1.
Introduction
# 1. Biology and the Scientific Method, Chapter 1
# 2. Cell Structure, Chapter 4
# 3. Protein Synthesis: Transcription and Translation, Chapters 9 and 10
2.
# 4. Cell-Cell Interactions, Chapter 5
# 5. From One Cell To Two: Cell Division and DNA Replication, Chapter 11
# 6. From Two Cells To Many: Cell Differentiation and Embryonic Development, Chapter 40
3.
# 7. From Genes To Traits: How Genotype Affects Phenotype, Chapters 12
# 8. From Genes To Species: A Primer on Evolution, Chapters 14, 15 and 16
4.
Exam I, Plant/Animal presentations
5.
# 9. Origin of Biological Diversity, Chapter 17
# 10. Evolution of Biological Diversity, Chapter 18
# 11. Current Biological Diversity, Chapters 19, 20, 21, 22, 23 and 24
6.
# 12. Organisms In Time and Space: Ecology, Chapters 26, 27, 28 and 29
# 13. What Creatures Do: Animal Behavior, Chapter 25
7.
# 14. Introduction to Anatomy and Physiology, Chapter 31
# 15. Physiology: Regulation and Control, Chapters 37, 38 and 39
# 16. Physiology: Coordinated Response, Chapters 32, 33, 34, 35 and 40
8.
Exam II and Organ System presentations
Filed under: Uncategorized | Tags: biology, philosophy of science, science, scientific method
Introduction to Biology and the Scientific Method
A. Biology and Life
Biology is the science that studies life. What is life?
Unlike non-living matter, living things exhibit the following properties:
Order: a hierarchical organization (a ‘nested hierarchy’, like Russian dolls). This means that organisms are composed of organs that work together in a systematic manner, the organs are composed of tissues, tissues of cells, cells of organelles, organelles of molecules and molecules of atoms, with the entire organization built in a way that maximizes the internal order, survival and reproduction of the organism.
Crystals exhibit order, but it is not hierarchical, and does not give the crystal a maximal chance of survival and reproduction. In living organisms, the properties of higher levels of organization cannot, unlike in crystals, be explained by the elements at the lower level of organization. Interactions between lower-level elements result in emergent properties at higher levels. For instance, from the order of nucleotides in the DNA we cannot infer how the whole organism looks like or behaves because the sequence does not specify the rules of interactions between the genes, gene-products (proteins), cells during development, and organisms inside their environments.
Sensitivity: response to stimuli in the environment. Even the simplest organisms, like bacteria, are capable of sensing changes in the environment and responding to such changes – they may swim away from or towards areas with higher concentrations of nutrients, salt, oxygen, or levels of illumination. Such responses (e.g., swimming) are active. A seed or a spore, seemingly “dead”, will actively respond to good growing conditions by germinating. A piece of dead matter may expand or even melt at high temperature, but that response is passive – due purely to the laws of physics.
Growth, Development and Reproduction: having a life-cycle. Crystals may grow, but the growth does not change the basic organization of the crystal. On the other hand, growth of an organism is accompanied by reorganization, cell division and cell differentiation. Each organism, at least during some parts of its life cycle, undergoes growth, developmental changes, and production of offspring. The results of reproduction – the offspring – are similar to the parent(s) due to the code inherited via a molecule, either DNA or RNA.
Regulation: All organisms have evolved well-orchestrated biochemical, physiological and behavioral mechanisms that regulate all the organism’s functions, which include finding and ingesting nutrients, processing nutrients and supplying all cells with the end-products of such processing, sequestering and eliminating the by-products of nutrient use. Likewise, every organism has evolved elaborate mechanisms for absorbing, storing, converting, using and dissipating energy – this last criterion may be the most important criterion for testing if something is alive or not, e.g., if one discovers a potentially living form on another planet.
Homeostasis: maintaining relatively constant internal conditions. We will cover this in much detail when we start the unit on human anatomy and physiology.
