Week 7

Ok, now this is going to seem like it doesn’t have anything to do with anything we have done so far, but it will! Here it goes:

This is a jar of flies (although I attempted to major in many different subjects before deciding on biology, art was NEVER really an option) (Figure 7.1a):

Figure 7.1a

These flies are just flying around doing fly things. They are eating fly food, having fly sex, having fly babies, and doing all kinds of stuff that flies do.

Now, I’m going to put a little tiny, tiny bit of Raid in the jar. I’m going to quickly open the lid and just spray 1⁄2 a spray or so....what do you think will happen? Well, a few of the flies will probably die but many will live...(Figure 7.2a)

Figure 7.2a

Now the ones that survive will have babies (and they are not really babies, they are eggs, but you get the idea). These will be the second generation. If I take those and spray them with the same amount of raid as I did before, I might get something like this (Figure 7.3a):

Figure 7.3a

Notice that fewer flies died this time. And, if I were to keep doing this, I could eventually get a jar of flies that would be pretty much immune to the can of raid all together. So why did this happen? Why do some flies live and others not?

Well, we are now getting down to the basics of Charles Darwin’s Theory of Evolution. We will talk more about Darwin and the others in a little while. But first, let’s spend some more time with our jar of flies.

Flies, like all living things, are made up of cells. Each cell has a nucleus with DNA. The DNA is used to make proteins. However, each fly has slightly different DNA. Therefore, each fly makes slightly different proteins and thus, each fly is a little bit different. If you were to weigh and measure each fly, you would notice that they are all a little bit different. The same thing would happen if you weighed and measured each of us. The collection of all of the genes in a population make up the gene pool. In our jar of flies, we started out with a certain gene pool. Over time, some of the flies had genes that made them more resistant to the Raid while others did not. Over the next several generations, our gene pool changes

slightly in that the genes that were not beneficial were wiped out. This is a good example of microevolution. Microevolution can be defined as small genetic changes in a gene pool over a relatively short amount of time. NOTICE that you don’t need any NEW genes. You don’t need to grow a leg or change colors or any of those types of things. If you start with 10 gene A’s and 10 gene B’s and after several generations you end up with 18 gene A’s and 2 gene B’s, you can say that microevolution has occurred. In microevolution, we are looking at genetic changes that occur at the population level. A group of organisms can change over time (genetically, that is). You don’t need to generate new species (which we will talk about next week).

Now let’s look at some of the ways that a population can end up having changes in its gene pool (we have already looked at one example which we will give a name to in just a second here).

Ways that Microevolution can occur:

Natural selection: Natural selection is the idea that nature “selects” which genes are good and which genes are bad. If you are an animal with a very thick coat of fur, are you going to live or die? Well, it depends on where you live. In the desert, nature would probably select against your thick fur coat because it would be too hot. In a polar environment, nature might select in favor of this trait because it can keep you warm. Our jar of flies was sort of an example of natural selection....but when humans intervene with some very unnatural force (such as the can of Raid), we call that artificial selection.

Natural selection can work in three basic ways. Let’s say you have a bunch of lizards (because I really like lizards!). Some are big and some are small. In one environment, being too big might make you slow but being too small might make you an easy target for predators. Therefore, the best size to be is in the middle, which is stabilizing seletion. In another environment (or even another type

of lizard all together) it might be best to be as big as possible (directional selection). Still in another environment (or again, in another lizard) being small might mean you can escape easily into a hole but being large might make you too big for predators to eat. In this case, being small or large is advantageous but being in the middle is not good (that would be an example of disruptive selection).

Figure 7.4a

In your book is an excellent, very famous example of how selection can change over the years in Galapagos finches (Figure7.5a). The Ground Finch has been studied by Peter and Rosemary Grant on the Galapagos islands for nearly 20 years. They were able to show that microevolution occurred in the finch when a severe drought drastically changed the plant composition and therefore the types of seeds available on the island. Here is the bird (Figure 7.5a) and here is a graph showing how the average beak size changed over time (Figure 7.6a):

Figure 7.5a

Figure 7.6a

Genetic Drift: Both bottleneck’s and founder effect’s are types of genetic drift.

