Category Archives: Readings

Reading from the text book by Mader & Windelspecht

The Impact of Acid Deposition

Acid Deposition

Normal rainwater has a pH of 5.6 because the carbon dioxide in the air combines with water to to give a weak solution of carbonic acid.

When fossil fuels burn, sulfur dioxide and nitrogen oxides combine with water to produce sulfuric and nitric acids, causing acid rain.

Impact on Lakes

Acid rain in Canada and New England has caused hundreds of lakes to be devoid of fish, and in some cases, any life at all.

Impact on Forest

In New England and the southern Appalachians, millions of acres of high elevation forests have been devastated (by acid rain.

Sulfur dioxide and nitrogen oxides, the main precursors of acid rain, have been steadily decreasing in the United States due to clean air legislation and strict emission limits.

Impact on Humans and Structures

Inhaling dry sulfate and nitrate particles appears to increase the occurrence of respiratory illnesses, such as asthma.  Buildings and monuments made of limestone and marble break down when exposed to acid rain.  The paint on homes and automobiles is likewise degraded.

Damage is decreased because of efforts to reduce chemicals that contribute to acid rain.

Conclusions from article and graph.

Acid rain emissions are trending downward.

Using less fossil fuels and capturing or converting the pollutants might help reduce sulfur dioxide and nitrogen oxide.

Acid rain converts mercury in lake bottom sediments to toxic methyl mercury.  Reducing acid rain emissions is essential to keep mercury from accumulating in fish.

 

Characteristics of Life

Dear Grandchildren

You ask…if snakes are mean,
..If turkeys hate Thanksgiving,
When “you know what happens”
..Does grandpa fear not living?

I’ll answer with rhyme of science,
..And leave feelings out for now.
It’s called biology
..The study of life it’s WOW!

You find in biology,
..an infinity of form.
Of function too, some funky ooh,
..Play with me, surprises are the norm

While some births are vomited
..Others violent.
Sometimes they’re born in trillions,
..Some are brief like rent.

Mating can occur
..Between an orchid and a bee.
Octopus solve problems
..With a brain that’s like a pea.

Life begins non-living
..With stuff it forms a cell
Some cells live independent
..A single life lived well.

Others clump together,
..We can’t tell who’s the wife.
Co-habitation suits them,
..Or not, but they serve life.

When many cells are similar,
..A tissue do they form.
Then tissues make up organs,
..Together they perform.

All these organs make an -ism,
..An organism birthed.
You may not think too much of some,
..Mother Nature knows their worth.

When organisms look alike,
..And really get along…
They tend to group together,
..To a population they belong.

Out back in the forest,
..Are animals and plants.
They form community,
..Picnicking with the ants.

In all they love the world outdoors,
..Weather, wind and rain.
A sphere within Earth’s sphere,
..Biosphere’s the name.

Life starts out really simple,
..Well, it’s not really life at all.
But then emerges complex mighty,
..Organizing the collected raw.

It’s just those raw materials,
..That manufacture life.
And they also must maintain it,
..To get life through life’s strife.

Nutrients, we call it food,
..Are organism’s friend.
They eat so they have energy,
..And thus their life extends.

The shining source of energy,
..Comes to plants from the sun.
Green ones magically change it,
..Then share with everyone.

Sun combines with soil,
..Producing food for us organics.
Food eats then we eat,
..A food chain’s base mechanics.

Plants turn in-organic,
..Into organic matter.
The cycle runs until it stops,
..Putting meat upon the platter.

Rain and sun determine much,
..From desert to coral reef.
Where they are abundant,
..Populations squeal and squeak.

While dry and dark communities,
..Exist in stark relief.
They seem to lack life on the surface,
..But team with it beneath.

Life requires balance,
..With tolerance the key.
Like temperature and moisture,
..Don’t forget acidity.

It’s those tissues mentioned earlier,
..And their organ system nerves.
That keep us all from crashing,
..Cashing food out of reserve.

Living things respond to things,
..that live and that live not.
Like environmental changes,
..And distant things that rot.

Some respond with movement,
..Ensuring they survive.
Behavior begets balance,
..Gets honey for the hive.

Life must bring more life,
..Reproduction it is called.
You might say mold develops,
..Offspring in it’s mold.

Single cells don’t marry,
..But they always have to split.
Multi-cell organics pair,
..Egg to sperm permit.

The reproduced new package,
..Instructions tucked inside.
Through genes offspring are similar,
..But different by design.

DNA is like a map,
..Within the gene’s deep pocket.
It turns genes on and off,
..Like many lights and sockets.

The difference you seem to see,
..Mutations they are called.
Inheritable changes,
..Variations sometimes bold.

Staggering diversity,
..Among identicals.
Allow inheritance,
..and better life all toll.

When mutation meets environment,
..Adaptation is its name.
Some feathers fly and others blubber.
..Survival is the game.

Environs change and so do we,
..If we’re improved then we’re evolved.
If we stay the same we lose,
..extincted by the stall.

Pinch a seed or hold an egg,
..Then pick up any stone.
One hand holds life’s potential,
..The other can’t be cloned.