We will study the details of all five of the above criteria in this course. During the first three lectures, we will look at general properties of living organisms at all levels, from molecules, organelles and cells, through tissues, organs, systems and organisms, to populations, species, communities and ecosystems. During the remainder of the course we will take a look at specific cases: bacteria, protista, fungi, plants and animals, as well as details of the functioning of the human body.
A. Scientific Method and Process
Deductive reasoning applies general principles to predict specific results. Inductive reasoning uses specific observations to construct general principles. Here is a brief description of the steps in the hypothetico-deductive method:
Scientists make observations of processes and events found in nature.
The observations lead to questions: what is this, how does it work, why does it work the way it does? This may necessitate further observations to be made.
The questions are then asked in a form that suggests a possible explanation (hypothesis) for the observations. Scientists try to come up with all possible explanations and pit them against each others as alternative hypotheses.
Using the available knowledge and understanding of the related phenomena, the scientist makes a best guess at which of the alternative hypotheses is most likely to be correct.
Experiments are designed in such a way that one or more hypotheses are tested. This means that the experiment is geared specifically towards rejecting one’s favored hypothesis: it is directly testing if that hypothesis is wrong. If the results are positive, the favored hypothesis is not rejected, but the alternative hypotheses may be rejected. If the results are negative, the favored hypothesis is rejected and one or more of the alternative hypotheses are accepted and further directly tested.
Often, two experiments are conducted at the same time. In one experiment, all the variables are kept constant except one, while the other experiment is called the control experiment, and in that experiment, that variable is left unaltered. The results of the two experiments are compared to each other using statistical methods to determine if the tested variable (the one not kept constant) indeed has an effect on the outcome.
After performing a series of experiments, a paper is written that provides some background information, describes the experimental methods and results, provides the statistical analysis, and draws conclusions from the results. The paper is then submitted for peer review and published in a scientific journal. We will take a look at some real scientific papers later on in the course, so you can see the structure and form of it and be able to find and read such primary literature.
Once all but one alternative hypothesis has been rejected over a series of experiments, the one remaining hypothesis is further tested. The hypothesis, if correct, can be used to make predictions which can be directly tested in subsequent experiments. Predictions provide a way to test the validity of a hypothesis.
As more and more studies are done and the hypothesis gets stronger and stronger (as all possible alternatives get rejected), it grows in its predictive power and it may also grow in its ability to explain a broader range of phenomena. Once a hypothesis reaches the stage at which it is supported with large amounts of evidence after repeated testing, it becomes a theory.
A theory is a body of interconnected concepts most strongly supported by scientific reasoning and experimental evidence. It is a scientific term that is used to denote the scientific concepts that have stood the test of time and are best supported by experimental evidence.
This sense of the word “theory” – the scientific ideas with the greatest certainty that they are correct – is in contrast to the colloquial use of the term, which means almost opposite – lack of certainty (as in “it’s my theory that Secretariat was the greatest American athlete of all times”, or “it’s just a theory – nothing you should trust on its face”). Purveyors of pseudoscience (for financial, religious or political reasons) like to utilize the difference between the two senses of the word, dishonestly implying that a scientific theory they don’t like is uncertain when just the opposite is true.
The strongest theories are those that are supported by a wide variety of kinds of evidence. Theory of evolution is one of the best supported theories of all science not only because it is backed up by mountains of evidence (and no evidence against it), but also because the evidence comes from many different areas of science: paleontology (fossils), biogeography, ecology, mathematical modeling, population and quantitative genetics, comparative genomics, medicine, agricultural breeding, study of animal behavior, comparative anatomy, comparative physiology and comparative embryology.
The way disparate data from quite different areas of science, when put together, all strengthen a single theory, is called consilience. Recently, this word has been misused in popular literature (including a book of the same name) and press to mean quite the opposite – taking the methodology or findings from one discipline and applying it to a variety of other disciplines, e.g., taking the logic of evolution by natural selection and applying it to chemistry, pharmacology, psychology or computer science. That is a worthy endeavor, but it not a correct meaning of the term ‘consilience’.
