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What is the point of being selection-free?

What is the point of being selection-free?


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I'm reading "Highly efficient endogenous human gene correction using designed zinc finger nucleases" by Urnov et al. They propose a way to use zinc finger proteins for gene therapy. They repeatedly claim their method is "selection free" and it seems they are claiming that as an advantage to their method.

Why would selection free be an advantage? Wouldn't you have to select for the transformed cells anyway to be relevant in a clinical setting?


Urnov et al. are trying to effect gene therapy - where a mutation causing a genetic form of severe combined immunideficiency (SCID) (also known as the bubble boy syndrome). Affected SCID patients can have little to no immunity to infection what so ever. SCID in this case is caused by a single site mutation in the IL2R-gamma gene.

Their method is to use a DNA binding protein (containing zinc finger domains that bind the DNA) which attracts a DNA repair enzyme.

The result is that 18% of the cells have the SCID gene repaired. This would have been a trivial result if they had applied selection, which generally refers to any method which eliminates cells which were not affected (in this case having their DNA repaired) by a transformation like their treatment. They claim that 18% of all the cells were repaired (I assume this is in a cell culture). This implies that if their treatment were applied to living tissue, 18% of the cells would be repaired in situ, which should be enough to restore immune function.

While its possible to apply a selection method to gene therapy, it would be far better if you did not. Cancer chemotherapy for instance is a selection based treatment for instance, relying on toxins which kill fast dividing or growing cells preferentially, leaving the slower growing tissues relatively viable. Still its quite toxic and disruptive to the patient.


College of Biological Sciences

Sehoya Cotner // Biology &rarr Well, ultimately, love is an adaptation for raising babies. We love our mates and our children, and everybody wins. In a proximate sense, love appears to be mitigated by the nine-unit neuropeptides oxytocin and vasopressin. Humans vary in their production of receptors for these wonder drugs, and thus vary somewhat in their capacity to love and respond to love. But that surge of well-being you feel when you nurse your baby? Or after sex? Oxytocin! That warm squishy feeling when you see an image of your mate? Vasopressin! (Well, at least if you're a prairie vole &hellip) Is this view dystopic? Perhaps. If we could get oxytocin and vasopressin in pill form, would we bother with the inconvenience of mating, the financial and emotional cost of raising children, or the pain of childbirth? Perhaps not! (You aren't going to show this to my husband, are you?)

Robert Elde // CBS Dean's Office and Neuroscience &rarrFirst, a disclaimer, my neuroscience expertise is pain, not love. Although, in some cases the two do seem to be related. Kidding aside, love is mostly a human attribute. Most of what we have in terms of behaviors are really important and have been selected for over evolutionary time. The stuff that&rsquos so particular about humans (as far as we know), is that top layer of feelings and emotions we connect with our concept of love. While love clearly co-evolved with sexual reproduction it's probably not all about that. We are a social animal and part of the social bonding is just extra affinity for one other individual or a small group of individuals to which that is really more profoundly manifest a condition otherwise known as love.

Michele Price // Biology &rarrYou are asking an entomologist and, let's face it, insects know how to find mates. As many animals do, from bugs to slugs to monkeys, they can locate a mate through chemicals in the air called pheromones. These airborne chemicals can affect the behavior or physiology in another organism of the same species. So, is love in the air when it comes to humans? Recent evidence suggests that this may be so. The smell of tears (sad tears, not tears of joy) can act like an anti-love pheromone leading to reductions in sexual arousal and testosterone levels in exposed men. Androstadienone (a component of male sweat) was found to increase cooperative behavior in the decision-making tasks between men and has been reported to influence women's attraction to men. Also of note is that one&rsquos nose can possibly seek out a genetically compatible mate as shown in another study where women preferred the smell of sweaty T-shirts worn by men with significantly different MHC (Major Histocompatibility Complex) genes. When it comes to physical attraction and falling in love, no doubt the eyes and brain are very much involved. But, with more research we may be interested in what the nose knows as well.

Clarence Lehman // CBS Dean's Office and Ecology, Evolution and Behavior &rarr

Adhere to the tenets of physical biology and you could conclude that love is merely electrochemical signals in the brain. Is it nothing more? Does it have no abstract existence in the realm of mind, independent of brain? For a parallel, think of mathematics. Pi=3.14159 arises in the human brain, so is it merely electrochemical signals as well? No, it has its own independent existence, its own claim on the structure of the universe. Minds alien to our own would discover and apply Pi as we do. On this Valentine's Day, let us contemplate the independent existence of love.

Emilie Snell-Rood // Ecology, Evolution and Behavior &rarr An animal behaviorist asked about the meaning of love might consider both a mechanistic (proximate) and functional (ultimate) explanation. At one level, we might think about love as the emergent result of neurons firing in the amygdala or hormones like oxytocin binding to receptors in brain regions such as the nucleus accumbens. At another level, we might explain love as an evolved emotion meant to solidify pair bonds in species that require intensive parental care of dependent young or to strengthen social relationships that lead to access to food or protection from predators. Some may see such biological explanations as detracting from the magic of emotions such as love. However, such a perspective allows us to hypothesize what other animals might feel similar emotions, while appreciating the evolutionary history that brought us to a point where we can recognize, understand and celebrate such emotions.

Robin Wright // CBS Dean's Office and Genetics, Cell Biology and Development &rarr When you snuggle with your special someone, your bloodstream and your brain are flooded with oxytocin. That oxytocin affects your body and your brain in strange and wonderful ways! To a cell biologist, love is oxytocin intoxication.


Wasteful lifestyle

Biologists have long struggled to understand why we mammals and our feathery cousins are warm-blooded. The standard explanation is that it evolved in small carnivores to enable an active, predatory lifestyle. Last year, however, a radical new idea was put forward&colon warm blood evolved not in carnivores but in herbivores, as a way of balancing their nutrient requirements. Though it is early days, this idea could explain not only why we have such an apparently &hellip

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Impact

Anyone who has ever had a goal (like wanting to lose 20 pounds or run a marathon) probably immediately realizes that simply having the desire to accomplish something is not enough. Achieving such a goal requires the ability to persist through obstacles and endurance to keep going in spite of difficulties.

