The Scientific Method PDF

8/29/24 The Scientific Method The scientific method describes the process of science Make an observation and ask a question about it Develop a testable explanation called a hypothesis Desi...

8/29/24 The Scientific Method The scientific method describes the process of science Make an observation and ask a question about it Develop a testable explanation called a hypothesis Design experiments to test the hypothesis Include a control to help rule out alternative explanations Do the experiment, collect and analyze data Draw a conclusion Communicate methods, results, and conclusions A scientific theory is an explanation supported by a large amount of evidence © McGraw Hill LLC 7 7 The Scientific Method The scientific method describes the process of science Make an observation and ask a question about it Can cycle here – Develop a testable explanation called a hypothesis Refine hypothesis and/or refine the Design experiments to test the hypothesis experiment. Include a control to help rule out alternative explanations Do the experiment, collect and analyze data Draw a conclusion Communicate methods, results, and conclusions A scientific theory is an explanation supported by a large amount of evidence © McGraw Hill LLC 8 8 4  8/29/24 Scientific Rules For this introductory course, I will frequently summarize material with a general rule. Know that every rule has exceptions. (including this one…) Understanding the exceptions frequently strengthens the utility of the rule. Exceptions may show up in special cases throughout the semester. Exceptions are also a good topic for office hours. Examples: Information always flows from DNA à RNA à Protein There are only four RNA BASES à A,G,C, & U 9 Information Stored in Nucleic Acids (DNA or RNA) MO Instruction and Grading are tougher than any course you’ve taken. Given a situation – you have to guess. If you guess wrong, you die. If you guess right, live, and reproduce -- Not only do you remember, but so do your offspring. Very slow process, and a lot of dead ends (literally!) But the time scale we are looking at is hard to imagine. 10 5  8/29/24 Universal Tree of Cellular Life Access the text alternative for slide images. © McGraw Hill LLC 15 15 Universal Tree Assesses the accumulation of mutations in DNA Lengths of lines correlate with evolutionary time Simplest assembly – all cellular life evolved from one single-celled ancestor Geological timeline Earth is ca. 4.6 billion years old Life started 3.5 – 3.8 billion years ago By 2.5 million years ago, single celled organisms were terraforming the planet, adding oxygen to the atmosphere. Spread and evolved to fit essentially every habitable zone on the planet. 16 8  8/29/24 Universal Tree of Cellular Life Access the text alternative for slide images. © McGraw Hill LLC 17 17 At this point – your reading went into the many ways MOs impact humans in the world today All true, all important (and probably worth an exam question) Microbiomes in humans (interesting sidebar on Clostridium difficile) Environmental impacts and Ecology Commercial uses Food production and preservation Biodegradation Production of specialized compounds Research tools But I promised you a bias for the course. Let’s dive straight into an overview of infectious disease. 18 9  8/29/24 Humankind has long recognized Diseases Illness and even death not related to physical injury and distinct from effect of poisons. Understanding of sanitation, all without knowing why! In many cases, the diagnosis of the disease was remarkably accurate, but without knowledge of MOs, etiology explanations were haphazard. Roman medicine included accurate descriptions of malaria fevers, but the only cause they could imagine was the poison of the “bad air” [“mal” “aria”] associated with swamps. Likewise, importance of good sanitation was understood, but not why. In Deuteronomy 23:12-14 we find explicit instructions for camp sanitation, requiring burial of human excrement outside of the camp. With no concept of infectious agents, the justification provided was that God walks through the camp at night, and we wouldn’t want his shoes to get dirty! We even learned how to use fermentation to preserve foods (beer, wine, mead, yoghurt, cheese, sauerkraut, kimchee, etc), frequently linking the preservation to to effects of selected caves or vats or whatever. 