Bottleneck: Another way that microevolution can occur (or another way that small genetic changes can happen in a population) is a bottleneck. In a bottleneck, you start out with a diverse population. But something happens that eliminates a great deal of the diversity. What you are left with is a small percentage of the original population that, when it repopulates, ends up having a very different look to it diversity-wise (it is usually far less diverse). One example of a bottleneck is the hunting of seals in the late 1800’s (Figure 7.7a)

Figure 7.7a

Founder Effect: Similar to a bottleneck, a new population can be started with a small piece of the diversity from an originally larger and more diverse population. The best example of this is when a couple of birds, mice, or lizards get blown out to sea and eventually land on an island that was never inhabited before. These small numbers of individuals repopulate the island which might

look very different from the mainland inhabitants. Let’s say you have a type of bird and on the mainland some of them are red, some are green, some are white and some are black. In other words, they are all the same kind of birds but they come in different colors. One day, 5 of the green birds get caught on a large gust of wind that blows them 20 miles offshore to an island. On this island, these birds do not exist until now. Once the birds reproduce and have lots of babies, you end up with a new population; but they are all green.

Gene Flow: Another way that microevolution can occur is through gene flow. Let’s say a large group of frogs is somehow divided into two populations (Figure 7.8a) by the separation of livable land masses by an expanse of barren terrain. Right now, they are still the same species BUT, they are two distinct populations (Pop A & Pop B) because they cannot reach each other to reproduce. However, sometimes, gene flow occurs. One of the frogs from Population B might sneak across the barren terrain to reach population A. That is how gene flow occurs and keeps diversity in each group.

Figure 7.8a

Let’s say a large group of frogs is somehow divided into two populations (Figure 7.8a) by the separation of livable land masses by an expanse of barren terrain. Right now, they are still the same species BUT, they are two distinct populations (Pop A & Pop B) because they cannot reach each other to reproduce. However, sometimes, gene flow occurs. One of the frogs from Population B might sneak across the barren terrain to reach population A. That is how gene flow occurs and keeps diversity in each group.

Mutation: The only NEW source of genes and genetic material is through mutations. Most of the time, mutations don’t do anything because there is so much DNA that isn’t actually used. Other times, mutations are harmful and end up killing the organism. BUT SOME mutations are actually good! If a mutation occurs that makes you faster or bigger it could be beneficial and might increase the chances of survival and reproduction. What

determines whether a mutation will be good or bad? Natural Selection!

Nonrandom Mating: Populations can also change because the members usually don’t just mate with anyone. They are selective. For example, a male sage grouse competes for females by a complex dance of chest swelling and strutting (Figure 7.9a).

Figure 7.9a

In some cases, two males will compete for mating rites to a female. The female chooses the male with the sexier dance. This is called sexual selection and it is a type of nonrandom mating. Do humans do this type of thing? Maybe a better question would be do humans ever NOT show signs of non-Random mating? I’m sure you have friends that spend a lot of time in dark bars that come pretty close to nonrandom mating!

Brief History of Ideas about how things came to be:

Darwin’s theory of evolution is the most widely accepted scientific explanation of how things came to be in the world. Meaning, where did all the plants and animals and humans come from? But how did we get to Darwin’s theory of evolution? Lets start a long, long time ago in a galaxy far, far away....

Plato (427-347 B.C.) – Plato believed in two worlds: a real world that was ideal and eternal and an illusory world of imperfection that we perceived through our senses. Plato believed that some god or gods created all of the plants and animals and they were designed perfectly. When we see an animal or plant with imperfections, we just see those imperfections because we have imperfect senses (which makes me think, why would we have imperfect senses if we were supposed to be designed perfectly!)

Aristotle (384-322) – Aristotle was Plato’s student. Aristotle believed that plants and animals could be arranged on a ladder of increasing complexity. This was called the scala naturae. So, worms, for example, would be low on the ladder. Then up a couple of steps might be birds. And then, of course, at the top of the ladder was humans. In this

Natural Theology – In the 1700’s biology in Europe and America was dominated by the idea of natural theology. Natural theology was heavily influenced by Judeo-Christian culture and by Aristotle’s idea of the scala naturae. The idea or goal of natural theology was this: to understand the creator’s plan, we must learn everything we can about the animals and plants around us and figure out how they fit on the scala naturae. By doing this, people would then understand God’s plan.

