2: The Nature and Process of Science - Biology

2: The Nature and Process of Science - Biology

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This chapter explains how scientists think and how they "do" science. The chapter also explains how science may be misused and how and why human subjects are protected in scientific research.

Thumbnail: This image describes the Scientific Method as a cyclic/iterative process of continuous improvement. Image used with permission (Public Domain).

The nature of science

Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids.

Part of the universality of life is the observation that all living organisms construct proteins out of the same pool of 20 amino acids. These 20 were identified in a rapid era of discovery after the development of partition chromatography in 1943. However, this has now been expanded to include two additional amino acids – selenocysteine and pyrrolysine, giving a total of 22 amino acids.

Selenocysteine, as the name suggests, is similar to the amino acid cysteine but it has a Selenium atom as part of its side-chain (R-Group). It is a highly reactive and potentially dangerous substance – cells have to use some tricky metabolic pathways in order to prevent it from moving freely and building up in the cytoplasm. It is used in certain redox reactions and has been found in all three domains of life, although it is not universal amongst them

Pyrrolysine is rarer, having only been found in some species of Archaeans and bacteria. It is structurally similar to lysine, but with the addition of a a pyrroline ring to the side-chain. It’s role and possible existence in other organisms is the focus of many ongoing studies.

Both of these amino acids are not encoded in the DNA – they are instead encoded by the stop codons UGA for selenocysteine and UAG for pyrrolysine and expressed via interactions with specific tRNA molecules, a process known as cotranslation. The biochemistry involved is fairly complex and difficult to summarise for IB biology purposes, but if you are interested the links below are a good place to start.

  • all living organisms use the traditional 20 amino acids to construct proteins and code for these amino acids in their DNA
  • all three domains of life (thought not every species in them) also use a 21st amino acid selenocysteine in some proteins (humans included)
  • Archaeans and bacteria have developed a mechanism to use a 22nd amino acid, pyrrolysine.
  • both of these amino acids are not coded for in the DNA but are expressed through the use of a stop codon and tRNA
  • the presence of Selenocysteine in all three domains strongly suggests it was present in the last universal common ancestor, and is thus a very ancient biochemical pathway

Selenocysteine and pyrrolysine are powerful examples of the versatility inherent in the genetic code. (Rother and Krzycki).

Like so many aspects of biology, once a rule is determined, the incredible variety of life shows us an exception.

For an interesting TOK-linked discussion, consider this quote, also from the Rother/Krzycki article:

They further provide examples of how precedent, though valuable, is not always the best predictor in scientific investigation…

What do the authors mean by this? Does this mean that inductive reasoning is not always a reliable form of reason? What other examples from science can you think of to illustrate this quote?

Das, Gunajyoti & Mandal, Shilpi. (2013). Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides. Biochemistry research international. ResearchGate. Accessed on 2 October, 2018

Dinmann, J. (2012). Control of gene expression by translational recoding. Advances in Protein Chemistry and Structural Biology via ScienceDirect. Accessed on 2 October, 2018.

Gutiérrez-Preciado, A., Romero, H. & Peimbert, M. (2010) An Evolutionary Perspective on Amino Acids. Nature Education. Accessed on 2 October, 2018.

Rother, Michael, and Joseph A. Krzycki. “Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea.” Archaea 2010 (2010): 453642. PMC. Web. 2 Oct. 2018.

Traditional approaches to teaching science

The root of the problem goes far deeper than our interaction over the course of the year. Throughout school, science is often portrayed in textbooks and even in the classroom as a series of "known" facts and figures for example, electrons are negatively charged, DNA is a double helix, earthquakes occur at plate boundaries, etc. Unfortunately, the process by which these discoveries were made and how they fit into scientific progress is often ignored in the classroom.

Figure 1: J.J. Thomson (1856 - 1940), a British physicist and Nobel laureate credited for discovering the electron.

Even when material is added to science lectures about the discovery of these concepts, they are often presented as an obvious and inevitable conclusion. For example, J.J. Thomson's experiments with a cathode ray tube are commonly discussed in chemistry classes (Figure 1). Few teachers present the critical components of the process that humanize Thomson, however, like the fact that when Thomson first presented his ideas on electron charge to the scientific community, a colleague asked him if he was joking! These details help illustrate the nature of scientific discoveries, the skepticism that accompanies new discoveries, and the process of review and validation they undergo before they are accepted. Yet this is rarely conveyed in the classroom along with the content, so it's no wonder these ideas seem like inevitable conclusions.