There are three major components of motivation: activation, persistence, and intensity.  

  • Activation involves the decision to initiate a behavior, such as enrolling in a psychology class.
  • Persistence is the continued effort toward a goal even though obstacles may exist. An example of persistence would be taking more psychology courses in order to earn a degree although it requires a significant investment of time, energy, and resources.
  • Intensity can be seen in the concentration and vigor that goes into pursuing a goal.   For example, one student might coast by without much effort, while another student will study regularly, participate in discussions, and take advantage of research opportunities outside of class. The first student lacks intensity, while the second pursues their educational goals with greater intensity.

The degree of each of these components of motivation can impact whether or not you achieve your goal. Strong activation, for example, means that you are more likely to start pursuing a goal. Persistence and intensity will determine if you keep working toward that goal and how much effort you devote to reaching it.

All people experience fluctuations in their motivation and willpower. Sometimes you might feel fired up and highly driven to reach your goals, while at other times you might feel listless or unsure of what you want or how to achieve it.

Even if you're feeling low on motivation, there are steps you can take that will keep you moving forward. Some things you can do include:

  • Adjust your goals to focus on things that really matter to you
  • If you're tackling something that is just too big or too overwhelming, break it up into smaller steps and try setting your sights on achieving that first step toward progress
  • Improve your confidence
  • Remind yourself about what you achieved in the past and what where your strengths lie
  • If there are things you feel insecure about, try working on making improvements in those areas so that you feel more skilled and capable.

Exposing the Inconsistency

Because an atheist does believe in God, but does not believe that he believes in God, he is simply a walking bundle of inconsistencies. One type to watch for is a behavioral inconsistency this is where a person’s behavior does not comport with what he claims to believe. For example, consider the atheist university professor who teaches that human beings are simply chemical accidents—the end result of a long and purposeless chain of biological evolution. But then he goes home and kisses his wife and hugs his children, as if they were not simply chemical accidents, but valuable, irreplaceable persons deserving of respect and worthy of love.

Consider the atheist who is outraged at seeing a violent murder on the ten o’clock news. He is very upset and hopes that the murderer will be punished for his wicked actions. But in his view of the world, why should he be angry? In an atheistic, evolutionary universe where people are just animals, murder is no different than a lion killing an antelope. But we don’t punish the lion! If people are just chemical accidents, then why punish one for killing another? We wouldn’t get upset at baking soda for reacting with vinegar that’s just what chemicals do. The concepts that human beings are valuable, are not simply animals, are not simply chemicals, have genuine freedom to make choices, are responsible for their actions, and are bound by a universal objective moral code all stem from a Christian worldview. Such things simply do not make sense in an atheistic view of life.

Many atheists behave morally and expect others to behave morally as well. But absolute morality simply does not comport with atheism. Why should there be an absolute, objective standard of behavior that all people should obey if the universe and the people within it are simply accidents of nature? Of course, people can assert that there is a moral code. But who is to say what that moral code should be? Some people think it is okay to be racist others think it is okay to kill babies, and others think we should kill people of other religions or ethnicities, etc. Who is to say which position should be followed? Any standard of our own creation would necessarily be subjective and arbitrary.

Now, some atheists might respond, “That’s right! Morality is subjective. We each have the right to create our own moral code. And therefore, you cannot impose your personal morality on other people!” But of course, this statement is self-refuting, because when they say, “you cannot impose your personal morality on other people” they are imposing their personal moral code on other people. When push comes to shove, no one really believes that morality is merely a subjective, personal choice.


What is the point of being selection-free? - Biology


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Introduction
Science is a way of knowing, a process for gaining knowledge and understanding of the natural world. The Science Core Curriculum places emphasis on understanding and using skills. Students should be active learners. It is not enough for students to read about science they must do science. They should observe, inquire, question, formulate and test hypotheses, analyze data, report, and evaluate findings. The students, as scientists, should have hands-on, active experiences throughout the instruction of the science curriculum.

The Science Core describes what students should know and be able to do at the end of each course. It was developed, critiqued, piloted, and revised by a community of Utah science teachers, university science educators, State Office of Education specialists, scientists, expert national consultants, and an advisory committee representing a wide diversity of people from the community. The Core reflects the current philosophy of science education that is expressed in national documents developed by the American Association for the Advancement of Science and the National Academies of Science. This Science Core has the endorsement of the Utah Science Teachers Association. The Core reflects high standards of achievement in science for all students.

Organization of the Science Core
The Core is designed to help teachers organize and deliver instruction. Elements of the Core include the following:

  • Each grade level begins with a brief course description.
  • The INTENDED LEARNING OUTCOMES (ILOs) describe the goals for science skills and attitudes. They are found at the beginning of each grade, and are an integral part of the Core that should be included as part of instruction.
  • The SCIENCE BENCHMARKS describe the science content students should know. Each grade level has three to five Science Benchmarks. The ILOs and Benchmarks intersect in the Standards, Objectives and Indicators.
  • A STANDARD is a broad statement of what students are expected to understand. Several Objectives are listed under each Standard.
  • An OBJECTIVE is a more focused description of what students need to know and be able to do at the completion of instruction. If students have mastered the Objectives associated with a given Standard, they are judged to have mastered that Standard at that grade level. Several Indicators are described for each Objective.
  • An INDICATOR is a measurable or observable student action that enables one to judge whether a student has mastered a particular Objective. Indicators are not meant to be classroom activities, but they can help guide classroom instruction.
  • SCIENCE LANGUAGE STUDENTS SHOULD USE is a list of terms that students and teachers should integrate into their normal daily conversations around science topics. These are not vocabulary lists for students to memorize.