Sometimes you will see (as opposed to the image on p.5 of your textbook) scientific method schematically depicted like this:
There are two reasons why the Biology textbook does not show a graph like this: a) it is not applicable to biology, and b) it is wrong.
It is wrong because it places “law” above the theory. Actually, the opposite is true – many laws (in physics, for instance) are elements of a greater theory and are parts of the evidence that the theory is correct. Laws are usually mathematical depictions of regular behavior of some aspect of nature. In other words, laws describe nature but do not explain it. Theories explain nature and are thus on the top of the hierarchy of scientific knowledge.
The model above is inapplicable to biology (it was probably drawn by a physicist) because there are no laws in biology. There are rules (like Bergmann-Allen Rule in ecology or Cope’s Rule in evolutionary biology), there are generalizations (e.g., Scaling), there are mathematical models (e.g., in population genetics) and there are Principles (e.g., the Principle of Natural Selection), but there are no laws. Biology deals with processes at much higher levels than does physics, where emergent properties of complex systems introduce a dose of unpredictability. All potential “laws” in biology have many exceptions, or have to be limited to a very small subset of processes, or to a small subset of organisms – they are not exception-less as laws of physics are.
Hypothetico-deductive method described above, while arguably the most powerful part of the scientific method, is not the only one. There is a continuum of scientific “methods” as depicted here (from Brandon 1996):
Collecting the information about all the species of birds and salamanders in the mountains of North Carolina is not a test of hypothesis and is not manipulative (and is not experimental) – yet it is certainly science (place a dot in the bottom right corner of the graph) – it provides important information about the natural world. If patterns emerge from such a survey and prompt new ideas about species distribution, this can then be tested in a more experimental fashion.
Human Genome Project is highly manipulative (and expensive!), yet it is not hypothesis-testing (place a dot in the bottom left corner). Nobody predicted that we would find anything but the four nucleotides known to make up DNA. We had no predictions as what the sequence will be and what would it all mean. Once the work was done, we could use the HGP as a tool for testing new hypotheses, e.g., how many genes do we have, how they are related to the genes of chimps, how diverse are particular gene sequences in human population as a whole, etc.
Paleontology is somewhere in the middle. It is somewhat manipulative (it takes hard work and a lot of people to do it) and it is somewhat hypothesis-testing (place a dot smack in the middle of the graph). Paleontologists do not dig randomly – they dig in particular places on the planet in particular layers of the sediment, looking for fossils of particular kinds of organisms. For instance, a group recently did an excavation in a particular bed of Late Silurian layer, looking specifically for a fossil of an early tetrapod, i.e., a transitional organism between fully aquatic and fully terrestrial mode of life. They discovered exactly that – a fossil named Tiktaalik whose fins were better suited for walking on land than that of fishes (like mudskippers, catfish and lungsfish), yet not completely evolved for land use as in amphibians.
Sometimes nature provides an experiment that tests a hypothesis (a dot in the top right corner). For instance, a biogeographical model of island succession was tested when the volcano Krakatoa erupted and eliminated all life from the island. The scientists went there and observed which organisms flew in from the mainland, in which order, and how the ecosystem passed through several stages until it reached its mature stage, thus confirming (and somewhat modifying) their hypotheses.