So where do we learn about how science is practiced? Those fortunate enough to be exposed to scientific research begin to understand because they are engaging in the process of science. After my experience with this student, we discussed the idea that science is not just a collection of known facts but a process by which we come to know things about the natural world. We discussed the purpose of experimentation, the role of reviewing the existing literature to identify possible research hypotheses, and the need to remain open to various interpretations of the data. Participating in mentored research is one way to learn how science is practiced.

This student went on to complete and publish her research, enroll in a PhD program, and become a qualified scientist in her own right (Mauclair, Layshock, & Carpi, 2008). When asked recently, she did not recall this specific interaction, but she did recall that despite having "The Scientific Method" drilled into her in many science classes, she had little understanding of what science entailed before her undergraduate research experience.

Natural Sciences

What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, computer sciences, psychology,biology, and mathematics. However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences and include the disciplines of physics, geology, biology, and chemistry. Environmental science is a cross-disciplinary natural science because it relies of the disciplines of chemistry, biology, and geology.


A variable is any part of the experiment that can vary or change during the experiment. Typically, an experiment only tests one variable and all the other conditions in the experiment are held constant.

  • The variable that is tested is known as the independent variable.
  • The dependent variable is the thing (or things) that you are measuring as the outcome of your experiment.
  • A constant is a condition that is the same between all of the tested groups.
  • A confounding variable is a condition that is not held constant that could affect the experimental results.

A hypothesis often has the format “If [I change the independent variable in this way] then [I will observe that the dependent variable does this] because [of some reason].” For example, the first hypothesis might be, “If you change the light bulb, then the light will turn on because the bulb is burned out.” In this experiment, the independent variable (the thing that you are testing) would be changing the light bulb and the dependent variable is whether or not the light turns on. It would be important to hold all the other aspects of the environment constant, for example not messing with the lamp cord or trying to turn the lamp on using a different light switch. If the entire house had lost power during the experiment because a car hit the power pole, that would be a confounding variable.

You may have learned that a hypothesis can be phrased as an “If..then…” statement. Simple hypotheses can be phrased that way (but they must also include a “because”), but more complicated hypotheses may require several sentences. It is also very easy to get confused by trying to put your hypothesis into this format. Hypotheses do not have to be phrased as “if..then..” statements, it is just sometimes a useful format.

Scientists think of nature as a single system controlled by natural laws. By discovering natural laws, scientists strive to increase their understanding of the natural world. Laws of nature are expressed as scientific laws. A scientific law is a statement that describes what always happens under certain conditions in nature.

Science is both a process and body of knowledge. Scientific knowledge is generated through systematic processes, such as observation and experimentation. Scientists are always testing and revising their ideas, and as new observations are made, existing ideas may be challenged. Ideas may be replaced with new ideas that better fit the facts, but more often, existing ideas are simply revised. Through many new discoveries over time, scientists gradually build an increasingly accurate and detailed understanding of the natural world.

Science, Evolution, and Creationism (2008)

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C h a p t e r O n e Evolution and the Nature of Science The scientific evidence supporting biological evolution continues to grow at a rapid pace. For more than a century and a half, scientists have been gathering evidence that expands our understanding of both the fact and the processes of biological evolution. They are investigating how evolution has occurred and is continuing to occur. In 2004, for example, a team of researchers made a remarkable discovery. On an island in far northern Canada, they found a four-foot-long fossil with features intermediate between those of a fish and a four-legged animal. It had gills, scales, and fins, and it probably spent most of its life in the water. But it also had lungs, a flexible neck, and a sturdy fin skeleton that could support its body in very shallow water or on land. Earlier scientific discoveries of fossilized plants and animals had already revealed a considerable amount about the environment in which this creature lived. About 375 million years ago, what is now Ellesmere Island in Nunavut Territory, Canada, was part of a broad plain crossed by many meandering streams. Trees, ferns, and other ancient plants grew on the banks of the streams, [Species: In sexual­ ly reproducing organ­ creating a rich environment for bacteria, fungi, and simple animals that fed on isms, species consist decaying vegetation. No large animals yet lived on the land, but Earth’s oceans of individuals that can contained many species of fish, and some of those species fed on the plants and interbreed with each animals in shallow freshwater streams and swamps. other.] Science, Evolution, and Creationism 