Seven Guidelines Were Used in Developing the Science Core

Reflects the Nature of Science: Science is a way of knowing, a process for gaining knowledge and understanding of the natural world. The Core is designed to produce an integrated set of Intended Learning Outcomes (ILOs) for students.

As described in these ILOs, students will:

  • Use science process and thinking skills.
  • Manifest science interests and attitudes.
  • Understand important science concepts and principles.
  • Communicate effectively using science language and reasoning.
  • Demonstrate awareness of the social and historical aspects of science.
  • Understand the nature of science.

Coherent: The Core has been designed so that, wherever possible, the science ideas taught within a particular grade level have a logical and natural connection with each other and with those of earlier grades. Efforts have also been made to select topics and skills that integrate well with one another and with other subject areas appropriate to grade level. In addition, there is an upward articulation of science concepts, skills, and content. This spiraling is intended to prepare students to understand and use more complex science concepts and skills as they advance through their science learning.

Developmentally Appropriate: The Core takes into account the psychological and social readiness of students. It builds from concrete experiences to more abstract understandings. The Core describes science language students should use that is appropriate to their grade level. A more extensive vocabulary should not be emphasized. In the past, many educators may have mistakenly thought that students understood abstract concepts (such as the nature of the atom) because they repeated appropriate names and vocabulary (such as "electron" and "neutron"). The Core resists the temptation to describe abstract concepts at inappropriate grade levels rather, it focuses on providing experiences with concepts that students can explore and understand in depth to build a foundation for future science learning.

Encourages Good Teaching Practices: It is impossible to accomplish the full intent of the Core by lecturing and having students read from textbooks. The Science Core emphasizes student inquiry. Science process skills are central in each standard. Good science encourages students to gain knowledge by doing science: observing, questioning, exploring, making and testing hypotheses, comparing predictions, evaluating data, and communicating conclusions. The Core is designed to encourage instruction with students working in cooperative groups. Instruction should connect lessons with students' daily lives. The Core directs experiential science instruction for all students, not just those who have traditionally succeeded in science classes.

Comprehensive: The Science Core does not cover all topics that have traditionally been in the science curriculum however, it does provide a comprehensive background in science. By emphasizing depth rather than breadth, the Core seeks to empower students rather than intimidate them with a collection of isolated and forgettable facts. Teachers are free to add related concepts and skills, but they are expected to teach all the standards and objectives specified in the Core for their grade level.

Useful and Relevant: This curriculum relates directly to student needs and interests. It is grounded in the natural world in which we live. Relevance of science to other endeavors enables students to transfer skills gained from science instruction into their other school subjects and into their lives outside the classroom.

Encourages Good Assessment Practices: Student achievement of the standards and objectives in this Core is best assessed using a variety of assessment instruments. The purpose of an assessment should be clear to the teacher as it is planned, implemented, and evaluated. Performance tests are particularly appropriate to evaluate student mastery of science processes and problem-solving skills. Teachers should use a variety of classroom assessment approaches in conjunction with standard assessment instruments to inform their instruction. Observation of students engaged in science activities is highly recommended as a way to assess students' skills as well as attitudes in science. The nature of the questions posed by students provides important evidence of students' understanding of and interest in science.

The Biology Core Curriculum has two primary goals: (1) students will value and use science as a process of obtaining knowledge based on observable evidence, and (2) students' curiosity will be sustained as they develop and refine the abilities associated with scientific inquiry.

Theme
The Biology Core has three major concepts for the focus of instruction: (1) the structures in all living things occur as a result of necessary functions. (2) Interactions of organisms in an environment are determined by the biotic and abiotic components of the environment. (3) Evolution of species occurs over time and is related to the environment in which the species live.

Inquiry
Biology students should design and perform experiments, and value inquiry as the fundamental scientific process. They should be encouraged to maintain an open and questioning mind, to pose their own questions about objects, events, processes, and results. They should have the opportunity to plan and conduct their own experiments, and come to their own conclusions as they read, observe, compare, describe, infer, and draw conclusions. The results of their experiments need to be compared for reasonableness to multiple sources of information. They should be encouraged to use reasoning as they apply biology concepts to their lives.

Good science instruction requires hands-on science investigations in which student inquiry is an important goal. Teachers should provide opportunities for all students to experience many things. Students should investigate living organisms from each kingdom. Laboratory investigations should be frequent and meaningful components of biology instruction. Students should enjoy science as a process of discovering and understanding the natural world.

Relevance
Biology Core concepts should be integrated with concepts and skills from other curriculum areas. Reading, writing, and mathematics skills should be emphasized as integral to the instruction of science. Personal relevance of science in students' lives is an important part of helping students to value science and should be emphasized at this grade level. Developing students' writing skills in science should be an important part of science instruction in biology. Students should regularly write descriptions of their observations and experiments. Lab journals are an effective way to emphasize the importance of writing in science.

Providing opportunities for students to gain insights into science related careers adds to the relevance of science learning. Biology provides students with an opportunity to investigate careers in genetics, biotechnology, wildlife management, environmental science, and many fields of medicine.

Character
Value for honesty, integrity, self-discipline, respect, responsibility, punctuality, dependability, courtesy, cooperation, consideration, and teamwork should be emphasized as an integral part of science learning. These relate to the care of living things, safety and concern for self and others, and environmental stewardship. Honesty in all aspects of research, experimentation, data collection, and reporting is an essential component of science.

Instructional Resources
This Core was designed using the American Association for the Advancement of Science's Project 2061: Benchmarks For Science Literacy and the National Academy of Science's National Science Education Standards as guides to determine appropriate content and skills.

Safety Precautions
The hands-on nature of science learning increases the need for teachers to use appropriate precautions in the classroom and field. Proper handling and disposal of chemicals is crucial for a safe classroom. The chemistry described in biology can be accomplished using safe household chemicals and microchemistry techniques. It is important that all students understand the rules for a safe classroom.

