BIODIVERSITY

Evolution Part 2

So far we have emphasized that life

is an interesting form of chemistry.

This helps understand its role in

transforming the biosphere.

But the most obvious feature of life is the

staggering DIVERSITY of its many forms

We will examine this diversity from

the two main perspectives

1. Evolution

2. Ecology

Looking closer at this diversity, various patterns emerge.

In order to make sense of this vast diversity,

we look for ways to classify it, to simplify

One natural classification scheme is to arrange organisms

into groups that look the same. This is the approach of

traditional taxonomy. This approach leads naturally to a

study of evolution - evolutionary relatedness and organismal

adaptation (form and function).

That is, organisms will look the same for two main reasons – they

are closely related, and/or they express similar functional ―designs‖

For example, butterflies, birds and bats all fly and they all

look similar because of the wings. But looking closer, there

are big differences too, so they are classified as separate

groups (there are many different kinds within each group)

Another natural classification scheme comes from noticing that

some organisms tend to live together in the same places (and not

in others) – that life is organized into natural ―communities‖ of

diverse organisms. This leads to the study of ecology, the logic

of how different organisms interact and coexist.

For example,

major ecosystem

types called

biomes (deserts,

rainforests etc.)

have characteristic

organisms and are

found distributed

in different places

on the earth

3-5/3-6

And the

distribution of

biomes is

closely related

to the

distribution of

climates.

12-2

Both evolution and ecology are important dimensions of the

multidimensional problem of understanding biodiversity.

But before we could think about understanding, a

huge effort had to be expended in collecting and

grouping organisms into logical classes.

All human cultures have developed systems for classifying life

The system used by our culture

was established by Carolus

Linnaeus in the 1700s in Sweden.

Taxonomy – the classification of life

http://www.ucmp.berkeley.edu/history/linnaeus.html

The Linnaean System

This system is based on the idea that life is separated into

distinct species that can be classified into a nested, or

hierarchical, increasingly inclusive set of groups.

Ultimately, each species is given a distinctive binomial – a

two word name referring to the species and the group to

which it belongs (this is called ―binomial nomenclature‖)

This is similar to our method of naming

people, family name and individual name

e.g. Jimmy Page

Leopard- Panthera pardus

Genus – Panthera

Species - pardus

Panthera tigris (tiger)

Panthera leo (lion)

Panthera pardus (leopard)

Panthera onca (jaguar)

http://home.globalcrossing.net/~brendel/index.html

Panthera uncia

(snow leopard)

And now, more

BIOLOGY

In The News!

Sunday, Mar. 01, 2009

Indonesian tiger catchers race against time

By ZAKKI HAKIM - Associated Press Writer SUNGAI GELAM, Indonesia --

Indonesia's tiger catchers have a double job - protecting humans from

tigers, and tigers from humans. The elite teams of rangers and conservationists

rush to the scene every time villagers report attacks or sightings of critically

endangered Sumatran tigers. First, they calm the people. And then, if there are

signs the animal is nearby, they return with steel cage traps, live bait, heat-

sensitive cameras and other equipment to capture the magnificent beasts.

This time Sartono, who at 40 has spent nearly half

his life in the job, arrives with his six-member squad

at a remote oil palm plantation in Sungai Gelam

district, 375 miles west of the capital, Jakarta,

knowing they'll have to act fast. Three people have

been killed in less than a week. Sartono knows if he

and his team cannot put a quick end to the killing

spree, residents will shoot or poison the Sumatran

tiger, which is already on the brink of extinction

because of rapid deforestation, poaching and

clashes with humans.

There are only around 250 of the cats left in the

wild, compared to about 1,000 in the 1970s,

according to the World Wildlife Fund, meaning

the Panthera tigris sumatrae could become

the first large predator to go extinct in the

21st century.

For the next few days, they hike beneath the equatorial sun, their

clothes soaked in sweat, in search of clues, while other team

members interview witnesses and check out rumors of more attacks

and sightings. Finally, they have one of their own.