Carolus Linneaus (1707-1778) – Carolus Linneaus was a major contributor to the field of study called Taxonomy. Taxonomy is the science of naming and classifying organisms. Linneaus came up with a two part, or binomial, system for naming and classifying organisms. Linneaus was a natural theologist who believed that

god had created all of these plants and animals and it was his job (Linneaus that is) to name them all.

Georges Cuvier (1769-1832) – Cuvier was a French Anatomist who greatly influenced the field of paleontology. Paleontology is the study of fossils. Cuvier noticed that in the fossil record he would find bones of animals that were similar to the bones of some of the animals we have now. But they were slightly different. He also noticed that the deeper fossil levels had animals with more and more differences. Furthermore, Cuvier noticed that you could find some fossils in some areas but not in others. This greatly puzzled Cuvier. Why weren’t there fossils that were exactly like the things we have now? And, why don’t we find the same fossils in the same area? Cuvier was strongly opposed to the idea of evolution. He came up with the idea of catastrophism. He reasoned that all of the plants and animals were designed at the same time and have always been around.

The fossil record is a record of the animals that died due to certain catastrophic events such as floods or hurricanes that wiped them out.

Jean Baptiste Lamarck – Although many people had suggested ideas about how life might evolve by the early 1800’s, Jean Baptist Lamarck was the first to develop and actually write up and publish a theory of evolution. This was in 1809*, the same year that Charles Darwin was born. Lamarck’s idea was that animals could evolve by passing on aquired characteristics. For example, a giraffe kind of looks like a horse but with a really long neck. Lamarck thought that a horse like animal spent its life stretching its neck to reach leaves that were higher up on the trees. This made the Giraffe’s neck a little bit longer. Therefore, its babies would start out with just slightly longer necks and if they spent their lives stretching their necks, then eventually you would get an animal with a really long neck. This idea of passing on acquired characteristics is believed not to be true anymore. We now know

that DNA is passed on from generation to generation and not the characteristics that we acquire such as large muscles, or tattoos, etc. Lamarck was ridiculed at the time (and sometimes even now) for his theory. But Lamarck should be given credit for having the courage to publish an unpopular idea at the time that greatly influenced the work of others to come.

James Hutton and Charles Lyell – Hutton and Lyell were geologists who greatly influenced our views on how the earth has changed over time. James Hutton came up with the idea of gradualism which basically states that features such as mountains and valleys could be developed over many, many thousands (or millions) of years. Charles Lyell incorporated Huttons idea into the theory of uniformitarianism which states that the same forces that build mountains and erode mountains are the same today as they were in the past. Hutton’s and Lyell’s ideas were very important because up until this time, most people believed that the world was only 6,000 years old. Now, these geological forces were starting to give us hints that perhaps the world was much older than that.

Charles Darwin – Darwin was born in 1809* in western England. As a child, Darwin was very interested in nature and spent a great deal of his time hunting, fishing and collecting insects. Darwin’s father, who was a famous physician at the time saw no future for Darwin as a natural theologist. So when Darwin was 16, he was sent off to Medical School. But Darwin didn’t like Medical School and dropped out before finishing. Instead, he went to Christ College in Cambridge to study natural theology. After he finished his B.A. in 1831, Darwin got a “job” with Captain Robert FitzRoy on the HMS Beagle (it wasn’t really a job because Darwin had to pay his own way). The HMS Beagle was getting ready for a trip to sail around the world. The primary mission was to chart poorly known segments of the South American Coastline. Here is their trip (Figure 7.10a):

Figure 7.10a

Darwin made many observations of the plants, animals, and fossils he found in South America which were clearly different from those he found in Europe. Of particular interest were the animals he found on the Galapogos islands. Mainly a group of birds called finches. These particular finches, Darwin later discovered, could be found no where else in the world (Figure 7.11a).