Appropriate Use of Living Things in the Science Classroom
It is important to maintain a safe, humane environment for animals in the classroom. Field activities should be well thought out and use appropriate and safe practices. Student collections should be done under the guidance of the teacher with attention to the impact on the environment. The number and size of the samples taken for the collections should be considered in light of the educational benefit. Some organisms should not be taken from the environment, but rather observed and described using photographs, drawings, or written descriptions to be included in the student's collection. Teachers must adhere to the published guidelines for the proper use of animals, equipment, and chemicals in the classroom. These guidelines are available on the Utah Science Home Page.

The Most Important Goal
Science instruction should cultivate and build on students' curiosity and sense of wonder. Effective science instruction engages students in enjoyable learning experiences. Science instruction should be as thrilling an experience for a student as opening a rock and seeing a fossil, tracing and interpreting a pedigree, or observing the affects of some chemical on the heartbeat of daphnia. Science is not just for those who have traditionally succeeded in the subject, and it is not just for those who will choose science-related careers. In a world of rapidly expanding knowledge and technology, all students must gain the skills they will need to understand and function responsibly and successfully in the world. The Core provides skills in a context that enables students to experience the joy of doing science.

Intended Learning Outcomes for Earth Systems Science, Biology, Chemistry and Physics

The Intended Learning Outcomes (ILOs) describe the skills and attitudes students should learn as a result of science instruction. They are an essential part of the Science Core Curriculum and provide teachers with a standard for evaluation of student learning in science. Instruction should include significant science experiences that lead to student understanding using the ILOs.

The main intent of science instruction in Utah is that students will value and use science as a process of obtaining knowledge based upon observable evidence.

By the end of science instruction in high school, students will be able to:

  1. Use Science Process and Thinking Skills
    1. Observe objects, events and patterns and record both qualitative and quantitative information.
    2. Use comparisons to help understand observations and phenomena.
    3. Evaluate, sort, and sequence data according to given criteria.
    4. Select and use appropriate technological instruments to collect and analyze data.
    5. Plan and conduct experiments in which students may:
      • Identify a problem.
      • Formulate research questions and hypotheses.
      • Predict results of investigations based upon prior data.
      • Identify variables and describe the relationships between them.
      • Plan procedures to control independent variables.
      • Collect data on the dependent variable(s).
      • Select the appropriate format (e.g., graph, chart, diagram) and use it to summarize the data obtained.
      • Analyze data, check it for accuracy and construct reasonable conclusions.
      • Prepare written and oral reports of investigations.
    6. Distinguish between factual statements and inferences.
    7. Develop and use classification systems.
    8. Construct models, simulations and metaphors to describe and explain natural phenomena.
    9. Use mathematics as a precise method for showing relationships.
    10. Form alternative hypotheses to explain a problem.
    1. Voluntarily read and study books and other materials about science.
    2. Raise questions about objects, events and processes that can be answered through scientific investigation.
    3. Maintain an open and questioning mind toward ideas and alternative points of view.
    4. Accept responsibility for actively helping to resolve social, ethical and ecological problems related to science and technology.
    5. Evaluate scientifically related claims against available evidence.
    6. Reject pseudoscience as a source of scientific knowledge.
    1. Know and explain science information specified for the subject being studied.
    2. Distinguish between examples and non-examples of concepts that have been taught.
    3. Apply principles and concepts of science to explain various phenomena.
    4. Solve problems by applying science principles and procedures.
    1. Provide relevant data to support their inferences and conclusions.
    2. Use precise scientific language in oral and written communication.
    3. Use proper English in oral and written reports.
    4. Use reference sources to obtain information and cite the sources.
    5. Use mathematical language and reasoning to communicate information.
    1. Cite examples of how science affects human life.
    2. Give instances of how technological advances have influenced the progress of science and how science has influenced advances in technology.
    3. Understand the cumulative nature of scientific knowledge.
    4. Recognize contributions to science knowledge that have been made by both women and men.
    1. Science is a way of knowing that is used by many people, not just scientists.
    2. Understand that science investigations use a variety of methods and do not always use the same set of procedures understand that there is not just one "scientific method."
    3. Science findings are based upon evidence.
    4. Understand that science conclusions are tentative and therefore never final. Understandings based upon these conclusions are subject to revision in light of new evidence.
    5. Understand that scientific conclusions are based on the assumption that natural laws operate today as they did in the past and that they will continue to do so in the future.
    6. Understand the use of the term "theory" in science, and that the scientific community validates each theory before it is accepted. If new evidence is discovered that the theory does not accommodate, the theory is generally modified in light of this new evidence.
    7. Understand that various disciplines of science are interrelated and share common rules of evidence to explain phenomena in the natural world.
    8. Understand that scientific inquiry is characterized by a common set of values that include logical thinking, precision, open-mindedness, objectivity, skepticism, replicability of results and honest and ethical reporting of findings. These values function as criteria in distinguishing between science and non-science.
    9. Understand that science and technology may raise ethical issues for which science, by itself, does not provide solutions.

    Core Standards of the Course

    Standard 1
    Students will understand that living organisms interact with one another and their environment.

    Objective 1
    Summarize how energy flows through an ecosystem.

    1. Arrange components of a food chain according to energy flow.
    2. Compare the quantity of energy in the steps of an energy pyramid.
    3. Describe strategies used by organisms to balance the energy expended to obtain food to the energy gained from the food (e.g., migration to areas of seasonal abundance, switching type of prey based upon availability, hibernation or dormancy).
    4. Compare the relative energy output expended by an organism in obtaining food to the energy gained from the food (e.g., hummingbird - energy expended hovering at a flower compared to the amount of energy gained from the nectar, coyote - chasing mice to the energy gained from catching one, energy expended in migration of birds to a location with seasonal abundance compared to energy gained by staying in a cold climate with limited food).
    5. Research food production in various parts of the world (e.g., industrialized societies’ greater use of fossil fuel in food production, human health related to food product).