On a scorching Sunday afternoon, an adult tiger charges out of dense

jungle brush and then suddenly retreats into the shrubbery. Slowly, as

Sartono aims his cocked rifle at the trembling bushes, the squad

walks backward.

"I was afraid, who wouldn't be!" the veteran tiger catcher later says

with an uneasy laugh. "We might have experience, but we don't have

superpowers!"

The squad finally snags her. When they pull up in their green pickup

truck on day eight, they find a tigress six feet long - excluding the tail -

crouched in the trap. First she is calm, then she explodes, growling and

throwing her 180-pound body against the steel bars.

"Easy, easy, we're here to save you," whispers

Nurazman Nurdin of the Nature Conservation Agency,

as the crew carefully approach the tigress, which has

since been named Salma. For the tiger catchers it is a

tense but thrilling moment.

For villagers - who have locked themselves up after dark, shuttered stores, and

canceled prayers in the mosque from dusk to dawn - it is a relief. Though some

support plans to relocate the animal into a jungle far away, others wish the rangers

would just shoot it. Many worry there may be more tigers out there.

They are right. Three more people have been mauled to death in the same area

since the capture, all of them illegal loggers. Since those attacks took place within

the cats' habitat, there are no immediate plans to catch or relocate them.

The men on the tiger team said it was disturbing - and rare - that Salma

ate one of the victim's remains. Normally, Sumatran tigers avoid humans,

but if they do kill a man, they usually leave the corpse untouched. The

tiger catchers saw the unusual behavior as a sign of how desperately

hungry the tigress must have been. "There's no place for its prey to live

here, all the land has been converted into oil palm plantations," said

Nurdin, the Nature Conservation Agency official, as he surveyed churned-

up wasteland and neat rows of trees. "You can't expect tigers to become

vegetarians," Nurdin said. "They need meat and humans trespassing their

territory are relatively easy targets."

As their name suggests, these tigers can only be found

in the wild on Sumatra island. Their habitat is

disappearing at an alarming rate, with 667,000 acres of

lowland forests being cleared annually, mostly for palm

oil, which is used in cosmetics and candy but also to

make "clean-burning" fuel for markets in the U.S. and

Europe. Other culprits are loggers and mining companies,

whose projects limit mating grounds, leave remaining

tiger populations isolated and scattered, and chase off the

majestic cats' prey.

On average, five to 10 Sumatran tigers have been

killed every year since 1998, the report said. "At this

rate, they will soon be extinct," said Hariyo

Wibisono of Harimaukita, an alliance that

coordinates 15 state agencies and tiger conservation

groups.

Sometimes the animals are killed by frightened villagers, other times by poachers

who sell their carcasses for trophies or to supply a growing demand for tiger

bones in traditional medicine. A poacher can get $3,300 for a dead tiger - what

some people in this impoverished nation of 235 million make in a year - but

Nurdin said trafficking operations are almost impossible to crack because they

involve syndicates.

"Only the well-connected would dare to buy such

things," he said, noting that the last person they caught

trying to sell a carcass was a soldier.

At the present rate of deforestation, there

will eventually be no safe place to release

the captured tigers. So international

wildlife experts are working with the

government to come up with a 10-year

conservation strategy. They want palm oil

and other companies to either help

monitor the activity of tigers on their

property or, better yet, put aside some

land as a sanctuary for wildlife.

"For years, we fought against land

conversion, but it did not work," said

Wibisono, of the tiger conservation

alliance. "We had to try a different

approach."