No matter how strongly a theory is supported by empirical evidence, it is always theoretically conceivable that one day, some data will come in that will force the scientists to modify or even eliminate the theory. Even if the scientists are 99.999999999999999999999999999999999% certain that the theory is true, it is philosophically incorrect to say that it is 100% true and to call it the Truth with the capital T. That is why scientists, when interviewed in the media, often sound uncertain and wishy-washy, while some quack or pseudoscientist pronounces his absolute certainty. Audience not educated in the scientific method is likely to swallow the pseudoscience bait, hook and sinker because we, as humans, crave certainty. It takes some scientific training to be able to fully embrace and even love uncertainty. That is why it is difficult for scientific knowledge to counteract financially, religiously and politically motivated assaults on it. However, nature does not care about what we like and wish for: the apples will continue to fall down, the continents will continue to move around the globe (causing earthquakes and volcanic eruptions) and the organisms will continue to evolve whether we like it or not, whether we believe in it or not.
References:
Audesirk, Audesirk and Byers, Biology, 8th edition., Chapter 1
Figure 1 from:
Earth Sciences 10, Lecture 1: Scientific Method by Greg Anderson
Figure 2 from:
Brandon, RN, Does biology have laws? The experimental evidence. PSA 1996, vol. 2, 444–457.
Filed under: Uncategorized | Tags: biology, cell structure, organelles, science
All living organisms are composed of one or more cells – the cell is the unit of organization of Life.
Most cells are very small. Exceptions? Ostrich egg is the largest cell. Nerve cell in a leg of a giraffe may be as long as 3m, but is very thin.
Basic Structure of the Cell
A cell is a small packet or bag of liquid. The liquid is cytoplasm (or cytosol), which is essentially salty water with various organic molecules suspended in it.
The cytoplasm is contained within a cell membrane. Cell membrane is a phospholypid bilayer – this means that it is composed of two layers of tighly packed molecules of fat. Within the membrane, proteins are embedded into the bilipid layer and are more or less free to move around within the membrane. These proteins are important for the communication between the inside and outside of the cell.
You can see a good image here.
On the outside of the membrane, some cells may have additional structures. For instance, many bacterial and plant cells have thick cell walls that confer more rigidity to the cell as well as better defense against mechanical, chemical or biological insults.
Some cells also have hair-like cilia on the surface (e.g., a protist called Silver Slipper), or long whip-like flagella at one end (e.g., sperm cells). Both of these structures allow the cell to move utilizing its own energy.
Inside every cell, there is hereditary material – DNA. Exceptions? Red blood cells which have a membrane and cytoplasm, but no hereditary material.
Differences between prokaryotes and eukaryotes:
Prokaryotes (bacteria) have a cell membrane and cytoplasm and no other organelles.
Eukaryotes (plants, animals, fungi, protista) have a number of different cell organelles.
The nuclear material in Prokaryotes is a single, circular strand of DNA.
The nuclear material in Eukaryotes is organized in multiple chromosomes contained with a nucleus.
Cell Organelles
Eukaryotic cells have organelles. Organelles are subcellular structures that provide internal compartmentalization and other functions.
Nuclues is a large membrane-bound organelle. Its function is to sequester the DNA from the rest of the cell. The nuclear membrane (or nuclear envelope), which is also a phospholipid bilayer, selectively allows molecules to pass between the nucleus and cytoplasm. Inside the nucleus, DNA is organized in chromosomes. A chromosome is a tighly coiled and wound strand of DNA packaged with various proteins (e.g,. histones).
Smooth endoplasmic reticulum is a system of membranes and is involved in carbohydrate and lipid synthesis.
Rough endoplasmic reticulum is a system of membranes that possesses ribosomes. Proteins are synthesized in the rough ER.
Golgi apparatus stores and packages various molecules. When a molecule is needed elsewhere in the cell, a portion of the Golgi membrane closes off and forms a vesicle that can be transported around the cell.
Some eukaryotic organelles contain a little bit of their own DNA: the mitochondria and the chloroplasts. These two organelles used to be intercellular parasites, i.e., different species of bacteria that, over time, became an integral part of a cell.
Chloroplasts are found in plant cells. Photosynthesis is the process that occurs in them.