    Objective 2
    Explain relationships between matter cycles and organisms.

    1. Use diagrams to trace the movement of matter through a cycle (i.e., carbon, oxygen, nitrogen, water) in a variety of biological communities and ecosystems.
    2. Explain how water is a limiting factor in various ecosystems.
    3. Distinguish between inference and evidence in a newspaper, magazine, journal, or Internet article that addresses an issue related to human impact on cycles of matter in an ecosystem and determine the bias in the article.
    4. Evaluate the impact of personal choices in relation to the cycling of matter within an ecosystem (e.g., impact of automobiles on the carbon cycle, impact on landfills of processed and packaged foods).

    Objective 3
    Describe how interactions among organisms and their environment help shape ecosystems.

    1. Categorize relationships among living things according to predator-prey, competition, and symbiosis.
    2. Formulate and test a hypothesis specific to the effect of changing one variable upon another in a small ecosystem.
    3. Use data to interpret interactions among biotic and abiotic factors (e.g., pH, temperature, precipitation, populations, diversity) within an ecosystem.
    4. Investigate an ecosystem using methods of science to gather quantitative and qualitative data that describe the ecosystem in detail.
    5. Research and evaluate local and global practices that affect ecosystems.

    Standard 2
    Students will understand that all organisms are composed of one or more cells that are made of molecules, come from preexisting cells, and perform life functions.

    Objective 1
    Describe the fundamental chemistry of living cells.

    1. List the major chemical elements in cells (i.e., carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfur, trace elements).
    2. Identify the function of the four major macromolecules (i.e., carbohydrates, proteins, lipids, nucleic acids).
    3. Explain how the properties of water (e.g., cohesion, adhesion, heat capacity, solvent properties) contribute to maintenance of cells and living organisms.
    4. Explain the role of enzymes in cell chemistry.

    Objective 2
    Describe the flow of energy and matter in cellular function.

    1. Distinguish between autotrophic and heterotrophic cells.
    2. Illustrate the cycling of matter and the flow of energy through photosynthesis (e.g., by using light energy to combine CO2 and H2O to produce oxygen and sugars) and respiration (e.g., by releasing energy from sugar and O2 to produce CO2 and H2O).
    3. Measure the production of one or more of the products of either photosynthesis or respiration.

    Objective 3
    Investigate the structure and function of cells and cell parts.

    1. Explain how cells divide from existing cells.
    2. Describe cell theory and relate the nature of science to the development of cell theory (e.g., built upon previous knowledge, use of increasingly more sophisticated technology).
    3. Describe how the transport of materials in and out of cells enables cells to maintain homeostasis (i.e., osmosis, diffusion, active transport).
    4. Describe the relationship between the organelles in a cell and the functions of that cell.
    5. Experiment with microorganisms and/or plants to investigate growth and reproduction.

    Standard 3
    Students will understand the relationship between structure and function of organs and organ systems.

    Objective 1
    Describe the structure and function of organs.

    1. Diagram and label the structure of the primary components of representative organs in plants and animals (e.g., heart - muscle tissue, valves and chambers lung - trachea, bronchial, alveoli leaf - veins, stomata stem - xylem, phloem, cambium root - tip, elongation, hairs skin - layers, sweat glands, oil glands, hair follicles ovaries - ova, follicles, corpus luteum).
    2. Describe the function of various organs (e.g. heart, lungs, skin, leaf, stem, root, ovary).
    3. Relate the structure of organs to the function of organs.
    4. Compare the structure and function of organs in one organism to the structure and function of organs in another organism.
    5. Research and report on technological developments related to organs.

    Objective 2
    Describe the relationship between structure and function of organ systems in plants and animals.

    1. Relate the function of an organ to the function of an organ system.
    2. Describe the structure and function of various organ systems (i.e., digestion, respiration, circulation, protection and support, nervous) and how these systems contribute to homeostasis of the organism.
    3. Examine the relationships of organ systems within an organism (e.g., respiration to circulation, leaves to roots) and describe the relationship of structure to function in the relationship.
    4. Relate the tissues that make up organs to the structure and function of the organ.
    5. Compare the structure and function of organ systems in one organism to the structure and function in another organism (e.g., chicken to sheep digestive system fern to peach reproductive system).

    There are predictable patterns of inheritance. Sexual reproduction increases the genetic variation of a species. Asexual reproduction provides offspring that have the same genetic code as the parent.

    Standard 4
    Students will understand that genetic information coded in DNA is passed from parents to offspring by sexual and asexual reproduction. The basic structure of DNA is the same in all living things. Changes in DNA may alter genetic expression.

    Objective 1
    Compare sexual and asexual reproduction.

    1. Explain the significance of meiosis and fertilization in genetic variation.
    2. Compare the advantages/disadvantages of sexual and asexual reproduction to survival of species.
    3. Formulate, defend, and support a perspective of a bioethical issue related to intentional or unintentional chromosomal mutations.

    Objective 2
    Predict and interpret patterns of inheritance in sexually reproducing organisms.

    1. Explain Mendel’s laws of segregation and independent assortment and their role in genetic inheritance.
    2. Demonstrate possible results of recombination in sexually reproducing organisms using one or two pairs of contrasting traits in the following crosses: dominance/recessive, incomplete dominance, codominance, and sex-linked traits.
    3. Relate Mendelian principles to modern-day practice of plant and animal breeding.
    4. Analyze bioethical issues and consider the role of science in determining public policy.

    Objective 3
    Explain how the structure and replication of DNA are essential to heredity and protein synthesis.

    1. Use a model to describe the structure of DNA.
    2. Explain the importance of DNA replication in cell reproduction.
    3. Summarize how genetic information encoded in DNA provides instructions for assembling protein molecules.
    4. Describe how mutations may affect genetic expression and cite examples of mutagens.
    5. Relate the historical events that lead to our present understanding of DNA to the cumulative nature of science knowledge and technology.
    6. Research, report, and debate genetic technologies that may improve the quality of life (e.g., genetic engineering, cloning, gene splicing).