19 With the discovery of a micro universe, people began to understand. Microorganisms can cause disease, but our disease and suffering is not their intent. Their billions of years of evolution have focused on surviving, growing, and reproducing. If they did want to kill us, we would be dead by now. Remember these tiny things terraformed a planet! If we can understand their specific needs, we can manipulate their activities to our benefit, to control infections, preserve foods, and stimulate good health. We are finding more cases where MOs even have a commensal relationship with us – with us supporting their growth and reproduction and them protecting us for other MOs! 20 10  8/29/24 Postulate two different categories of infectious diseases. Some diseases have evolved to be in a state of balance with us and with our defense systems. These organisms see no advantage to killing us, at least not quickly. They want to give us time to let them grow and reproduce and spread to other people. Other diseases are an unfortunate accident or mistake. MOs that evolved in a different environment or organism – new to us and out of balance. In the worst cases, deadly to us and no benefit to MO. 21 Remember how MOs “Learn”? If MO kills too quickly, no growth/transmission. (Ebola) àNo advantage à No learning If MO is quickly killed by host, no growth/transmission. (Tetnus) àNo advantage àNo learning But in a Goldilocks environment... MO and host can learn! Evolving into a balance. Still can be a crappy deal for the patient... 22 11  8/29/24 Some infectious disease concepts Most microorganisms are not harmful – some are even beneficial Those that cause disease are called pathogens. They can cause disease by Directly damaging body cells and tissues. Creating toxins that damage cells and tissues. Releasing waste products (from MO growth) that damage cells and tissues. Stimulating the body’s defense mechanisms, resulting in collateral damage. 23 Their impact can far exceed anything we have done to ourselves (so far) Influenza in 1918 to 1919 killed more Americans than died in WWI, WWII, and the Korean, Vietnam, and Iraq wars combined The COVID-19 pandemic has resulted in the death of more than 15 million people worldwide, including over 1 million Americans 24 12  8/29/24 MOs don’t even have to infect us to impact us! The great famine in Ireland in the 1800s was largely due to a microbial disease of potatoes A bacterial disease that kills olive trees, first seen in southern Italy in 2013, has spread to Spain and France, contributing to a recent worldwide drop in olive oil production A fungal disease called “wheat blast” devastated wheat crops in South America, then spread to Bangladesh in 2016, resulting in the loss of over 35,000 acres of crops that year. Two years later it was found in Zambia Frog populations around the world have been decimated by a fungal disease called chytridiomycosis Not just impacting frog-leg diners – think insect control! 25 Some specific successes (but...) Smallpox eradicated! The disease once killed one-third of its victims; left others blind or scarred Devastated unexposed populations, such as native inhabitants of Americas World-Wide vaccination program – can tell you stories of real heroes! No reported cases since 1977, but laboratory stocks of virus remain And Monkey pox is emerging... Plague deaths less than 100 per year Killed one-third of population of Europe (approximately 25 million people) between 1347 and 1351 Control of rodent populations and human respiratory secretions to prevent spread Antibiotics for treatment But we still have plague throughout the southwest region, just not human spread! Polio nearly eliminated by vaccination Emphasis on “nearly”. Eliminating the last human reservoirs stymied by religion and politics. Measles also “nearly” in US. Don’t get me started... 26 13  8/29/24 Remember those “accidental” pathogens, out of balance? Emerging Infections – frequently a Zoonosis. Also, Climate change facilitated spread! COVID-19—caused by a virus called SARS-CoV-2 mpox (previously called monkeypox) Ebola virus disease Congenital Zika syndrome Middle East respiratory syndrome (MERS) Influenza (certain types) Lyme disease AIDS Hantavirus pulmonary syndrome Mad cow disease (bovine spongiform encephalopathy) 27 Emerging Infectious Diseases Accidental crossover (e.g., zoonosis) E. coli O104:H4 Ebola HIV-1 COVID-19 Climate change exacerbated Lyme disease Chagas disease Malaria Societal exacerbation Drug resistance (e.g., Tuberculosis, Staph.) Rapid world-wide travel/connections. Unequal access to medical care and treatments. Misinformation preventing application of medical care and treatments. 