Mitochondria are found in all Eukaryotic cells. Breakdown of glucose begins in the cytoplasm and ends in the mitochondria, where the final products of the breakdown are ATP, water, CO2 and heat. This process requires oxygen – that is why we breath: to provide the oxygen for the mitochodria and to get rid of carbon dioxide produced in the mitochondria.
ATP (adenosine triphosphate) is the energy currency of the living world. Every cellular process that requires energy gets it from ATP. Thus, mitochondria are sometimes refered to as “factories of the cell”.
The final portion of the process of glucose digestion (the Krebs cycle) is, like any process, not 100% efficient. Errors happen and not every atom of every glucose molecule ends up where it should: in ATP, water or CO2. The result of this inefficiency is production of heat and production of highly reactive small molecules called free radicals (e.g., hydrogen peroxyde, H2O2). Free radicals tend to quickly react with whatever molecule they first encounter upon leaving the mitochondria. Such reactions damage those molecules, be they proteins, lipids, sugars or nucleic acids. The intercellular damage caused by free radicals is one aspect of the process of aging.
Some animals – birds and mammals – have harnessed the heat production by the mitochondria to keep a stable internal temperature. The efficiency of the mitochondrial “machine” is held low under the control of hormones like thyroid hormones. As a result, there is a greater production of free radicals, so warm-blooded animals evolved particularly good mechanisms for neutralizing free radicals and for repairing the damage. If a person keeps a constant low temperature or constant low-grade fever, the first thing the physician will check is the function of the thyroid gland.
The cytoskeleton, composed of filaments and microtubules, anchors the organelles and gives a cell its shape. Microtubules move organelles, including vesicles, within a cell. They also move the membrane-embedded proteins around where they are needed.
References:
Audesirk, Audesirk and Byers, Biology, 8th edition., Chapter 4
Check this video on YouTube:
Filed under: Uncategorized | Tags: biology, cell, DNA, protein, RNA, science, transcription, translation
The DNA code
DNA is a long double-stranded molecule residing inside the nucleus of every cell. It is usually tightly coiled forming chromosomes in which it is protected by proteins.
Each of the two strands of the DNA molecule is a chain of smaller molecules. Each link in the chain is composed of one sugar molecule, one phosphate molecule and one nucleotide molecule. There are four types of nucleotides (or ‘bases’) in the DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). The two strands of DNA are structured in such a way that an adenine on one strand is always attached to a thymine on the other strand, and the guanine of one strand is always bound to cytosine on the other strand. Thus, the two strands of the DNA molecule are mirror-images of each other.
The exact sequence of nucleotides on a DNA strand is the genetic code. The total genetic code of all of the DNA on all the chromosomes is the genome. Each cell in the body has exactly the same chromosomes and exactly the same genome (with some exceptions we will cover later).
A gene is a small portion of the genome – a sequence of nucleotides that is expressed together and codes for a single protein (polypeptide) molecule.
Cell uses the genes to synthetise proteins. This is a two-step process. The first step is transcription in which the sequence of one gene is replicated in an RNA molecule. The second step is translation in which the RNA molecule serves as a code for the formation of an amino-acid chain (a polypeptide).
Transcription
For a gene to be expressed, i.e., translated into RNA, that portion of the DNA has to be uncoiled and freed of the protective proteins. An enzyme, called DNA polymerase, reads the DNA code (the sequence of bases on one of the two strands of the DNA molecule) and builds a single-stranded chain of the RNA molecule. Again, where there is a G in DNA, there will be C in the RNA and vice versa. Instead of thymine, RNA has uracil (U). Wherever in the DNA strand there is an A, there will be a U in the RNA, and wherever there is a T on the DNA molecule, there will be an A in the RNA.
Once the whole gene (100s to 10,000s of bases in a row) is transcribed, the RNA molecule detaches. The RNA (called messenger RNA or mRNA) may be further modified by addition of more A bases at its tail, by addition of other small molecules to some of the nucleotides and by excision of some portions (introns) out of the chain. The removal of introns (the non-coding regions) and putting together the remaining segments – exons – into a single chain again, is called RNA splicing. RNA splicing allows for one gene to code for multiple related kinds of proteins, as alternative patterns of splicing may be controlled by various factors in the cell.