    Standard 5
    Students will understand that biological diversity is a result of evolutionary processes.

    Objective 1
    Relate principles of evolution to biological diversity.

    1. Describe the effects of environmental factors on natural selection.
    2. Relate genetic variability to a species’ potential for adaptation to a changing environment.
    3. Relate reproductive isolation to speciation.
    4. Compare selective breeding to natural selection and relate the differences to agricultural practices.

    Objective 2
    Cite evidence for changes in populations over time and use concepts of evolution to explain these changes.

    1. Cite evidence that supports biological evolution over time (e.g., geologic and fossil records, chemical mechanisms, DNA structural similarities, homologous and vestigial structures).
    2. Identify the role of mutation and recombination in evolution.
    3. Relate the nature of science to the historical development of the theory of evolution.
    4. Distinguish between observations and inferences in making interpretations related to evolution (e.g., observed similarities and differences in the beaks of Galapagos finches leads to the inference that they evolved from a common ancestor observed similarities and differences in the structures of birds and reptiles leads to the inference that birds evolved from reptiles).
    5. Review a scientific article and identify the research methods used to gather evidence that documents the evolution of a species.

    Objective 3
    Classify organisms into a hierarchy of groups based on similarities that reflect their evolutionary relationships.

    1. Classify organisms using a classification tool such as a key or field guide.
    2. Generalize criteria used for classification of organisms (e.g., dichotomy, structure, broad to specific).
    3. Explain how evolutionary relationships are related to classification systems.
    4. Justify the ongoing changes to classification schemes used in biology.

    These materials have been produced by and for the teachers of the State of Utah. Copies of these materials may be freely reproduced for teacher and classroom use. When distributing these materials, credit should be given to Utah State Board of Education. These materials may not be published, in whole or part, or in any other format, without the written permission of the Utah State Board of Education, 250 East 500 South, PO Box 144200, Salt Lake City, Utah 84114-4200.


    These manuscripts should present well-rounded studies reporting innovative advances that further knowledge about a topic of importance to the fields of biology or medicine. The conclusions of the Original Research Article should clearly be supported by the results. These can be submitted as either a full-length article (no more than 6,000 words, 8 figures, and 4 tables) or a brief communication (no more than 2,500 words, 3 figures, and 2 tables). Original Research Articles contain five sections: abstract, introduction, materials and methods, results and discussion.

    Reviewers should consider the following questions:

    • What is the overall aim of the research being presented? Is this clearly stated?
    • Have the Authors clearly stated what they have identified in their research?
    • Are the aims of the manuscript and the results of the data clearly and concisely stated in the abstract?
    • Does the introduction provide sufficient background information to enable readers to better understand the problem being identified by the Authors?
    • Have the Authors provided sufficient evidence for the claims they are making? If not, what further experiments or data needs to be included?
    • Are similar claims published elsewhere? Have the Authors acknowledged these other publications? Have the Authors made it clear how the data presented in the Author’s manuscript is different or builds upon previously published data?
    • Is the data presented of high quality and has it been analyzed correctly? If the analysis is incorrect, what should the Authors do to correct this?
    • Do all the figures and tables help the reader better understand the manuscript? If not, which figures or tables should be removed and should anything be presented in their place?
    • Is the methodology used presented in a clear and concise manner so that someone else can repeat the same experiments? If not, what further information needs to be provided?
    • Do the conclusions match the data being presented?
    • Have the Authors discussed the implications of their research in the discussion? Have they presented a balanced survey of the literature and information so their data is put into context?
    • Is the manuscript accessible to readers who are not familiar with the topic? If not, what further information should the Authors include to improve the accessibility of their manuscript?
    • Are all abbreviations used explained? Does the author use standard scientific abbreviations?

    Case reports describe an unusual disease presentation, a new treatment, an unexpected drug interaction, a new diagnostic method, or a difficult diagnosis. Case reports should include relevant positive and negative findings from history, examination and investigation, and can include clinical photographs. Additionally, the Author must make it clear what the case adds to the field of medicine and include an up-to-date review of all previous cases. These articles should be no more than 5,000 words, with no more than 6 figures and 3 tables. Case Reports contain five sections: abstract introduction case presentation that includes clinical presentation, observations, test results, and accompanying figures discussion and conclusions.

    Reviewers should consider the following questions:

    • Does the abstract clearly and concisely state the aim of the case report, the findings of the report, and its implications?
    • Does the introduction provide enough details for readers who are not familiar with a particular disease/treatment/drug/diagnostic method to make the report accessible to them?
    • Does the manuscript clearly state what the case presentation is and what was observed so that someone can use this description to identify similar symptoms or presentations in another patient?
    • Are the figures and tables presented clearly explained and annotated? Do they provide useful information to the reader or can specific figures/tables be omitted and/or replaced by another figure/table?
    • Are the data presented accurately analyzed and reported in the text? If not, how can the Author improve on this?
    • Do the conclusions match the data presented?
    • Does the discussion include information of similar case reports and how this current report will help with treatment of a disease/presentation/use of a particular drug?

    Reviews provide a reasoned survey and examination of a particular subject of research in biology or medicine. These can be submitted as a mini-review (less than 2,500 words, 3 figures, and 1 table) or a long review (no more than 6,000 words, 6 figures, and 3 tables). They should include critical assessment of the works cited, explanations of conflicts in the literature, and analysis of the field. The conclusion must discuss in detail the limitations of current knowledge, future directions to be pursued in research, and the overall importance of the topic in medicine or biology. Reviews contain four sections: abstract, introduction, topics (with headings and subheadings), and conclusions and outlook.