Panthera tigris sumatrae

―A man-eating tiger is a tiger that has been compelled,

through stress of circumstances beyond its control, to

adopt a diet alien to it. The stress of circumstances is, in

nine out of ten cases, wounds, and in the tenth case old

age.‖

―There is , however, one point on which I am

convinced that all sportsmen … will agree with

me, and that is that a tiger is a large-hearted

gentleman with boundless courage and that

when he is exterminated – and exterminated he

will be unless public opinion rallies in his

support – India will be the poorer, having lost

the finest of her fauna.‖

Jim Corbett “Man-eaters of Kumaon” and other books

-from the Author’s Note

As we were saying -The Linnaean System

This system is based on the idea that life is separated into

distinct species that can be classified into a nested, or

hierarchical, increasingly inclusive set of groups.

Ultimately, each species is given a distinctive binomial – a

two word name referring to the species and the group to

which it belongs (this is called ―binomial nomenclature‖)

This is similar to our method of naming

people, family name and individual name

e.g. Jimmy Page

Leopard- Panthera pardus

Genus – Panthera

Species - pardus

Some interesting examples of species names (NY Times Feb 20 2005):

Bittium (mollusk) has a related

genus Ittibittium

Ba humbugi (snail)

Insects:

Heerz tooya

Apopyllus now

Pieza pi, Pieza rhea, Pieza

deresistans

Phthireia relativitae

For more check this out: http://home.earthlink.net/~misaak/taxonomy.html

The Linnaean System

Updated link - http://www.curioustaxonomy.net/

And now, more

BIOLOGY

In The News!

Saturday, Feb. 28, 2009

Indonesia's psychedelic fish named a new species

By ROBIN McDOWELL - Associated Press Writer

JAKARTA, Indonesia

A funky, psychedelic fish that bounces on the ocean floor

like a rubber ball has been classified as a new species, a

scientific journal reported. The frogfish - which has a

swirl of tan and peach zebra stripes that extend from its

aqua eyes to its tail - was initially discovered by scuba

diving instructors working for a tour operator a year ago

in shallow waters off Ambon island in eastern Indonesia.

The fish - which the University of Washington professor has named

"psychedelica" - is a member of the antennariid genus, Histiophryne, and like

other frogfish, has fins on both sides of its body that have evolved to be leg-like.

But it has several behavioral traits not previously known to the others, Pietsch

wrote. Each time the fish strike the seabed, for instance, they push off with their

fins and expel water from tiny gill openings to jet themselves forward. That, and an

off-centered tail, causes them to bounce around in a bizarre, chaotic manner.

The fish, which has a gelatinous fist-sized body covered

with thick folds of skin that protect it from sharp-edged

corals, also has a flat face with eyes directed forward,

like humans, and a huge, yawning mouth.

Mark Erdman, a senior adviser to the Conservation International's marine

program, said Thursday it was an exciting discovery. "I think people thought

frogfishes were relatively well known and to get a new one like this is really

quite spectacular. ... It's a stunning animal," he said, adding that the fish's

stripes were probably intended to mimic coral.

"It also speaks to the tremendous diversity in this region and to fact that there

are still a lot of unknowns here - in Indonesia and in the Coral Triangle in

general."

Ques – so what is the correct

binomial for this species?

Jimmy Page

Led Zeppelin

English Rock Bands

Music groupsHierarchical classification is

totally natural for us –

although the ―ideal‖ system

of classification can be

elusive

The Linnaean System

Dec. 10, 2007

Stairway to Heaven (R. Plant & J. Page)

There's a lady who's sure

All that glitters is gold

And she's buying a stairway to heaven.

When she gets there she knows

If the stores are all closed

With a word she can get what she came for.

Ooh, ooh, and she's buying a stairway to heaven.

There's a sign on the wall

But she wants to be sure

cause you know sometimes words have two meanings.

In a tree by the brook

There's a songbird who sings,

Sometimes all of our thoughts are misgiven.

Ooh, it makes me wonder,

Ooh, it makes me wonder.

There's a feeling I get

When I look to the west,

And my spirit is crying for leaving.

In my thoughts I have seen

Rings of smoke through the trees,

And the voices of those who stand looking.

Ooh, it makes me wonder,

Ooh, it really makes me wonder.