Figure 7.11a

Darwin was looking at these finches and noticed that although they were unique they resembled finches found on the mainland of South America. He began to read Charles Lyell’s book on the Principles of Geology. Darwin began thinking, if the world can change over time, maybe plants and animals can change over time as well. In 1844, Darwin wrote up a long manuscript about how populations of animals could evolve over time through the process of natural selection. But he didn’t publish his manuscript. Darwin was afraid of being attacked by the scientific community. He talked with Lyell about his idea and Lyell told him he should

publish it. But he still did not. In 1858, another person working independently of Darwin named Alfred Wallace sent Darwin a copy of his own theory of evolution by natural selection. It was almost identical. Darwin wrote to Lyell and told him that he was right and he should have published the paper. Now all of Darwin’s work was to be lost. But have you ever heard of Alfred Wallace until now? Probably not. That’s because Charles Lyell presented Wallace’s paper along with pieces of Darwin’s manuscript to the Linnaean Society of London on July 1, 1858. Darwin quickly finished his manuscript and published The Origin of Species in 1859. Although Wallace prepared his manuscript first, the Linnaean Society of London was convinced that Darwin had proven that he had developed the idea first and had it defended so much better that he was to receive the credit.

Microevolution has been well studied and is pretty much agreed upon by anyone who knows anything about science. Now, if you take the same basic process of microevolution and instead, give it millions of years, the idea is that you can get very large changes. This can result in a new species or even new groups of species. This is called macroevolution (and we will revisit this later). This is not as agreed upon as microevolution. Either way, there is a great diversity of life on this planet and this is a little tour of it:

Biodiversity is basically a measure of how many different kinds of species you have in an area. I want you to flip through chapters 20 and 21 and just look at the pictures of all of the different kinds of living organisms there are in the world. We cannot even begin to discuss each one. So, I will just pick several groups to talk about. Also, whenever appropriate, I will introduce various aspects of one of my favorite classes to teach: Animal Behavior!

Bacteria: Bacteria are the smallest living organisms that we know of in the world and they are AMAZING. Bacteria have been found almost everywhere including almost 2 miles below the surface of the earth and 27,000 feet above sea level in the Himalayas. Based

on what little we know about the fossil history of bacteria, they appear to be the first organisms dating back to about 3.5 billon years ago. Because bacteria are so small and so abundant, your body actually has more bacterial cells on it than your own cells! Also, remember that bacteria are prokaryotic organisms and they do not have most of the organelles found in the larger Eukaryotic cells (such as a nucleus, mitochondria, and chloroplasts).

Archeae: These are also organisms made up of prokaryotic cells. Some examples include the Aracheae that live down near the hydrothermal vents at the bottom of the ocean or in highly salty pools of water (such as in the Great Salt Lake in Utah).

Protozoa: Protozoa are small, single-celled, eukaryotic organisms that are very diverse (many different types and styles). Some of them are human parasites (such as Plasmodium which causes Malaria and Trypanosoma which causes African Sleeping Sickness and Chagas disease). Many others live in ponds or lakes and some are photosynthetic. The protozoa is longer considered just one group; is has been broken down into 4-6 large groups which also consist of ancestors that eventually lead to animals, plants, and fungi)

Plants and Trees: There are 290,000 different kinds of plants and trees. Plants can be distinguished from other living organisms because they have cell walls made of cellulose. The oldest living organisms in the world turn out not to be humans or turtles, but some species of trees. A bristlecone pine living in eastern California has been dated at 4,900 years old!

Fungi: This group of organisms includes things such as mushrooms and molds. Fungi (which is plural for fungus) are important in ecosystems because they decompose dead materials and recycle them into reusable nutrients.

The largest living organism in the world is not a whale or

elephant....it’s actually a fungus. In 1992, researchers found a fungus growing in Washington State that was 1,500 acres large! Much of this fungus was underground but still all one giant organism.

Many fungi are edible. One very expensive and popular type of fungi you might have heard of before is called a truffle. Truffles are fungi that basically grow underground. Apparently, pigs have excellent noses for smelling out truffles and are often used to collect them.

Animals:

Above, we just lumped all the bacteria and trees and fungi into three big categories. They can actually be subdivided into many, many categories but it becomes very complex and most of us are not familiar enough with the groups. For the animals, I will break them down in a few groups that should be familiar to all of us.

