Daily Newsletter April 19, 2012

Daily Newsletter April 19, 2012

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Today's Topic: Macroevolution
Readings:

• Patterns of Evolution
• Evolution Is Change in the Inherited Traits of a Population through Successive Generations
• Volvox, Chlamydomonas, and the Evolution of Multicellularity
• Neutral Theory: The Null Hypothesis of Molecular Evolution
• Trait Evolution on a Phylogenetic Tree: Relatedness, Similarity, and the Myth of Evolutionary Advancement

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Daily Challenge: Discuss the patterns in evolution using the readings above. Remember, this is worth 6 points.

Daily Newsletter                               April 18, 2012

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Today's Topic: Speciation

Suggested Readings:
Speciation: Evolution 101
Speciation: The Origin of New Species
Hybrid Incompatibility and Speciation
Why Should We Care about Species?

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Daily Challenge: Speciation
In your own words, discuss the concept of speciation. Take a look at the mechanisms of speciation and the outcomes. Why is the concept of a species important to us?

Daily Newsletter April 17, 2012

Daily Newsletter April 17, 2012

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Today's Topic: Microevolution

Suggested Readings:

• Microevolution
• This is a page from Berkley Universities 'Evolution 101' project.
• Use the 'next' button to move through the microevolution section.
• Evolution Is Change in the Inherited Traits of a Population through Successive Generations
• A short article that uses the concepts of microevolution.

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Daily Challenge: Microevolution
Discuss the concept of microevolution and the mechanisms involved in microevoltuion.

Daily Newsletter                                                      April 13, 2012

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Evolution Friday the 13^th!

Daily Challenge: Evolution and Ecology
From what you have learned this week, how does our knowledge of population, community, and ecosystem ecology help inform the modern concept of evolution?

Daily Newsletter                                                                        April 12, 2012

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Today's Topic: Ecosystem Ecology

Readings:  The following readings support your daily challenge.  You are encouraged to read the corresponding chapter of your textbook.

• Ecosystem Ecology
• This is a topics page, and the following articles are linked from this page.  There are other articles you may find interesting, so I encourage you to explore more of this topic.
• Energy Economics in Ecosystems
• A basic overview that puts metabolism into an ecological prospective.  An important context for you to keep in mind.
• Biodiversity and Ecosystem Stability
• A critical concept that has come out of ecology is that biodiversity is important for environmental stability.  Community members rely on each other.
• Terrestrial Primary Production: Fuel for Life
• This puts photosynthesis in an environmental perspective.  As with "Energy Economics in Ecosystems", this provides a valuable perspective on why metabolic pathways are so important.  Both of these article also help demonstrate the importance of the second law of thermodynamics.
• The Conservation of Mass
• We know of the conservation of energy, but what of the conservation of mass?
• What happens to all the carbon you take in as food?  Does it disappear?  This article brings another perspective to metabolic functions you may not have considered.
• The Nitrogen Cycle: Processes, Players, and Human Impact
• An important aspect of ecosystems are the Nutrient Cycles.  If mass is neither created nor destroyed, then it must be recycled.  So, how do we recycle the nutrients needed by our body?

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Daily Challenge: Ecosystem perspective on metabolism
After reading the articles above, you will start seeing that there is an ecosystem perspective on metabolic functions. Briefly describe the focus of ecosystem ecology (as it is broader than metabolism), and then discuss how ecosystem studies takes metabolic functions to a new perspective. How does the second law of thermodynamics work in living systems? Why is it important that we consider the conservation of matter?

Daily Newsletter April 11, 2012

Daily Newsletter                                                                              April 11, 2012

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Today's Topic: Community Ecology
Readings: The following readings will support your daily challenge. You are encouraged to read the textbook chapter on community ecology.

• Community Ecology
• This is a topic page.  The following articles are linked from here.  If you find this topic interesting, please review some of the other short articles.
• Characterizing Communities
• Succession: A Closer Look
• Keystone Species
• Neutral Theory of Species Diversity

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Daily Challenge: Community Ecology
In your own words, what is the study of community ecology? Take one aspect of community ecology you find interesting and delve a little deeper. Discuss this aspect of community ecology, and help your readers understand it a little better.