And its whispered that soon

If we all call the tune

Then the piper will lead us to reason.

And a new day will dawn

For those who stand long

And the forests will echo with laughter.

If there's a bustle in your hedgerow

Don't be alarmed now,

Its just a spring clean for the May Queen.

Yes, there are two paths you can go by

But in the long run

There's still time to change the road you're

on.

And it makes me wonder.

Your head is humming and it won’t go

In case you don't know,

The piper’s calling you to join him,

Dear lady, can you hear the wind blow,

And did you know

Your stairway lies on the whispering wind

And as we wind on down the road

Our shadows taller than our soul.

There walks a lady we all know

Who shines white light and wants to show

How everything still turns to gold.

And if you listen very hard

The tune will come to you at last.

When all are one and one is all

To be a rock and not to roll.

And she's buying a stairway to heaven.

The Linnaean system uses a

particular set of levels that has

been modified over time –

genus, family, order, etc.

The Linnaean System

The Tree of Life

The Linnaean system was developed before ideas about

evolution and the relatedness of all life, yet it is consistent with

that view (and inspired it) and has remained in wide use

The evolutionary view adds an historical component – that

the species we see today derive by a process of speciation

(separation of one species into two over time), creating a

―family tree‖ of ancestral and descendant species

These relationships are usually

depicted as a branching tree, or

phylogeny (or ―phylogenetic tree‖)

The Y-axis is time – down is

longer into the past, branching

implies speciation events

The hierarchical

branch ―clusters‖

correspond to the

taxonomic levels

This is a ―rough‖

correspondence but

overall traditional

taxonomy has been

an excellent guide to

modern phylogenetic

reconstruction

The Tree of Life

The Tree of Life

Phylogenetics – determining these trees for taxonomic

groups is a very active area of research. The ultimate

goal is to construct the complete family tree of life, and to

make this the basis of our taxonomic system.

You can find out the current status of this effort at

http://tolweb.org/tree/phylogeny.html

The basic idea of this approach is to classify

species by their various characteristics, or

traits, and to identify which traits are newer and which

older. Traits that are relatively older are called ancestral,

more recently evolved are called derived.

The Tree of Life

This style of reasoning

is essentially the same

as traditional taxonomy

The Tree of Life

The current explosion in tree of life research has been fueled

by our new knowledge about gene (and protein) sequences.

This is essentially an entirely

new and extremely precise array

of species traits from which

detailed phylogenies can be

constructed – independently of

traditional observable traits.

This independence creates a welcome check on traditional

taxonomy. So far it has mostly confirmed the traditional approach,

but in some cases has provided interesting new insights.

For example, traditionally reptiles and birds are

separated into different classes: Reptilia and Aves

But the genetic evidence suggests that crocodiles,

traditionally considered reptiles, are really closer to

birds than to other reptiles.

Reptilia Aves

Naturally, there is a lot of discussion about how to sort this out

What would you suggest?

The Tree of Life

Here are some of the contenders – is your solution here?

The Tree of Life

http://www.eidnesfurs.com/index.html

What is a gene sequence?

Recall: Gene expression is the protein

production machinery of a cell’s

biochemistry. Proteins are used in

various ways, but especially in the form

of enzymes, that catalyze reactions – they

regulate what reactions happen when –

that is, they control everything.

How can a gene sequence be used to create a phylogenetic tree?

- a long chain molecule, or polymer, a chain of small organic

molecules amino acids (20 different types), that when

assembled, folds itself into a 3-dimensional shape that can

catalyze a reaction.

What is a protein?

The final protein structure is determined by the

sequence of amino acids in the protein polymer.

What controls the amino acid sequence of a protein?

The DNA molecule is also

a long chain of simpler

organic molecules

(―nucleic acids‖) that

contains the protein

sequence in coded form,

using the genetic code

The genetic code is not a simple one-for-one code because there are

only four different nucleic acids (A,T,G,C) to code for 20 amino acids.