Poriferans: Sponges belong to the group called the Porifera. They are the most primitive and simplistic animals. They do not even contain true tissues like other animals. They are filter feeders that primarily live in the ocean.

Cnidarians: Jelly fish and Sea Anemones are scientifically called cnidarians. Cnidarians have specialized cells called cnidocytes that have a stinging harpoon like structure called a nematocyst. These nematocyst are often used to sting and poison prey that they then eat. Cnidarians are one of the most primitive types of animals.

Arthropods: The group called Arthropoda are the “jointed foot” animals. They generally have a hard exoskeleton. They are also the largest of all groups. It contains many subgroups including insects, arachnids, and crusteaceans.

Insects: As far as species go, most of the animals that we have described have been insects. Currently, there are over 1.5 million

species of organisms that have been described and about 1 million of these have been insects. Most of these (about 300,000 of them) are beetles.

Insects can be identified by the fact that they have a total of six legs when they are adults. Insects include things such as grasshoppers, flies, ants, bees, wasps, and so forth.

Arachnids: Arachnids include things such as spiders and scorpions. Arachnids have two distinct body regions and have a total of eight legs. Many arachnids are highly poisonous, however, most are generally harmless to people.

Crustaceans: Crustaceans are a very large group of the arthropods that include animals such as crabs and lobsters. The Crustaceans are mostly marine.

The largest spiders in the world are tarantulas (of which there are many different species). Some tarantulas can have a leg span of up to 11 inches. Because of their larger size, many people believe that tarantulas are highly venomous This is not true; in fact the bite of smaller spiders such as a black widow can be more dangerous (not because they are small; some species are just more venomous than others).

Annelids: Annelids are segmented worms. The most familiar example that you would know are earthworms. Annelids have segmented bodies and tiny little hairs that stick out of the side of the segments that help them move through dirt. Some annelids have little paddles that stick off the side of their body that help them crawl or swim (if they live in the ocean and many of them do).

Mollusk: Mollusks are a very large group of animals that include animals such as squid, octopods, clams, snails and slugs (among a few others that are not as common). Most mollusks have a specialized feeding structure called a “radula”. A radula is like a

tiny file and it is found in the mouths of most mollusks and it is used for scraping algae and stuff off of the rocks.

Echinoderms: Echinoderms include animals like sea stars, sea cucumbers, brittle stars and sea urchins. Their name means the “spiny skinned animals”. They have a specialized group of tubes called a water vascular system that they use to adjust the pressure in their tiny little suckers called “tube feet”. The “tube feet” are what hold a sea star to a rock so tightly.

Reptiles: Reptiles include animals such as lizards, snakes, and turtles. Reptiles can be identified by the fact that they have scales. At one time, birds were considered a separate group of organisms. But for quite some time now, we have known that birds are closely related to alligators and crocodiles. Therefore, birds are considered reptiles.

There are so many different kinds of interesting reptiles. Just to pick one, the largest lizard in the world is called the Komodo Dragon. They live on an island off of Indonesia. Komodo Dragons can grow to 10 feet in length.

Birds: Although birds are really a type of reptile, I will talk about them as a separate group for now. If I ask you on an exam or quiz, however, you should be aware that birds are really a type of reptile that most closely relate to crocodiles and alligators.

Birds can be distinguished from other animals by the fact that they have feathers. Feathers are actually highly modified scales. Birds are endothermic animals which means that most of their body heat comes from their own metabolism. This is basically what we do.

One of the fairly unique things about birds is that most of them can fly. In fact, the fastest moving animal in the world is actually a Peregrine Falcon. Peregrine Falcons (which live here in Southern California) can reach speeds of about 150 miles an hour when in a full dive.

Mammals: We are of course, members of the group mammalia. Mammals have hair, usually give live birth (except for two odd animals found in Australia), and usually have mammary glands that produce milk that is fed to the young. The largest of these, the Blue Whale, happens to also be largest animal that has ever lived (even larger than all of the dinosaurs we have discovered thus far!) Figure 7.12a

Figure 7.12a

Coming Up....(but you need to know at least this part for this coming quiz!)...

