyond experiments: Observational studies and natural experiments - Some aspects of the natural world aren't manipulable, and hence can't be studied with direct experiment. We simply can't go back in time and introduce finches to three separate islands groups to see how they evolve. We can't move the planet around to see how their orbits would be altered by a new configuration. In such cases, we can still figure out what expectations a hypothesis generates and make observations to test the idea. For example, we can't actually experiment on distant stars in order to test ideas about which nuclear reaction occurs withing them, but we can test those ideas building sensors that allow us to observe what forms of radiation the stars emit. - Natural experiments occur when the universe, in a sense, performs an experiment for us --- that is, the relevant experimental set up already exist, and all we have to do is observe the results. For example, researchers in England wanted to know if a program to improve the health and well-being of young children and their families was effective. Enrolling some children in the program and randomly excluding others to create a controlled experiment would be unethical. However, for other reasons, the program was rolled out in some geographic areas, but not in others. This set up a natural experiment that the researchers could take advantage of by comparing outcomes in families who received the program with outcomes in similar families who did not receive the program. Analyzing the results of this natural experiment suggested that the program helped children develop socially, encouraged families to build better learning environments for their kids, and discouraged poor parenting. Hypothesis testing - A hypothesis a potential explanation that can be tested experimentally. - Alternative hypothesis: a second hypothesis. - Without testing we cannot know which hypothesis makes sense. Testing Hypothesis - requires a controlled observation. - Each hypothesis leads to a prediction, which goes something like "if x, then Y ". - To be useful, a hypothesis must be testable. - A hypothesis should also be falsifiable, meaning that observations can support or refuse the hypothesis. - To test a hypothesis, a researcher must conduct one or more experiments designed to refute the hypothesis. An experiment provides means to reject a hypothesis but can never prove a hypothesis. - Rejecting one hypothesis does not mean that another hypothesis is supported. Can you describe the key features of testing a hypothesis? Scientific method - Observation - Causal Question: write what causes the beginning of the question - Hypothesis (if X and i do G, then Y" - Plan experiment - Prediction Cog 1.3Why scientists believe in evolution Evolutionary ideas before Darwin - In the 18th century, a French naturalist named Georges-Louis Leclerc reintroduced the concept of evolution, noting that plants and animals vary among regions even when environments are similar. In addition to this observation, many naturalists realized that some species that lived in the past were now extinct. - In the early 19th century, Jean-Baptiste Lamarck proposed a mechanism referred to as the inheritance of acquired characteristics. In Lamarck\'s model, changes that affect an organism during its lifetime would be passed to its offspring. These changes might result from stress in the environment or behavior of the organism. For example, Lamarck\'s model predicts that giraffes that stretch their necks to reach leaves on tall trees would have offspring with longer necks. Although simple experiments eventually refuted this model, Lamarck's ideas influenced evolutionary thought in general and Darwin in particular. - Around the same time, a Scottish naturalist named James Hutton proposed that geological change occurs gradually, by small changes that gradually accumulate to create a large change over millions of years. Hutton\'s view contrasted with the predominant view that Earth had been shaped by catastrophic events that occurred during a brief history. Hutton's view was popularized by the geologist Charles Lyell, who later became Darwin\'s friend. Lyell's ideas influenced Darwin greatly, even before he started to think about evolution. The notion of an ancient Earth was like a seed planted in Darwin\'s mind, which wo