[Paleontologist: Paleontologists had previously found the fossils of some of these shallow- A scientist who water fishes. The bones in their fins were sturdier and more complex than in studies fossils to other fish species, perhaps allowing them to pull themselves through plant- learn about ancient filled channels, and they had primitive lungs as well as gills. Paleontologists organisms.] had also found, in somewhat younger sediments, fossils of fishlike animals that likely spent part of their time on land. Known as early tetrapods (a Paleontologists word referring to their four legs), they had modified front and back fins that searched this valley in Nunavut, near the resembled primitive legs and other features suited for life out of the water. But Arctic Circle in north paleontologists had not found fossils of the transitional animals between shal- central Canada, for low-water fishes and limbed animals. fossils when they learned that it con- The team that discovered the new fossil decided to focus on far northern tained sedimentary Canada when they noticed in a textbook that the region contained sedimentary rocks deposited dur- rock deposited about 375 million years ago, just when shallow-water fishes ing the period when were predicted by evolutionary science to be making the transition to land. The limbed animals were first starting to live team had to travel for hours in planes and helicopters to reach the site, and they on land. Fossils of could work for just a couple of months each summer before snow began to fall. Tiktaalik were dis- In their fourth summer of fieldwork they found what they had predicted they covered on the dark would find. In an outcropping of rock on the side of a hill, they uncovered the outcropping of rock on the right side of fossil of a creature that they named Tiktaalik. (The name means “big freshwater this photograph. fish” in the language of the Inuit of northern Canada.) Tiktaalik still had many site of fossils Tiktaalik’s left and right fins had a single upper bone (the large bone at the bot- tom of each of these drawings) followed by two intermediate bones, giving the creature an elbow and a wrist, as in more recent organisms.  Science, Evolution, and Creationism

Tiktaalik lived during the period when freshwa- ter fishes were evolving Ichthyostega the adaptations that enabled four-legged animals to live out of water. Tiktaalik may have Tiktaalik lived somewhat before or somewhat after the ancestral species that gave rise to all of today’s limbed animals, including Panderichthys humans. The evolution- ary lineage that contained Tiktaalik may have gone extinct, as shown in this diagram by the short line branching from the main evolutionary lineage, or it may have been part of the evolutionary line leading to all modern tetrapods (animals with four legs). The last com- mon ancestor of humans and all modern fishes also gave rise to evolution- ary lineages that led to modern lobe-finned fishes of the features of fish, but it also had traits characteristic of early tetrapods. (represented today by Most important, its fins contained bones that formed a limb-like appendage that the coelacanth). In this and succeeding figures, the animal could use to move and prop itself up. time is represented by the A prediction from more than a century of findings from evolutionary biol- lengths of the lines mod- ogy suggests that one of the early species that emerged from the Earth’s oceans ern groups of organisms about 375 million years ago was the ancestor of amphibians, reptiles, dino- are listed at the top of the figure. saurs, birds, and mammals. The discovery of Tiktaalik strongly supports that prediction. Indeed, the major bones in our own arms and legs are similar in overall configuration to those of Tiktaalik. The discovery of Tiktaalik, while critically important for confirming predic- tions of evolution theory, is just one example of the many findings made every year that add depth and breadth to the scientific understanding of biological evolution. These discoveries come not just from paleontology but also from physics, chemistry, astronomy, and fields within biology. The theory of evolu- tion is supported by so many observations and experiments that the overwhelm- ing majority of scientists no longer question whether evolution has occurred and continues to occur and instead investigate the processes of evolution. Scientists are confident that the basic components of evolution will continue to be sup- ported by new evidence, as they have been for the past 150 years. Science, Evolution, and Creationism 