28 14  8/29/24 Back to the “Usual Suspects” All living cells can be classified into the three domains we saw earlier. Bacteria Archaea Eukarya All three domains include known or suspected pathogens (Archaea sidebar and optional reference) 29 ” A rose by any other name....” Quick sidebar on Binomial System of Nomenclature Generally two words Genus (capitalized) species name (not capitalized) Both genus and species are either italicized or underlined Genus may be abbreviated (E. coli) if clear from context But note Escherichia coli and Entamoeba coli are both E. coli! Also, can use ‘spp.’ for multiple species: Plasmodium spp. 30 15  8/29/24 More on Scientific Names Name often reflects characteristic of organism or honors a scientist who worked with it Escherichia (honors Theodor Escherich) coli (indicates the colon, where the bacteria live) Members of a species with important minor differences may be indicated with a strain designation (E. coli K12) Informal names that resemble genus names are not italicized Members of the genus Staphylococcus are often called staphylococci © McGraw Hill LLC 31 31 Members of the Microbial World—Table 1.1 Table 1.1 Characteristics of Members of the Three Domains Characteristic Bacteria Archaea Eukarya Cell type Prokaryotic Prokaryotic Eukaryotic Number of cells Unicellular Unicellular Unicellular or multicellular Membrane-bound No No Yes organelles Ribosomal RNA Yes Yes Yes sequences unique to the group Peptidoglycan in Yes No No cell wall Typical size range 0.3–2 μm 0.3–2 μm 5–50 μm © McGraw Hill LLC 32 32 16  8/29/24 Bacteria Single-celled prokaryotes Most have a Rigid cell wall containing ‘peptidoglycan’ (polymer that is unique to bacteria) Many move using one or more ‘flagella’ Multiply via binary fission Obtain energy from a wide variety of sources; some are photosynthetic Most species have a consistent, specific shape. 33 Fancy names for bacterial shapes... Coccus (plural: cocci) Spherical cells, may be flattened on one end or slightly oval Bacillus (plural: bacilli) A rod shaped, cylindrical cell (length can vary with different species) Vibrio (plural: vibrios) A short, curved rod Spirillum (plural: spirilla) A curved rod long enough to form spirals Spirochete (plural: spirochetes) A long, spiral-shaped cell with a flexible cell wall and a unique mechanism of motility Pleomorphic Refers to bacteria that characteristically vary in their shape or mix two or more shapes 34 17  8/29/24 Some bacteria form characteristic clusters (especially when growing on solid media) Cocci that remain as pairs are called diplococci Division in one plane can form long chains, such as the members of the genus Streptococcus strepto means “twisted chain” Cocci that divide in perpendicular planes form cubical packets Members of the genus Sarcina form such packets Cocci that divide randomly in several planes may form grape-like clusters Staphylococcus species, typically form grape-like clusters staphylo means “bunch of grapes” 35 Archaea Single-celled prokaryotes similar in size, shape, and properties to bacteria Major differences from Bacteria in chemical composition Cell walls lack peptidoglycan Ribosomal RNA sequences different To date, most research is on “extremophiles” High salt concentration, temperature Many are common in moderate environments Also found in human microbiomes (intestine, oral cavity) See optional (i.e., not on exam) article from CDC, this year. 36 18  8/29/24 Common Cell Arrangements—Figure 1.9 a (top): Dennis Kunkel Microscopy/SPL/Science Source; a (bottom): BSIP SA/Alamy Stock Photo; b: CDC/Betsy Crane/Janice Haney Carr; c: Eye of Science/Science Source Access the text alternative for slide images. © McGraw Hill LLC 37 37 Eukarya Eukarya: single-celled or multicellular eukaryotes Eukaryotes studied by microbiologists include fungi, algae, protozoa, and helminths (worms) Algae and protozoa also referred to as protists Table 1.3 Eukaryotic Organisms Studied by Microbiologists Organism Characteristics Fungi Use organic material for energy. Size range from microscopic (yeasts) to macroscopic (molds; mushrooms) are the reproductive structures of some fungi. Algae Use sunlight for energy. Size range from microscopic (single- celled algae) to macroscopic (multicellular algae). Protozoa Use organic material for energy. Single-celled microscopic organisms. Helminths Use organic material for energy. Adult worms are typically macroscopic and often quite large, but their eggs and larval forms are microscopic. © McGraw Hill LLC 38 38 19  8/29/24 Fungi Fungi: diverse group ranging from single- celled yeasts to multicellular filamentous molds The microscopic filaments of molds, called hyphae, form a visible mat called a mycelium Filamentous molds spread by release of microscopic