Birth she is uncertain,
..But her conditions are finite.
And death is always certain,
..We live between these plights.

Love

 

Your Yopa

 

Microscopy Today

Cells were not discovered until the seventeenth century, when the microscope was invented.

Three different microscopes produce images for different purposes:

  • Compound: for viewing by human eye.
  • Transmission Electron (TEM): for photographic film.
  • Scanning Electron (SEM): three dimensions.

Magnification, Resolution and Contrast

  • Magnification…The path of light rays and electrons moving through space is wavelike but the wavelength of electrons is much shorter than the wavelength of light.
  • Resolution… is the minimum distance between two objects that allows them to be seen as two separate objects.
  • Contrast… a difference in the shading of an object compared to its background.

Illumination, Viewing, and Recording

The human eye can view microscopic images when:

  • Light rays are bent (refracted) and brought to focus as they pass through glass lenses.
  • Electrons are directed toward a screen that are sensitive to their presence.

Confocal Microscopy… can create a three-dimensional image from a laser beam scanning across a specimen and producing a series of optical sections.

Video-enhanced Contrast Microscopy… a television camera converts the light image into an electronic image, which can be entered into a computer.  The computer makes the darkest areas of the original image darker and the lightest areas of the original much lighter.

 

 

Epigenetics

Same but not the same – the role of Epigenetics

Two people with the same genes can be different.  Scientists attribute this to nature (genes) and nurture (lifestyle & environment).  A third force affecting overall welfare, a bridge between nature and nurture, is epigenetics.

DNA methylation (a methyl group attaches to the cytosine base of DNA) weakens a gene, transcription cannot occur.

Epigenetics are heritable changes in gene expression without changing the DNA sequence.  Chemical reactions due to environmental exposures influence how genes are turned on or off (strengthened or weakened).

Discordant diseases in identical twins have different DNA methylation on certain genes.

Anxiety and calmness can be created by injecting or removing methyl groups with drugs.  Epigenetic medicines could correct or reverse disorders.

Questions to Consder

  1.  How does epigenetics affect transcription and translation?

Methyl group attachment prevents transcription and the gene can not translate.

2.  What lifestyle choices most likely negatively impact a person’s epigenetics?

 

Smoking dope may be fun

and more when you add beer.

Sex is even better

and those piercing look so dear.

Add a back tatoo,

and start to cut yourself.

Soon your twin won’t look the same,

and you’ll become an elf.

 

Possibly, another answer is:

 

If one twin trips to Chernobyl

and the other lips Liberia,

The methyl grips upon their genes

is worse than bland hysteria.

WHAT DID I LEARN?

A parent should allow nature and apply nurture but the environment always holds a trump card – and its blowin’ in the wind.  Class mates and food takes can grab your tikes by the genes and never let go.  It’s no wonder non-twins from the same parents with the more or less same nature and nurture grow up to become so different when you consider all of the environmental factors which are out of the parents control and growing, literally, out of control.

 

 

Metagenomics

Preface

Metagenomics Definition: The study of metagenomes – genetic material obtained directly from envronmental sample.

Traditionally, a scientist would isolate one species to culture enough DNA for sequencing resulting in the loss of the true biodiversity that existed in the sample.

Shotgun Sequencing (SS)

SS randomly shears DNA, sequences the short fragments, then reassembles these sequences into the correct order – called consensus sequence.

Eukaryotic DNA can be identified and removed, leaving the microbial DNA behind for analysis.

Studies Using Metagenomics

…does each type of mammal have its own community of (gut) microbes?

…the diet of mammals, not the specfic species of that mammal, determines what microorgansms live in the gut.

Metagenomics can also be used as a diagnostic tool to discover causative agents of diseases.

Questions to Consider

  1. Why is metagnomics used versus traditional genomic techniques?

Traditional science isolated and cultured only the most abundant species, resulting in the loss of the true biodiversity that actually existed in the collected sample, metagenomics allows for determining evolutionary interactions in a particular environment by revealing the hidden biodiversity of microscopic life.

2. Why is shotgun sequencing used in the field of study?

In order to gain knowledge on the true biodiversity of all species in a given environmental sample:

SS takes pieces of DNA and sequences the short fragments into the correct order.

The result is defined as a consensus sequence.

3. Why is metagenomics closely tied to evolutionary biology?

When used as a diagnostic tool, it can be used to discover causative agents of disease, such viral evolution, by filtering out DNA of a healthy species to reveal the disease in a sick subject.

Comment:

I don’t get the explanation of Shotgun Sequencing provided by the author.  SS got its name from the broad trajectory of buckshot a shotgun blast produces.  Then, SS is likened to putting ten copies of the textbook in a shredder, taking those pieces out and reassembling a complete book.

Without going further, two consecutive metaphors (1 metaphor, 1 simile) leaves a cub-metagenomicist with a rapidly spinning propeller.  I think I would try to reconcile the two metaphors before giving an explanation that doesn’t seem to address either.  There must be a better definition of Shotgun Sequencing out there.