Biological evolution is the central organizing principle of modern biology. [Trait: A physical The study of biological evolution has transformed our understanding of life or behavioral on this planet. Evolution provides a scientific explanation for why there are so characteristic of many different kinds of organisms on Earth and how all organisms on this plan- an organism.] et are part of an evolutionary lineage. It demonstrates why some organisms [DNA: Deoxyribo­ that look quite different are in fact related, while other organisms that may look nucleic acid. A biolog­ similar are only distantly related. It accounts for the appearance of humans on ical molecule composed Earth and reveals our species’ biological connections with other living things. It of subunits known details how different groups of humans are related to each other and how we as nucleotides strung acquired many of our traits. It enables the development of effective new ways together in long chains. to protect ourselves against constantly evolving bacteria and viruses. The sequences of these nucleotides contain the Biological evolution refers to changes in the traits of organisms over multiple information that cells generations. Until the development of the science of genetics at the beginning need in order to grow, of the 20th century, biologists did not understand the mechanisms responsible to divide into daughter for the inheritance of traits from parents to offspring. The study of genetics cells, and to manufac­ showed that heritable traits originate from the DNA that is passed from one ture new proteins.] generation to the next. DNA contains segments called genes that direct the pro- [Protein: A large duction of proteins required for the growth and function of cells. Genes also molecule consisting of orchestrate the development of a single-celled egg into a multicellular organism. a chain of smaller mol­ DNA is therefore responsible for the continuity of biological form and function ecules called amino across generations. acids. The sequence However, offspring are not always exactly like their parents. Most organ- of amino acids and isms in any species, including humans, are genetically variable to some extent. the molecule’s three- dimensional structure In sexually reproducing species, where each parent contributes only one-half determine a protein’s of its genetic information to its offspring (the offspring receives the full amount specific function in of genetic information when a sperm cell and an egg cell fuse), the DNA of the cells or organisms.] two parents is combined in new ways in the offspring. In addition, DNA can undergo changes known as mutations from one generation to the next, both in [Mutation: A change sexually reproducing and asexually reproducing organisms (such as bacteria). in the sequence of nucleotides in DNA. When a mutation occurs in the DNA of an organism, several things can Such changes can alter happen. The mutation may result in an altered trait that harms the organism, the structure of pro­ making it less likely to survive or produce offspring than other organisms in teins or the regulation the population to which it belongs. Another possibility is that the mutation of protein production.] makes no difference to the well-being or reproductive success of an organ- ism. Or the new mutation may result in a trait that enables an organism to [Population: A group of organisms take better advantage of the resources in its environment, thereby enhancing of the same species that its ability to survive and produce offspring. For example, a fish might appear are in close enough with a small modification to its fins that enables it to move more easily through proximity to allow shallow water (as occurred in the lineage leading to Tiktaalik) an insect might them to interbreed.]  Science, Evolution, and Creationism

acquire a different shade of color that enables it to avoid being seen by preda- tors or a fly might have a difference in its wing patterns or courtship behav- iors that more successfully attracts mates. If a mutation increases the survivability of an organism, that organism is like- ly to have more offspring than other members of the population. If the offspring inherit the mutation, the number of organisms with the advantageous trait will increase from one generation to the next. In this way, the trait — and the genetic material (DNA) responsible for the trait — will tend to become more common in a population of organisms over time. In contrast, organisms possessing a harmful or deleterious mutation are less likely to contribute their DNA to future generations, and the trait resulting from the mutation will tend to become less frequent or will be eliminated in a population. Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms. The differential reproductive success of organisms with advantageous traits is known as natural selection, because nature “selects” traits that enhance [Natural selection: the ability of organisms to survive and reproduce. Natural selection also can Differential survival reduce the prevalence of traits that diminish organisms’ abilities to survive and reproduction of organisms as a and reproduce. Artificial selection is a similar process, but in this case humans consequence of the rather than the environment select for desirable traits by arranging for animals characteristics of the or plants with those traits to breed. Artificial selection is the process responsible environment.] for the development of varieties of domestic animals (e.g., breeds of dogs, cats, and horses) and plants (e.g., roses, tulips, corn). Evolution in Medicine: Combating New Infectious Diseases In late 2002 several hundred Immediately, work began on a people in China came down blood test to identify people with with a severe form of pneu- the disease (so they could be monia caused by an unknown quarantined), on treatments for infectious agent. Dubbed the disease, and on vaccines to “severe acute respiratory syn- prevent infection with the virus. drome,” or SARS, the disease An understanding of evolu- soon spread to Vietnam, Hong tion was essential in the identi- Kong, and Canada and led to fication of the SARS virus. The hundreds of deaths. In March genetic material in the virus 2003 a team of researchers at was similar to that of other the University of California, San viruses because it had evolved Francisco, received samples of from the same ancestor virus. a virus isolated from the tissues of a SARS patient. Furthermore, knowledge of the evolutionary history Using a new technology known as a DNA micro­ of the SARS virus gave scientists important informa- array, within 24 hours the researchers had identi- tion about the disease, such as how it is spread. fied the virus as a previously unknown member of Knowing the evolutionary origins of human patho- a particular family of viruses — a result confirmed gens will be critical in the future as existing infectious by other researchers using different techniques. agents evolve into new and more dangerous forms. Science, Evolution, and Creationism 