This molecule can be copied,

keeping the sequence intact

DNA sequence

becomes a protein

sequence

There is an

intermediate

step involving

an RNA

sequence

It is a ―triplet code‖ – every three nucleic acids code

for each subsequent amino acid

The genetic code

As far as we know,

the code is pretty

arbitrary – could

have been different

and still work fine

Yet, all species use

the same genetic

code, supporting idea

of a common origin

of all life

The DNA stores the sequence information for all the proteins

needed by the organism

―Gene expression‖ is this

conversion – protein production.

Which genes are ―turned on‖ when

Since enzymes regulate

biochemistry, including gene

expression, the regulation of gene

expression is the ultimate controller

Gene expression is responsive to the

environment (internal and external)

A ―gene‖ is a particular DNA

sequence that codes for a

particular protein

And now, more

BIOLOGY

In The News!

Friday, Feb. 27, 2009

Gene therapy might regrow teeth

By Lauran Neergaard - Associated Press

WASHINGTON — Ever wonder why sharks get several

rows of teeth and people get only one? Some geneticists

did, and their discovery could spur work to help adults

grow new teeth when their own wear out.

If scientists knew exactly what triggers a new tooth to grow in the first

place, it's possible they could switch that early-in-life process on again

during adulthood to regenerate teeth. Also intriguing: All the mice

born without this gene, called Osr2, had cleft palates severe enough

to kill. So better understanding of this gene might play a role in efforts

to prevent that birth defect, the Rochester team reported in the journal

Science.

A single gene appears to be in charge, preventing additional tooth formation in

species destined for a limited set. When the scientists bred mice that lacked

that gene, the rodents developed extra teeth next to their first molars —

backups like sharks and other non-mammals grow, University of Rochester

scientists reported Thursday.

"It's almost a self-generating propagation of the signal" that leads to one tooth after

another forming all in a row, he explained. Knocking that molecular pathway out of

whack causes either missing or extra teeth to result, Jiang showed in a series of

mouse experiments.

Think of the Osr2 gene as a control switch, a

kind of gene that turns on and off the downstream

actions of other genes and proteins. The Osr2 gene

works in concert with two other genes to make

sure budding teeth form in the right spot, said

lead researcher Dr. Rulang Jiang, a geneticist at

Rochester's Center for Oral Biology.

'It's exciting. We've got a clue what to do,' said

Dr. Songtao Shi of the University of Southern

California School of Dentistry, who said the

Rochester discovery will help his own research

into how to grow a new tooth from scratch.

Saturday, Dec. 26, 2009

UK researcher helps develop

Ruppy, a glowing dog

By Cheryl Truman, Herald Leader

Ruppy, a genetically engineered

beagle that glows, lives in Korea,

but he's creating a stir at the

University of Kentucky.

The fluorescent canine, infused

with a gene from a sea anemone

and known as the world's first

transgenic dog, isn't really a single

animal.

Even in broad daylight, this is a dog of a different

color: You can see it in the red flush of the pads on the

bottoms of his feet.

Why a red flush? Because researchers needed a trait

that would be visible immediately. A color change in a

puppy does just that.

Initially there were three "Ruppy" puppies — short for ruby puppy— all beagles,

part of a project that UK fertility researcher Chemyong Jay Ko was involved

with at Seoul University in South Korea. Now, Ko says, there are several groups

of cloned Ruppys — maybe 30.

Ko is emphatic that the latter-day Ruppys not be called offspring or siblings or

even the next generation of transgenic puppyhood: They're clones, he says, and

clones do not follow the standard order of beagle family trees.

Ko, who came to UK as a post-doctoral student in 1998,

says he spends several weeks a year in Korea working

with the research team that developed Ruppy. In 2005,

Snuppy, a cloned Afghan hound, was introduced. Ko

then contacted the researchers and became involved in

the research that resulted in Ruppy.