    Reviewers should consider the following questions:

    • Is the review accessible to readers of YJBM who are not familiar with the topic presented?
    • Does the abstract accurately summarize the contents of the review?
    • Does the introduction clearly state what the focus of the review will be?
    • Are the facts reported in the review accurate?
    • Does the Author use the most recent literature available to put together this review?
    • Is the review split up under relevant subheadings to make it easier for the readers to access the article?
    • Does the Author provide balanced viewpoints on a specific topic if there is debate over the topic in the literature?
    • Are the figures or tables included relevant to the review and enable the readers to better understand the manuscript? Are there further figures/tables that could be included?
    • Do the conclusions and outlooks outline where further research can be done on the topic?

    Perspectives provide a personal view on medical or biomedical topics in a clear narrative voice. Articles can relate personal experiences, historical perspective, or profile people or topics important to medicine and biology. Long perspectives should be no more than 6,000 words and contain no more than 2 tables. Brief opinion pieces should be no more than 2,500 words and contain no more than 2 tables. Perspectives contain four sections: abstract, introduction, topics (with headings and subheadings), and conclusions and outlook.

    Reviewers should consider the following questions:

    • Does the abstract accurately and concisely summarize the main points provided in the manuscript?
    • Does the introduction provide enough information so that the reader can understand the article if he or she were not familiar with the topic?
    • Are there specific areas in which the Author can provide more detail to help the reader better understand the manuscript? Or are there places where the author has provided too much detail that detracts from the main point?
    • If necessary, does the Author divide the article into specific topics to help the reader better access the article? If not, how should the Author break up the article under specific topics?
    • Do the conclusions follow from the information provided by the Author?
    • Does the Author reflect and provide lessons learned from a specific personal experience/historical event/work of a specific person?

    Analyses provide an in-depth prospective and informed analysis of a policy, major advance, or historical description of a topic related to biology or medicine. These articles should be no more than 6,000 words with no more than 3 figures and 1 table. Analyses contain four sections: abstract, introduction, topics (with headings and subheadings), and conclusions and outlook.

    Reviewers should consider the following questions:

    • Does the abstract accurately summarize the contents of the manuscript?
    • Does the introduction provide enough information if the readers are not familiar with the topic being addressed?
    • Are there specific areas in which the Author can provide more detail to help the reader better understand the manuscript? Or are there places where the Author has provided too much detail that detracts from the main point?
    • Does the Author provide balanced viewpoints on a specific topic if there is debate over the topic in the literature?
    • If necessary, does the Author divide the article into specific topics to help the reader better access the article? If not, how should the Author break up the article under specific topics?
    • Do the conclusions follow from the information provided by the Author?

    Profiles describe a notable person in the fields of science or medicine. These articles should contextualize the individual’s contributions to the field at large as well as provide some personal and historical background on the person being described. More specifically, this should be done by describing what was known at the time of the individual’s discovery/contribution and how that finding contributes to the field as it stands today. These pieces should be no more than 5,000 words, with up to 6 figures, and 3 tables. The article should include the following: abstract, introduction, topics (with headings and subheadings), and conclusions.

    Reviewers should consider the following questions:

    • Does the abstract accurately summarize the contents of the manuscript?
    • Does the Author provide information about the person of interest’s background, i.e., where they are from, where they were educated, etc.?
    • Does the Author indicate how the person focused on became interested or involved in the subject that he or she became famous for?
    • Does the Author provide information on other people who may have helped the person in his or her achievements?
    • Does the Author provide information on the history of the topic before the person became involved?
    • Does the Author provide information on how the person’s findings affected the field being discussed?
    • Does the introduction provide enough information to the readers, should they not be familiar with the topic being addressed?
    • Are there specific areas in which the Author can provide more detail to help the reader better understand the manuscript? Or are there places where the Author has provided too much detail that detracts from the main point?
    • Does the Author provide balanced viewpoints on a specific topic if there is debate over the topic in the literature?
    • If necessary, does the Author divide the article into specific topics to help the reader better access the article? If not, how should the Author break up the article under specific topics?
    • Do the conclusions follow from the information provided by the Author?

    Interviews may be presented as either a transcript of an interview with questions and answers or as a personal reflection. If the latter, the Author must indicate that the article is based on an interview given. These pieces should be no more than 5,000 words and contain no more than 3 figures and 2 tables. The articles should include: abstract, introduction, questions and answers clearly indicated by subheadings or topics (with heading and subheadings), and conclusions.


    • All vaccines are genetically modified in a way. A gene may be programmed to produce an antiviral protein in a bacterial cell. Once sealed into the DNA, the bacteria is now effectively re-programmed to replicate this new antiviral protein.
    • Recombinant engineered vaccines are being extensively explored, especially to eradicate infectious diseases, allergies, and cancers.
    • Protocols for genetically engineered vaccines raise issues on their efficacy and overall benefit.
    • FDA: Food and Drug Administration, an agency of the United States Department of Health and Human Services.
    • vaccine: a substance given to stimulate the body&rsquos production of antibodies and provide immunity against a disease, prepared from the agent that causes the disease, or a synthetic substitute.
    • genetic engineering: The deliberate modification of the genetic structure of an organism. The term genetic modification is used as a synonym.

    Genetic engineering, also called genetic modification, is the direct manipulation of an organism &lsquos genome using biotechnology. New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest using molecular cloning methods to generate a DNA sequence, or by synthesizing the DNA and then inserting this construct into the host organism. Genes may be removed, or &ldquoknocked out,&rdquo using a nuclease. Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations.

    Genetic engineering alters the genetic makeup of an organism using techniques that remove heritable material, or that introduce DNA prepared outside the organism either directly into the host or into a cell that is then fused or hybridized with the host. This involves using recombinant nucleic acid (DNA or RNA) techniques to form new combinations of heritable genetic material, followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection and micro-encapsulation techniques.