Evolution in Agriculture: The Domestication of Wheat When humans understand a phenomenon that wild wheat so that seeds remained on the plant occurs in nature, they often gain increased control when ripe and could easily be separated from their over it or can adapt it to new uses. The domesti- hulls. Over the next few millennia, people around cation of wheat is a good example. the world used similar processes of evolution- By recovering seeds from dif- ary change to transform many other ferent archaeological sites and wild plants and animals into the noticing changes in their char- crops and domesticated animals acteristics over the centuries, we rely on today. scientists have hypothesized In recent years, plant sci- how wheat was altered by entists have begun making humans over time. About hybrids of wheat with some 11,000 years ago, people of their wild relatives from in the Middle East began the Middle East and else- growing plants for food where. Using these hybrids, rather than relying entirely they have bred wheat varieties on the wild plants and ani- that are increasingly resistant mals they could gather or hunt. to droughts, heat, and pests. These early farmers began sav- Most recently, molecular biologists ing seeds from plants with particu- have been identifying the genes in larly favorable traits and planting those the DNA of plants that are responsible for seeds in the next growing season. Through this their advantageous traits so that these genes can process of “artificial selection,” they created a be incorporated into other crops. These advances variety of crops with characteristics particularly rely on an understanding of evolution to analyze suited for agriculture. For example, farmers the relationships among plants and to search for over many generations modified the traits of the traits that can be used to improve crops. Evolution can result in both small and large changes in populations of organisms. Evolutionary biologists have discovered structures, biochemical processes and pathways, and behaviors that appear to have been highly conserved within and across species. Some species have undergone little overt change in their body structure over many millions of years. At the level of DNA, some genes that control the production of biochemicals or chemical reactions that are essential for cellular functioning show little variation across species that are only distantly related. (See, for example, the DNA sequences for two different genes that are conserved in closely related as well as more distantly related species that are described on pages 30 and 31.) However, natural selection also can have radically different evolutionary effects over different timescales. Over periods of just a few generations (or,  Science, Evolution, and Creationism

in some documented cases, even a single generation), evolution produces relatively small-scale microevolutionary changes in organisms. For example, [Microevolution: many disease-causing bacteria have been evolving increased resistance to anti- Changes in the traits biotics. When a bacterium undergoes a genetic change that increases its ability of a group of organ­ isms that do not result to resist the effects of an antibiotic, that bacterium can survive and produce in a new species.] more copies of itself while nonresistant bacteria are being killed. Bacteria that cause tuberculosis, meningitis, staph infections, sexually transmitted diseases, and other illnesses have all become serious problems as they have developed resistance to an increasing number of antibiotics. Another example of microevolutionary change comes from an experiment on the guppies that live in the Aripo River on the island of Trinidad. Guppies that live in the river are eaten by a larger species of fish that eats both juveniles and adults, while guppies that live in the small streams feeding into the river are eaten by a smaller fish that preys primarily on small juveniles. The guppies in the river mature faster, are smaller, and give birth to more and smaller offspring than the guppies in the streams do because guppies with these traits are better able to avoid their predator in the river than are larger guppies. When guppies were taken from the river and introduced into a stream without a preexisting population of guppies, they evolved traits like those of the stream guppies within about 20 generations. Incremental evolutionary changes can, over what are usually very long Studies of guppies in Trinidad have demon- periods of time, give rise to new types of organisms, including new species. strated basic evolution- The formation of a new species generally occurs when one subgroup within a ary mechanisms. species mates for an extended period largely within the subgroup. For exam- ple, a subgroup may become geographically separated from the rest of the species, or a subgroup may come to use resources in a way that sets them apart from other members of the same species. As members of the subgroup mate among themselves, they accumulate genetic differences compared with the rest of the species. If this reproductive isolation continues for an extended period, How long could it take to produce 1,000 generations? How many generations might occur in a million years? 1 Generation 1,000 Generations Generations per 1 million years Bacteria 1 hour to 1 day 1,000 hours (42 days) to 2.7 years 8.7 billion to 370.4 million Pets: dog/cat 2 years 2,000 years 500,000 Humans 22 years 22,000 years 45,000 Science, Evolution, and Creationism 