Daily Newsletter April 10, 2012

Daily Newsletter                                                        April 10, 2012

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Today's Topic:  Population Ecology

Readings: While you are encouraged to read chapter 55 of your textbook, the follow readings can be used to answer the daily challenge.

• Population Ecology
• This is a topics page of Scitable by Nature.  The following three articles are specific subjects found on this topics page.  While it provides a basic definition of population ecology, the power of this page is in the links.
• If you are interested about population ecology, explore the links.
• Each of the linked articles is rather short.
• Game Theory, Evolutionary Stable Strategies and the Evolution of Biological Interactions
• The idea of game theory is a critical intellectual model.  This article holds only the basic concept of game theory, but you will see how important it is when you start looking at populations and natural selection.
• Population Limiting Factors
• There is no such thing as unlimited growth.  All growth has limits.  This article talks about some of the most important limiting factors affecting populations.
• How Populations Grow: The Exponential and Logistic Equations
• This article looks at the math behind population growth.  It first looks at single cells, and then moves to how this can be used with larger animals.
• Survivorship Curves
• This short article looks at one of the critical aspects of population ecology, the survivorship curve.  This is a tool to look at the general life expectancy of members of a population, but as you will see, it can provide much more information.

Population ecology deals with research involving individuals, and the interaction of individuals, of the same species that live within the same time and space (as described by the researcher).  So we are looking at birth rates, death rates, survivorship, intraspecies competition, and other aspects of how individuals of a given species live.  Occassionally we will look at two species, such as predator-prey models, or specific examples of competition between two species (game theory).  Research involving more than this is usually handled under the rubric of Community Ecology.

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Daily Challenge
Your challenge today is to describe population ecology in your own words. This is a broad field, so your not expected to talk about every aspect of the field. Give a general account, in your own words, about population ecology; then talk about some aspect that you find interesting.

Daily Newsletter April 9, 2012

Daily Newsletter April 9, 2012

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Today's Topic:  Introduction to Ecology
Ecology is a life science discipline that studies the interaction and interrelation of organisms with each other and the physical environment.  It is important to remember that Ecology is a scientific discipline seeking to understand natural phenomena in order to predict and control.  Environmentalism is a human social activity in which people advocate for policy changes dealing with environmental resources.  Ecology informs environmentalism, but they are not the same.

When we look at Ecology, we can divide the discipline into different fields:

• Population Ecology:  We look at the interactions between individuals of the same species that live in the same time and place.
• Time and place is important:  The population of Atlanta is different than the population of Denver.  This is also true of animals and plants.  Time is important, because the populations of 100 years ago may not be the same populations we see today.
• Studies of different time points are important, and constitute subfield.
• Studies of different places are used for comparison.
• You look at births vs. death, intraspecies competition (competition between members of the same species), and various aspects of the organisms life cycle.
• How would intraspecies competition play into evolution? (HINT: natural selection)
• Predator-Prey:  A sub-class of Population studies are classic predator-prey models. 
• Community Ecology:  We look at the interaction between species living in the same time and space.
• Here we have the concept of a NICHE.
• The niche is an organism's "position" in an environment; that of it as it's living space (habitat), eating (food preference), and job (function in the environment-predator, prey, consumer, etc...).
•  Every organism has its fundamental niche (what it can do), and its realized niche (what it actually does).
• Interspecies competition (between species) forces organisms into a realized niche.
• How does this play into evolution?  (Hint: Natural Selection).
• There are other aspects of community ecology (food chains, food webs) that we will look at throughout the week.
• Ecosystem Ecology:  This is where we look at the interaction between the living (biotic) and non-living (abiotic) components of the environment
• This is where we look at energy flow through the system, as well as nutrient cycles.  We will look at nutrient cycles later in the week.
• One major emphasis is the movement of energy.
• Remember your 2^nd law of thermodynamics!
•  Photosynthesis converts Photons into Reducing Power.
• Question:  If you consume 1 mole of glucose produced from a plant, how many moles of ATP could you form?
• Question:  How many glucose molecules could you remake from the ATP generated?
• Just to make is easier:  Would you generate <More/Same/Less) glucose?
• Applied Ecology:
• Applied Ecology uses the theories produced in the previous fields to make changes in the world.
• Examples include:
• Resource Management.
• Endangered Species Management.
• Landscape Management.
• Landscape Remediation.
• Chemical/Pollutant Remediation.
• Landfills and Waste Water treatement. 