Unlike DNA, the mRNA molecule is capable of exiting the nucleus through the pores in the nuclear membrane. It enters the endoplasmatic reticulum and attaches itself to one of the membranes in the rough ER.
Translation
Three types of RNA are involved in the translation process: mRNA which carries the code for the gene, rRNA which aids in the formation of the ribosome, and tRNA which brings individual amino-acids to the ribosome. Translation is controlled by various enzymes that recognize specific nucleotide sequences.
The genetic code (nucleotide sequence of a gene) translates into a polypeptide (amino-acid sequence of a protein) in a 3-to-1 fashion. Three nuclotides in a row code for one amino-acid. There are a total of 20 amino-acids used to build all proteins in our bodies. Some amino-acids are coded by a single triplet code, or codon. Other amino-acids may be coded by several different RNA sequences. There is also a START sequence (coding for fMet) and a STOP sequence that does not code for any amino-acid. The genetic code is (almost) universal. Except for a few microorganisms, all of life uses the same genetic code.
When the ribosome is assembled around a molecule of mRNA, the translation begins with the reading of the first triplet. Small tRNA molecules bring in the individual amino-acids and attach them to the mRNA, as well as to each other, forming a chain of amino-acids. When a stop signal is reached, the entire complex disassociates. The ribosome, the mRNA, the tRNAs and the enzymes are then either degraded or re-used for another translational event.
Protein synthesis – post-translational modifications
Translation of the DNA/RNA code into a sequence of amino-acids is just the beginning of the process of protein synthesis.
The exact sequence of amino-acids in a polypeptide chain is the primary structure of the protein.
As different amino-acids are molecules of somewhat different shapes, sizes and electrical polarities, they react with each other. The attractive and repulsive forces between amino-acids cause the chain to fold in various ways. The three-dimensional shape of the polypeptide chain due to the chemical properties of its component amino-acids is called the secondary structure of the protein.
Enzymes called chaperonins further modify the three-dimensional structure of the protein by folding it in particular ways. The 3D structure of a protein is its most important property as the functionality of a protein depends on its shape – it can react with other molecules only if the two molecules fit into each other like a key and a lock. The 3D structure of the fully folded protein is its tertiary structure.
Prions, the causes of such diseases as Mad Cow Disease, Scabies and Kreutzfeld-Jacob disease, are proteins. The primary and secondary structure of the prion is almost identical to the normally expressed proteins in our brain cells, but the tertiary structure is different – they are folded into different shapes. When a prion enters a healthy brain cell, it is capable of denaturing (unwinding) the native protein and then reshaping it in the same shape as the prion. Thus one prion molecule makes two – those two go on and make four, those four make eight, and so on, until the whole brain is just one liquifiied spongy mass.
Another aspect of the tertiary structure of the protein is addition of small molecules to the chain. For instance, phosphate groups may be attached to the protein (giving it additional energy). Also, short chains of sugars are usually bound to the tail-end of the protein. These sugar chains serve as “ZIP-code tags” for the protein, informing carrier molecules exactly where in the cell this protein needs to be carried to (usually within vesicles that bud off the RER or the Golgi apparatus). The elements of the cytoskeleton are used as conduits (“elevators and escalators”) to shuttle proteins to where in the cell they are needed.
Many proteins are composed of more than one polypeptide chain. For instance, hemoglobin is formed by binding together four subunits. Each subunit also has a heme molecule attached to it, and an ion of iron attached to the heme (this iron is where oxygen binds to hemogolobin). This larger, more complex structure of the protein is its quaternary structure.
See animations:
Transcription
Translation
Watch videos:
DNA Structure
DNA Transcription
References:
Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 9 and 10.