What makes each thing above different is that they have different DNA. That might sound pretty obvious, but it is very important. DNA is an important molecule that basically is a set of instructions on how to build proteins. DNA is made up of smaller subunits called nucleotides. A similar molecule, called RNA is also made up of nucleotides.

Making a protein basically has two stages. During the first stage, a special enzyme called RNA polymerase is used to copy a piece of the DNA into RNA. This stage is called transcription and takes place in the nucleus of a cell. From there, the RNA leaves and travels out into the cytoplasm.

During translation, the RNA (specifically called mRNA or messenger RNA at this point) then gets read by the ribosome. The ribosome is a meeting place between the mRNA and another kind of RNA called tRNA. What happens is this: the mRNA is going to get read in sections of three. A section of three nucleotides in a row is called a codon. The tRNA has parts that are compliments or opposites to the codons that are called anti-codons. Also, the tRNA has an amino acid attached to it. Thus, the mRNA binds with only certain specific anti-codons (on the tRNA) and so only certain amino acids are put in one at a time. These amino acids hook together to form a polypeptide chain and eventually this folds up into a three dimensional protein. Proteins (many of them being enzymes) regulate growth and development and this how DNA is used to make each of the above organism different (and also why two people look different). The above couple of paragraphs are overwhelming, I’m sure. We will learn this in more detail during lab and during next weeks stuff. For now, try to read through it again and follow the picture below to get an idea of the steps of transcription and translation (Figure 7.12a).

Figure 7.12a

ASSIGNMENT #7 – Print this sheet off and turn it in with your lab next week. This sheet of paper goes on top (then the lab).

1) The most toxic poison in the world comes from a/an:

A) Frog

B) Lizard

C) Snake

D) Bacteria

E) Cnidarian

2) The largest lizard in the world is the:

A) Australian Frilled Lizard

B) The Komodo Dragon

C) The Western Fence Lizard

D) Day Gecko

E) Chinese Water Dragon

3) Which of the following is a geologist who influenced Darwin?

A) Gregor Mendel

B) Charles Lyell

C) Aristotle

D) Socrates

E) Jean Baptiste Lamarck

4) The sum or collection of all of the genes in a population make up the:

A) Gene Pool

B) Habitat

C) Alleles

D) DNA

E) Proteins

5) Seals were hunted to near extinction in the 1800’s. This resulted in a drastic reduction in the various phenotypes. When seals rebounded in population, they were all basically one color. This is an example of a/an:

A) Sexual Selection

B) Bottleneck

C) Founder Effect

D) Disruptive Selection

7) Describe the journey of the HMS Beagle (internet or book).

8) What are “extremophiles? (internet or book)

9) What are lichens (internet or book)?

10) Name and very briefly describe the nine phyla of animals.

Words that you may be asked to define or use in fill-in-the blank types of questions:

Microevolution, macroevolution, gene pool, Darwin, Lyell, Hutton, Aristotle, Lamarck, Socrates, Cuvier, Linnaeus, Natural Theology, Disruptive Natural Selection, Stabilizing Natural

Selection, Directional Natural Selection, Mutation, Genetic Drift, Founder Effect, Bottleneck, Sexual Selection, Artificial Selection, Bacteria, Fungi, Arthropods,

Arachnids, Reptiles, Amphibians, Plants, Mammals, Birds, Cnidarians, Echinoderms, Archeae, Protozoa, Plasmodium, Malaria, Trypanosoma, African Sleeping Sickness, Chagas Disease, DNA, RNA, tRNA, mRNA, ribosome, codon, anticodon, amino acid, polypeptide

* You should also know your base pair rulings in DNA and RNA. That is, “A” nucleotides always pair up with “T” nucleotides and “G” nucleotides always pair up with “C” nucleotides in DNA. This is also true of RNA EXCEPT, there is no “T” in RNA; instead, there is a different nucleotide called uracil, or “U”. So, if a DNA strand is GGGCCCAAA on one side, the other side is going to be CCCGGGTTT. If you want to know what RNA nucleotides are going to pair up with which DNA nucleotides, it would look like this (for the same DNA molecules used above): CCCGGGUUU (the “U” is there because there is no “T” in RNA.