A final topic is that of coevolution, which is informed by work done in population and community ecology.  There are many examples of this phenomena in which one organism experiences a change in response to a change in another organism.   Specific examples include:

• Hummingbirds and ornithophilous flowers 
• Angraecoid orchids and African moths 
• Old world swallowtail and fringed rue 
• Garter snake and rough-skinned newt 
• Acacia ant and bullhorn acacia tree 
• Yucca Moth and the yucca plant

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Daily Challenge: Coevolution
Today, you are to discuss how population and community level effects can influence the interaction between two species and result in coevolution. For this you will use the following example: The leaf-cutting ant (genus: Acromyrnex) and the farmed fungus (genus: Leucocoprinus). The ants in this example cut and chew leaves to build a medium to grow fungus. The fungus is then harvested and eaten by the colony.
Suggested Readings:
A Farming Ant and Its Fungus Are Ancient Cohabitants
Ants Are Experienced Fungus Farmers
Fungus-Farming Ants First To Find Natural Pesticides

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Optional Readings:  These three articles are presented in case you want to see other aspects of ecology.
Energy Economics in Ecosystems
The Ecology of Fire
Restoration Ecology

Daily Newsletter April 6, 2012

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Today's Topic: Regulation and Evolution

Please read the following article: The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise

Hopefully this week has introduced you to the importance of genetic regulation. 

Multicellular organisms, such as humans, need coordinated development, from a zygote (fertilized ovum), through embryonic stages, fetal development, and then the stages of growth and development into an adult.  Each of these changes is marked by changes in gene regulation.

To save energy, cells will keep non-essential genes turned off.  In they receive different signals, or encounter different environments, cells can adapt their physiology by altering gene expression.  Remember, building mRNA and then a Protein is energetically very costly to the cell.  Cells have to be masters of energy maintenance, so the ability to regulate gene expression is critical. 

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Daily Challenge: The Evolution of Gene Regulation
From readings in your textbook and throughout the week, discuss the evolution of gene regulation, and the importance of gene regulation to evolution.

Daily Newsletter April 5, 2012

Daily Newsletter                                                                             April 5, 2012

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Today's Topic: Eukaryotic Gene Regulation

Yesterday, we looked at the Lac operon, a classic example of bacterial gene regulation.  The majority of prokaryotic gene regulation is handled at the transcriptional level.  As we move to eukaryotic cells, we find that there are other ways that genetic expression can be regulated.

•   Epigenome:  This occurs in both prokaryotes and eukaryotes.  In eukaryotes, the epigenome is noted by chemical changes to DNA and histone molecules that result in changes to the chromatin strand.  These changes can "lock down" genes, preventing even the recognition of the promoter.
• IMPORTANT:  the epigenome does not represent mutations.  Instead it is a reversible chemical alteration to chromatin structure.
• This chromatin alteration can be passed vertically to offspring.
• Changes to the epigenome occur due to chemical signals and environmental changes (they change the organisms adaptation range).
• Check out the movies embedded on the MOOC site.   They give a good perspective on epigenetics.
•  Transcriptional control:  This is control of the promoter and operator, and is very similar to what was seen with the Lac operon.
• Post-Transcription regulation:  If you don't add the 5' cap, then RNA can't leave the nucleus.  If you don't add the 3' poly-A tail, RNA is digested.  If you don't splice out the introns, you don't have a code.  Prevention of post-transcriptional modification can play a role in gene expression.