members of the subgroup may no longer respond to court- ship or other signals from members of the original population. Eventually, genetic changes will become so substantial that the members of different subgroups can no longer produce viable offspring even if they do mate. In this way, existing species can continually “bud off” new species. Over very long periods of time, continued instances of speciation can produce organisms that are very different from their ancestors. Though each new species resembles the species from which it arose, a succession of new species can diverge more and more from an ancestral form. This divergence from an ancestral form can be especially dramatic when an evolu- tionary change enables a group of organisms to occupy a new habitat or make use of resources in a novel way. Consider, for example, the continued evolution of the tet- When tetrapods (such rapods after limbed animals began living on land. As new species of plants as this sea turtle laying evolved and covered the Earth, new species of tetrapods appeared with features its eggs on a coastal beach) evolved the abil- that enabled them to take advantage of these new environments. The early tetra- ity to lay hard-shelled pods were amphibians that spent part of their lives on land but continued to lay eggs, they no longer their eggs in the water or in moist environments. The evolution about 340 million had to return to the years ago of amniotic eggs, which have structures such as hard or leathery shells water to reproduce. The last common ances- tor of the four-legged animals living today gave rise to amphibians and was the predeces- sor of reptiles. Birds and mammals evolved from different lineages of ancient reptiles.  Science, Evolution, and Creationism

Evolution in Industry: Putting Natural Selection to Work The concept of natural selection has been applied in many fields outside biology. For example, chemists have applied principles of natural selection to develop new molecules with specific functions. First they create variants of an existing molecule using chemi- cal techniques. They then test the variants for the desired function. The variants that do the best job are used to generate new variants. Repeated rounds of this selection process result in molecules that have a greatly enhanced ability to perform a given task. This technique has been used to create new enzymes that can convert cornstalks and other agricultural wastes into ethanol with increased efficiency. and additional membranes that allow developing embryos to survive in dry environments, was one of the key developments in the evolution of the reptiles. The early reptiles split into several major lineages. One lineage led to reptiles, including dinosaurs, and also to birds. Another lineage gave rise to mammals between 200 million and 250 million years ago. The evolutionary transition from reptiles to mammals is particularly well documented in the fossil record. Successive fossil forms tend to have larger brains and more specialized sense organs, jaws and teeth adapted for more efficient chewing and eating, a gradual movement of the limbs from the sides of the body to under the body, and a female reproductive tract increasingly able to support the internal development and nourishment of young. Many of the biological novelties seen in mammals may be associated with the evolution of warm-bloodedness, which enabled a more active lifestyle over a much larger range of temperatures than in the cold-blooded reptilian ancestors. Then, between 60 million and 80 million years ago, a group of mammals known as the primates first appeared in the fossil record. These mammals had grasping hands and feet, frontally directed eyes, and even larger and more complex brains. This is the lineage from which ancient and then modern humans evolved. Science, Evolution, and Creationism 