spores (conidia) Mushroom: macroscopic reproductive structure characteristic of some fungi Secrete enzymes onto organic materials, and then take in the released nutrients Opportunistic infections (e.g., yeast) Janice Haney Carr/CDC Also, systemic infections on skin and in lungs. Access the text alternative for slide images. © McGraw Hill LLC 39 39 Algae Diverse group of photosynthetic eukaryotes Single-celled or multicellular Photosynthesis in algae occurs in chloroplasts which contain chlorophyll or other pigments that give characteristic colors Usually live near surface of water or in moist habitat Rigid cell walls and flagella distinct from those of prokaryotes Only rarely a pathogen, but some species secrete toxins into water. (Note: Cyanobacter are bacteria, NOT algae) Lisa Burgess/McGraw Hill © McGraw Hill LLC 40 40 20  8/29/24 Protozoa Diverse group of single-celled eukaryotes Complex, larger than prokaryotes Most ingest organic compounds No rigid cell wall Most are motile Energy from ingested organic material Pathogenic protozoa are often included under the term Parasites. Melba Photo Agency/Alamy Stock Photo © McGraw Hill LLC 41 41 Helminths Parasitic helminths are worms that live at the expense of a host Adult worms of most species can be seen with the naked eye. However, these stages are often embedded within the body and not easily viewed. The diagnostic stages (larvae and ova (or eggs) usually require use of a microscope – hence their inclusion under Microbiology. Helminths include roundworms (Ascaris), tapeworms (Taenia), and flukes © McGraw Hill LLC 42 42 21  8/29/24 Another Group: Acellular Infectious Agents As name implies – they are not cells à Not on the universal tree of life Unlike cells, they have originated many times They are the lawyers of the Microbiology Universe They start perfectly reasonable laws and rules Then twist them beyond recognition for their own benefit. Not clear if they are alive (depends on definitions) but they learn in the same evolutionary classroom as cells And two of them use the same nucleic acid memory. By definition, they are all pathogenic to something! 43 Acellular Infectious Agents—Table 1.4 Agent Characteristic Viruses Consist of either DNA or RNA, surrounded by a protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate. Viroids Consist only of RNA; no protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate. Prions Consist only of protein; no DNA or RNA. Misfolded versions of normal cellular proteins that cause the normal versions to misfold. © McGraw Hill LLC 44 44 22  8/29/24 Viruses Nucleic acid packaged in protein coat Infect living cells, referred to as hosts Obligate intracellular agents Multiply using host cell machinery and nutrients Inactive outside of host All forms of life can be infected by different types May kill host cell May remain within host cell and replicate viral genetic information as host cell multiplies Fun fact – your genome is carrying thousands of viral genomes (ca 8% of your DNA). Fortunately, most of Cynthia S. Goldsmith and Thomas Rowe/CDC them have been enjoying a free ride for so long they have forgotten how to get out, replicate, and kill us.... © McGraw Hill LLC 45 45 Viroids Consist only of a single short piece of RNA (They generally need a buddy to get them into the plant in the first place) Obligate intracellular agents Cause a number of plant diseases To date, only one known human disease – Hepatitis D © McGraw Hill LLC 46 46 23  8/29/24 Prions (aka “slow viruses”) Infectious proteins: misfolded versions of normal cellular proteins found in the brain Misfolded version in contact with normal version causes it to also misfold Abnormal proteins form fibrils Cells die leaving spaces in brain (spongiform encephalopathy) Resistant to usual sterilization EM Unit, VLA/Science Source procedures © McGraw Hill LLC 47 47 If time – Scientific Method and information transfer 1900s – was “obvious” that proteins were the only molecule sufficiently complex to transfer information. Carbohydrates were polymers of sugar, for energy. DNA was polymer of nucleic acids for nitrogen storage. 1930-1944, Avery, MacLeod, & McCarty claimed that DNA was actually the transmitting molecule. Long, drawn out fight. Final nail in coffin was Watson & Crick (& ) showing how DNA replicated information. 1970-1988, Pruisner claimed that protein, alone could carry the information to cause disease. Same long, drawn arguments as before, but with roles reversed. There are exceptions to every rule – whatever the rule is. And the Scientific Method will (eventually) sort it out! 48 24