Suggested Reading:
Eukaryotic Gene Regulation
Tissue Specific Gene Regulation
Gene Regulation in Eukaryotes (advanced)
Eukaryotic Gene Expression Problem Set (advanced)

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Daily Challenge: Eukaryotic Gene Expression
Pick one topic regarding eukaryotic gene regulation that you are interested in, and in your own words, discuss that form of eukaryotic regulation.

Daily Newsletter April 4, 2012

Daily Newsletter                                                                        April 4, 2012

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Today's Topic: Lac Operon
One of the most well studied gene regulation systems is the Lac Operon found in Escherichia coli.  To understand this system, it is important to first understand that bacteria do not experience Transcription and Translation in exactly the same way as eukarotes  (the mechanics are very similar, but there are some distinct differences).

Bacteria lack a nucleus, thus transcription takes place in the cytosol.  There is no need for a tag to get out of the nucleus, so there is no need for capping.  Also, there are no introns, so no need for splicing.  Basically, there is no processing of RNA to make mRNA.  What is transcribed is mRNA.

Since there is no membrane separating transcription from translation,  you can couple these to processes.  As mRNA is made, it can be translated.

Bacteria also have a single circular molecule of DNA (a genophore, not a chromosome).  They have to conserve their genetic space, so bacteria combine genes in a single mRNA.  IMPORTANT:  bacteria can combine genes for a metabolic pathway into a sequential sequence with a single promoter.  Thus, when you transcribe, you get all the genes for a given metabolic pathway.

The word OPERON describes this unique arrangement of prokaryotic genes:  One promoter and one operator for a given series of metabolically linked genes.

The Lac Operon holds three genes that give the cell the ability to take in and use the sugar LACTOSE.  For E. coli, glucose is the preferred sugar.  When glucose is present, there is no need to use lactose:  these genes are not transcribed.  When there is no glucose, E. coli has to use other sugars.  IF lactose is present, the genes for lactose utilization will be made.  Conversely, if there is no lactose, they genes remain locked down.

Here are three articles that go over different aspects of prokaryotic regulation and the Lac Operon:

• Operons and Prokaryotic Gene Regulation
• Negative Transcription Regulation in Prokaryotes
• Positive Transcription Control: The Glucose Effect

NOTE:  In this example, there are two ways to control the expression of a gene or operon:
1)  You can block the operator of the gene.  This prevents RNA polymerase from making RNA.
2)  You can alter the promoter (or the interaction between transcription factors and DNA) to prevent binding of the Transcription Complex (RNA polymerase).

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Daily Challenge:
In your own words, describe the regulation of the Lac Operon.  Start with a brief discussion of the nature of an operon using the Lac Operon as your model.  Then discuss the control of the Lac Operon expression.

Daily Newsletter April 2, 2012

Daily Newsletter April 2, 2012

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Today's Topic: Gene Regulation

Suggested Reading - Operons and Prokaryotic Gene Regulation

Do we express all of our genes at the same time?  Why?
Do we need all of our genes expressed all the time?  Why?
Why do we have so many genes?

These are just a few of the questions you need to start asking yourself.  Humans have hundreds of thousands of genes.  Many are needed all the time (constitutive), but others are only needed when the cell get's certain signals.

During mitosis, for example, did you see the production of DNA polymerase and the replication complex during the start of G1, or did you only see it after you passed the first restriction point?  Do we keep DNA polymerase around just in case we are going to do some nuclear division?

Consider:  The first restriction point determines if you are going to prep for division.  When you have enough cyclin-dependent kinase available, you pass the restriction point.  CDK signals the cell to get ready for division.  How does this signal work?  It changes gene expression (i.e., we activate regulated genes).

Think about the human body and homeostasis.  Think about hormones.  Are you always producing everything, or do you need to trigger some events?  Could that trigger then be a regulated gene?

Today, your goal is to reflect on why some genes are regulated and some are constitutionally produced. 

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Daily Challenge: Why do we need gene regulation? Today, reflect on the need and use of gene regulation. Why would an organism need to have some genes that it could turn on or off? Why would you need to control gene expression? Can gene regulation affect evolution?