Scientists seek explanations of natural phenomena based on empirical evidence. Advances in the understanding of evolution over the past two centuries provide a superb example of how science works. Scientific knowledge and understanding accumulate from the interplay of observation and explanation. Scientists gather information by observing the natural world and conducting experiments. They then propose how the systems being studied behave in general, basing their explanations on the data provided through their experi- ments and other observations. They test their explanations by conducting additional observations and experiments under different conditions. Other scientists confirm the observations independently and carry out additional studies that may lead to more sophisticated explanations and predictions about future observations and experiments. In these ways, scientists continu- ally arrive at more accurate and more comprehensive explanations of particu- lar aspects of nature. In science, explanations must be based on naturally occurring phenomena. Natural causes are, in principle, reproducible and therefore can be checked independently by others. If explanations are based on purported forces that are outside of nature, scientists have no way of either confirming or disprov- ing those explanations. Any scientific explanation has to be testable — there must be possible observational consequences that could support the idea but also ones that could refute it. Unless a proposed explanation is framed in a way that some observational evidence could potentially count against it, that explanation cannot be subjected to scientific testing. Definition of Science The use of evidence to construct testable explanations and predictions of natural phenomena, as well as the knowledge generated through this process. Because observations and explanations build on each other, science is a cumulative activity. Repeatable observations and experiments generate expla- nations that describe nature more accurately and comprehensively, and these explanations in turn suggest new observations and experiments that can be used to test and extend the explanation. In this way, the sophistication and scope of scientific explanations improve over time, as subsequent generations of scientists, often using technological innovations, work to correct, refine, and extend the work done by their predecessors. 10 Science, Evolution, and Creationism

Is Evolution a Theory or a Fact? It is both. But that answer requires looking more vations and experiments that were not possible deeply at the meanings of the words “theory” previously. and “fact.” One of the most useful properties of scientific In everyday usage, “theory” often refers to theories is that they can be used to make predic- a hunch or a speculation. When people say, “I tions about natural events or phenomena that have have a theory about why that happened,” they not yet been observed. For example, the theory of are often drawing a conclusion based on frag- gravitation predicted the behavior of objects on the mentary or inconclusive evidence. Moon and other planets long before the activities The formal scientific definition of theory is of spacecraft and astronauts confirmed them. The quite different from the everyday meaning of evolutionary biologists who discovered Tiktaalik the word. It refers to a comprehensive explana- (see page 2) predicted that they would find fossils tion of some aspect of nature that is supported intermediate between fish and limbed terrestrial by a vast body of evidence. animals in sediments that were about 375 million Many scientific theories are so well estab- years old. Their discovery confirmed the prediction lished that no new evidence is likely to alter made on the basis of evolutionary theory. In turn, them substantially. For example, no new evi- confirmation of a prediction increases confidence in dence will demonstrate that the Earth does that theory. not orbit around the Sun (heliocentric theory), In science, a “fact” typically refers to an obser- or that living things are not made of cells (cell vation, measurement, or other form of evidence theory), that matter is not composed of atoms, that can be expected to occur the same way under or that the surface of the Earth is not divided similar circumstances. However, scientists also use into solid plates that have moved over geologi- the term “fact” to refer to a scientific explanation cal timescales (the theory of plate tectonics). that has been tested and confirmed so many times Like these other foundational scientific theo- that there is no longer a compelling reason to keep ries, the theory of evolution is supported by so testing it or looking for additional examples. In many observations and confirming experiments that respect, the past and continuing occurrence of that scientists are confident that the basic com- evolution is a scientific fact. Because the evidence ponents of the theory will not be overturned supporting it is so strong, scientists no longer ques- by new evidence. However, like all scientific tion whether biological evolution has occurred and theories, the theory of evolution is subject to is continuing to occur. Instead, they investigate the continuing refinement as new areas of science mechanisms of evolution, how rapidly evolution can emerge or as new technologies enable obser- take place, and related questions. In science it is not possible to prove with absolute certainty that a given explanation is complete and final. Some of the explanations advanced by sci- entists turn out to be incorrect when they are tested by further observations or experiments. New instruments may make observations possible that reveal the inadequacy of an existing explanation. New ideas can lead to explana- tions that reveal the incompleteness or deficiencies of previous explanations. Many scientific ideas that once were accepted are now known to be inaccurate or to apply only within a limited domain. Science, Evolution, and Creationism 11