    In medicine, genetic engineering has been used to mass-produce insulin, human growth hormones, follistim (for treating infertility), human albumin, monoclonal antibodies, antihemophilic factors, vaccines,and many other drugs. Vaccination generally involves injecting weak live, killed, or inactivated forms of viruses or their toxins into the person being immunized. Genetically engineered viruses are being developed that can still confer immunity, but lack the infectious sequences. Mouse hybridomas, cells fused together to create monoclonal antibodies have been humanised through genetic engineering to create human monoclonal antibodies.

    Figure: Genetically modified viruses: Scientist studying the H5N1 influenza virus to design a vaccine.

    The process of genetic engineering involves splicing an area of a chromosome, a gene, that controls a certain characteristic of the body. The enzyme endonuclease is used to split a DNA sequence and to split the gene from the rest of the chromosome. For example, this gene may be programmed to produce an antiviral protein. This gene is removed and can be placed into another organism. For example, it can be placed into a bacteria, where it is sealed into the DNA chain using ligase. When the chromosome is once again sealed, the bacteria is now effectively re-programmed to replicate this new antiviral protein. The bacteria can continue to live a healthy life, though genetic engineering and human intervention has actively manipulated what the bacteria actually is.

    Despite the early success demonstrated with the hepatitis B vaccine, no other recombinant engineered vaccine has been approved for use in humans. It is unlikely that a recombinant vaccine will be developed to replace an existing licensed human vaccine with a proven record of safety and efficacy. This is due to the economic reality of making vaccines for human use. Genetically engineered subunit vaccines are more costly to manufacture than conventional vaccines, since the antigen must be purified to a higher standard than was demanded of older, conventional vaccines. Each vaccine must also be subjected to extensive testing and review by the FDA, as it would be considered a new product. This is costly to a company in terms of both time and money and is unnecessary if a licensed product is already on the market. Although recombinant subunit vaccines hold great promise, they do present some potential limitations.

    In addition to being less reactogenic, recombinant subunit vaccines have a tendency to be less immunogenic than their conventional counterparts. This can be attributed to these vaccines being held to a higher degree of purity than was traditionally done for an earlier generation of licensed subunit vaccines. Ironically, the contaminants often found in conventional subunit vaccines may have aided in the inflammatory process, which is essential for initiating a vigorous immune response. This potential problem may be overcome by employing one of the many new types of adjuvants that are becoming available for use in humans. Recombinant subunit vaccines may also suffer from being too well-defined, because they are composed of a single antigen. In contrast, conventional vaccines contain trace amounts of other antigens that may aid in conferring an immunity to infectious agents that is more solid than could be provided by a monovalent vaccine. This problem can be minimized, where necessary, by creating recombinant vaccines that are composed of multiple antigens from the same pathogen.


    AP Biology: How to Approach Free-Response Questions

    For Section II, the AP Biology free-response section, you’ll have 80 minutes (after the reading period) to answer six questions. You will likely spend more time on each of the two long free-response questions than on each of the four short-response questions. A fair balance is 22 minutes per long free-response question and 9 minutes per short free-response question. Take the time to make your answers as precise and detailed as possible while managing the allotted time.

    Important Distinctions on the AP Biology Exam

    Each free-response question will, of course, be about a distinct topic. However, this is not the only way in which these questions differ from one another. Each question will also need a certain kind of answer, depending on the type of question it is. Part of answering each question correctly is understanding what general type of answer is required. There are five important signal words that indicate the rough shape of the answer you should provide:

    Each of these words indicates that a specific sort of response is required none of them mean the same thing. Questions that ask you to describe, discuss, or explain are testing your comprehension of a topic. A description is a detailed verbal picture of something a description question is generally asking for “just the facts.” This is not the place for opinions or speculation. Instead, you want to create a precise picture of something’s features and qualities. A description question might, for example, ask you to describe the results you would expect from an experiment. A good answer here will provide a rich, detailed account of the results you anticipate.

    A question that asks you to discuss a topic is asking you for something broader than a mere description. A discussion is more like a conversation about ideas, and— depending on the topic—this may be an appropriate place to talk about tension between competing theories and views. For example, a discussion question might ask you to discuss which of several theories offers the best explanation for a set of results. A good answer here would go into detail about why one theory does a better job of explaining the results, and it would talk about why the other theories cannot cope with the results as thoroughly.

    A question that asks you to explain something is asking you to take something complicated or unclear and present it in simpler terms. For example, an explanation question might ask you to explain why an experiment is likely to produce a certain set of results, or how one might measure a certain sort of experimental result. A simple description of an experimental setup would not be an adequate answer to the latter question. Instead, you would need to describe that setup and talk about why it would be an effective method of measuring the result.

    COMPARE VS. CONTRAST QUESTIONS

    Questions that ask you to compare or contrast are asking you to analyze a topic in relation to something else. A question about comparison needs an answer that is focused on similarities between the two things. A question that focuses on contrast needs an answer emphasizing differences and distinctions.


    Tragedy of the commons

    Overharvesting is a serious threat to many species, especially aquatic ones. Common resources &ndash or resources that are shared, such as fisheries &ndash are subject to an economic pressure known as &ldquothe tragedy of the commons,&rdquo in which essentially no harvester has a motivation to exercise restraint in harvesting from a certain area, because that area is not owned by that harvester. The natural outcome of harvesting common resources is their overexploitation.

    For example, most fisheries are managed as a common resource even when the fishing territory lies within a country&rsquos territorial waters because of this, fishers have very little motivation to limit their harvesting, and in fact technology gives fishers the ability to overfish. In a few fisheries, the biological growth of the resource is less than the potential growth of the profits made from fishing if that time and money were invested elsewhere. In these cases (for example, whales) economic forces will always drive toward fishing the population to extinction.

    Figure (PageIndex<1>): Cod trawler and net: Overharvesting fisheries is an especially salient problem because of a situation termed the tragedy of the commons. In this situation, fishers have no real incentive to practice restraint when harvesting fish because they do not own the fisheries.


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