This new proof-of-principle experiment should

open the door for transgenic dog models of

human disease, says Ko. "The next step for us

is to generate a true disease model," he says.

His lab hopes to knock out a specific oestrogen

receptor in dogs to understand the hormone's

effects on fertility.

Ruppy is almost too cute to be thought of as a research subject.

There are two ways of looking at this: You can think, as Ko does, that the

development of a glowing beagle is a step forward in genetic science that

points the way to all manner of advances — from commercial development

of dogs bred with specific traits, such as green eyes, or developing a gene

that could address a specific disease, to changes in the way researchers

collect blood for research. [He says that dogs have a lot more blood than a

lab mouse. Further, he says that lab technology has evolved to allow for a

nearly painless withdrawal of blood.]

The other way to look at the moral implications of Ruppy raises questions about

whether there's a difference between exhausting a supply of lab mice and

keeping dogs for experiments. Where in the mammalian line the difference

comes, where humans start to look at animals as companions and defend their

welfare rather than writing them off as commodities is difficult to say. But the

idea of tinkering with dogs strikes some as far more awful than making Glo Fish,

which are available at many pet stores. The genetically altered fish are available

in "Starfire Red," "Electric Green," and "Sunburst Orange," although sale of the

designer fish has been banned in California.

[Ko] professes some amazement in dealing with the aftermath of the

announcement of Ruppy's existence. Network news has been in touch.

Animal-rights activists are posting on The New York Times Web site,

where Ruppy made the Times magazine's list of the top ideas of 2009, and

the Ruppy project has been kicked around on various blogs.

"You can make thousands of kinds of transgenic animals," Ko says.

Sara Rosenthal, director of the UK Program for Bioethics, says that

humans tend to assign greater moral worth to larger animals and those

who resemble us. Nonetheless, she notes, even primates such as

chimpanzees are used in research because such research spares human

suffering; to humans, and in research circles, that is the most unsettling

research.

"We use animals because we find that animals are in service to reduce the

number of humans" that have to be used for medical advances, Rosenthal

says. "The ethical justification for using animals in research has to be

very strong."Some medical advances, such as the discovery of insulin in

1921, would not have been possible without using dogs in research,

Rosenthal said.

Genes are the third key ingredient, or

resource, in the recipe for life – information

1. Energy

2. Materials

3. Information

Information encoded in the sequences of

DNA can be thought of as a kind of

knowledge, often referred to as a library

This information has accumulated over the billions of years

of life’s history on earth. It is reasonable to think of it as a

natural resource, built into the structure of living organisms.

The differences between organisms

are due to differences in their genes

Each species carries

genes that are unique

to that species – unique

information

DNA sequences can be used to create phylogenies

by assuming that the more similar the gene

sequences, the more closely related the species are

What is the logic behind this assumption?

Reptilia Aves

3. Given 1 & 2, the current diversity must have resulted

from a diversification of the genetic makeup of organisms.

1. All life arose from a single common ancestor

2. Organisms differ primarily in their genes

4. The diversification was one step at a time –

biochemistry is too complicated to change radically

5. The more time has elapsed since lineages

diverged, the more steps have been taken

Interestingly, these assumptions don’t require any specific

knowledge about gene function – it even applies to genes

that have no known function (silent or ―junk‖ DNA)

What is the logic behind this assumption?

Human ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTT...

Yeast ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTT...

Corn ...GCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTT...

Escherichia coli ...GCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGT...

Methanococcus sp. ...GCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCT...

Some genes have changed very little, and can help

compare very distant relatives (here a segment of rRNA)

Some regions change very fast – what would they reveal?

http://www.bact.wisc.edu/Bact303/Phylogeny

This work has led to

a detailed ―big

picture‖ view of the

tree of life, including

the establishment of

the ―Three Domain‖

concept

Also, much fine detailed

study of evolutionary

changes within-species

End Evolution part 2