However, many scientific explanations have been so thoroughly tested that they are very unlikely to change in substantial ways as new observations are made or new experiments are analyzed. These explanations are accepted by scientists as being true and factual descriptions of the natural world. The atomic structure of matter, the genetic basis of heredity, the circulation of blood, gravitation and planetary motion, and the process of biological evolution by natural selection are just a few examples of a very large number of scientific explanations that have been overwhelmingly substantiated. Science is not the only way of knowing and understanding. But science is a way of knowing that differs from other ways in its dependence on empirical evidence and testable explanations. Because biological evolution accounts for events that are also central concerns of religion — including the origins of biological diversity and especially the origins of humans — evolution has been a conten- tious idea within society since it was first articulated by Charles Darwin and Alfred Russel Wallace in 1858. Acceptance of the evidence for evolution can be compatible with religious faith. Today, many religious denominations accept that biological evolution has produced the diversity of living things over billions of years of Earth’s his- tory. Many have issued statements observing that evolution and the tenets of their faiths are compatible. Scientists and theologians have written eloquently about their awe and wonder at the history of the universe and of life on this planet, explaining that they see no conflict between their faith in God and the evidence for evolution. Religious denominations that do not accept the occur- rence of evolution tend to be those that believe in strictly literal interpretations of religious texts. Science and religion are based on different aspects of human experience. In science, explanations must be based on evidence drawn from examining the natural world. Scientifically based observations or experiments that conflict with an explanation eventually must lead to modification or even abandon- ment of that explanation. Religious faith, in contrast, does not depend only on empirical evidence, is not necessarily modified in the face of conflicting evidence, and typically involves supernatural forces or entities. Because they are not a part of nature, supernatural entities cannot be investigated by sci- ence. In this sense, science and religion are separate and address aspects of human understanding in different ways. Attempts to pit science and religion against each other create controversy where none needs to exist. 12 Science, Evolution, and Creationism

Excerpts of Statements by Religious Leaders Who See No Conflict Between Their Faith and Science Many religious denominations and individual religious leaders have issued statements acknowledging the occurrence of evolution and pointing out that evolution and faith do not conflict. “[T]here is no contradiction between an evolutionary theory of human origins and the doctrine of God as Creator.” “[S]tudents’ ignorance about evolution will seriously undermine their understanding — General Assembly of the Presbyterian Church of the world and the natural laws gov- erning it, and their introduction to other explanations described as ‘scientific’ will give them false ideas about scientific methods and criteria.” — Central Conference of American Rabbis “In his encyclical Humani Generis (1950), my predecessor Pius XII has already affirmed that there is no conflict between evolution and the doctrine of the faith regarding man and his vocation, provided that we do not lose sight of certain fixed points. . . . Today, more than a half-century after the appearance of that encyclical, some new findings lead us toward the recognition of evolution as more than an hypothesis. In fact it is remarkable that this theory has had progressively greater influence on the spirit of researchers, following a series of discoveries in different scholarly disciplines. The convergence in the results of these independent studies — which was neither planned nor sought — constitutes in itself a signifi- cant argument in favor of the theory.” — Pope John Paul II, Message to the Pontifical Academy of Sciences, October 22, 1996. Science, Evolution, and Creationism 13


In contrast to the SARS-CoV epidemic of almost 20 years ago, improved technologies, such as transcriptomics, proteomics, single-cell RNA sequencing, global single-cell profiling of patient samples, advanced primary 3D cell cultures and rapid reverse genetics, have been valuable tools to understand and tackle SARS-CoV-2 infections. Furthermore, several existing animal models initially established for SARS-CoV are applicable to study SARS-CoV-2 and will help to identify the critical viral and host factors that impact on COVID-19. We need to understand why SARS-CoV-2, in contrast to SARS-CoV, is replicating so efficiently in the upper respiratory tract and which viral and host determinants are decisive on whether COVID-19 patients will develop mild or severe disease 152,153,154 . Finally, we need to put the first encouraging studies on SARS-CoV-2 into the context of coronavirus biology to develop efficacious strategies to treat COVID-19 and to develop urgently needed vaccines.

The advent of functional genomics has enabled the molecular biosciences to come a long way towards characterizing the molecular constituents of life. Yet, the challenge for biology overall is to understand how organisms function. By discovering how function arises in dynamic interactions, systems biology addresses the missing links between molecules and physiology. Top-down systems biology identifies molecular interaction networks on the basis of correlated molecular behavior observed in genome-wide ‘omics’ studies. Bottom-up systems biology examines the mechanisms through which functional properties arise in the interactions of known components. Here, we outline the challenges faced by systems biology and discuss limitations of the top-down and bottom-up approaches, which, despite these limitations, have already led to the discovery of mechanisms and principles that underlie cell function.

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Watch the video: Functions, Nature, and Process of Communication (October 2022).