The Scientific Method of Evolution

Discussion about scientific issues as they relate to God and Christianity including archaeology, origins of life, the universe, intelligent design, evolution, etc.
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BGoodForGoodSake
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Post by BGoodForGoodSake »

Before the discovery of DNA most scientists beleived that the hereditary information must be in the form of proteins.

Oswald Avery 1944
http://particle.physics.ucdavis.edu/bios/Avery.html
Discovered that DNA was the material which held the hereditary information.

After this discover some scientists continued to beleive that proteins contained the hereditary information simply because the sugar molecules DNA consists of seemed too simple to convey any information.

In 1953 this all changed when Watson and Crick discovered the double helix. This structure allowed researchers to glean at the duplication process, and how the information is stored.

Now it seemed that the decoding of the code of life would soon comence.

But before we get into genetic analysis, let us see what scientists did with Darwins new idea.

Georges Cuvier
http://www.ucmp.berkeley.edu/history/cuvier.html
The founder of vertebrate paleontology, he also developed a classification system of strict divisions of types based on function. A strict opponent of linnean evolution he did not beleive in evolution. He stated that any small changes would render an animal useless and thus would make it unable to survive.

Étienne Geoffroy St. Hilaire
http://www.ucmp.berkeley.edu/history/hilaire.html
Was a proponent that form defines function, one of the first practicioners of teratology, the study of development. Hilaire beleived that all animals shared a body plan. Cuvier found that this idea was not supported by his own studies. In a famed debate on the similarities of cephalopod and vertebrate design Cuvier convincingly argued that these similarities were contrived. Although not an evolutionist he would set the scene for comparative developmental studies.

August Weismann
http://www.britannica.com/eb/article-9076462
Founder of genetics, theorized on how genetic material must pass onto the next generation.

Julian Huxley
http://noosphere.cc/huxleymenu.html
Julian Huxley did some rather interesting studies on embryology and noted the development of embryos of sea squirts and sea urchins.

During the same time mathmeticians were beginning to see how the laws of heredity along with natural selection can account for change within a population.
J.B.S. Haldane
http://en.wikipedia.org/wiki/J._B._S._Haldane
Sewall Wrighthttp://www.harvardsquarelibrary.org/uni ... ewall.html
Sir Ronald Fisher
http://www.mrs.umn.edu/~sungurea/intros ... isher.html

Theodosius Dobzhansky
http://en.wikipedia.org/wiki/Theodosius_Dobzhansky
Studies with ladybugs revealed that individuals within a population had variations which were not needed for the environment they were found in. Leter he discovered that the more successful species tend to have greater variety present in the population.

Hugo de Vries
http://www.nceas.ucsb.edu/~alroy/lefa/deVries.html
Showed that new charachteritics appear suddenly and that they were inheritable.

At this point it is not generally accepted that all life is related only an idea that there is a parent type for each species.

Studies of cell biology soon changed this as it soon became apparant that all multicellular life at the cellular level was strikingly similar. From plants to birds, to paramecium.

Now to cap we have a theory. Evolution is the idea that species change over time and eventually become a new species resulting in all the variety we have on this planet.

What are the mechanisms for this theory?
Natural Selection.
Mutation.
Genetic Drift.

What are some ways that these mechanisms have been tested.
As seen before organisms go through a developmental embryonic or larval stage where a single cell becomes a complex multicellular organism.

The similarities between different species in embryological development were noted early on.
http://www.pbs.org/wgbh/evolution/libra ... 042_03.pdf

Also noted was that alterations early in the development phase has greater impact than changes which occur later in development.

Later discoveries show how mutations cause changes in development.

Many tests were put together to test natural selection, including inlab.
http://www.genetics.org/cgi/content/full/149/1/189
And in the field.
http://intl.sciencemag.org/cgi/content/ ... 7/5451/306

Mutations were found to add variety to a population.
Mostly from studies on rats and fruit flies.

Other studies of isolated pockets of species, lent credence to the idea of genetic drift. Lab experiments confirmed this idea, with the above mentioned discoveries of mutations.

Isolated populations could not share the same mutations.

So to sumarize, the questions posed by Darwins idea were as follows,

:arrow: Do species change over time?
It would appear that they do. Experiments have shown that new traits occur.
:arrow: Does natural selection occur?
Experiments have confirmed the mechanism.
:arrow: How does variation arise?
Through Mutations.
:arrow: How does natural selection work.
It works by selecting from existing traits.
:arrow: Is it gradual?
We are assuming so, but this will turn out to be more complicated than originally anticipated.
:arrow: What about the problems with the phylogenic chart?
At this point we are unaware of how large this problem actually is.

Now we bring up new questions.
How do we go from one form to another? How does a new species form?
Is all life related?
Is evolution gradual?
How do mutations actually work to add traits?

From our earlier discussion we see that the cell is like a controlled lab experiment. Add in some proteins and they will interact with other proteins in the cell in a cascade of reactions.

Proteins are a result of the amino acid chains encoded in the DNA.
The function of a protein is a result of its shape. There are areas of a protein which are functionally unimportant, we will address this next in the next to final section on comparative genetic analysis.
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Post by BGoodForGoodSake »

Wall-dog wrote:Take your time BeGood!

I'm enjoying the reading. I'm also learning an embarassing amount considering that I consider myself a reasonably well educated individual. Please - take your time and be as thorough as you think appropriate. There is nothing wrong with supplying a firm base of understanding.
Thank You.
Wall-dog wrote:I just wanted to make sure that you understood that the cumulative length of your posts isn't in and of itself going to constitute evidence supporting evolution.
Of course.
Wall-dog wrote:You could have summarized the entire thing prior to actual evolution with something like:
Evolution is not a theory based on a quagmire of speculation. It is a theory firmly rooted in mankind's base of knowledge, built on and interwoven within such differing disciplines as cellular biology, ... If I blow by anyone, please let me know and I'll slow down to fill in the blanks. What is important is that people understand that just as Darwin provided for the Tree of Life, science - of which evolution is a big part - provides for the Tree of Knowledge.
The problem with this approach is that most people eyes glaze over when you jump straight into it, that's why they teach high school biology, chemistry geology, and the basic courses in College. Without a foundation it's all greek.
Wall-dog wrote:I would have thought something like that would have sufficed. But that said, you are a great writer, I'm learning a tremendous amount, and I encourage you to continue.
Again Thank you.
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Post by Wall-dog »

BeGood,

Thank you for that very thorough synopsis!

I want to clarify right from the very beginning that I don't question most of the theory of evolution. I don't think anyone seriously questions the concept of species changing over time. What many scientists question is the notion that 1) evolutionary divergence can lead to new species, and 2) sufficient time existed for evolutionary divergence to create the initial complex species.

These scientists classified evolutionary theory into two groups. It is important to note that these groups aren't different in process - only in effect.

First we have micro-evolution. These are small changes within a species that can over time lead to variation such as different breeds of dogs or different ethnicities among humans.

Next we have macro-evolution. Macro-evolution is the notion that the changes observed in micro-evolution can, given time, create new species.

Pro-evolution scientists like to point out that macro-evolution doesn't really exist because at no time does one species just suddenly become another species. Rather, small changes over a vast array of time lead to different lineages and at some point the species in existence from those different lineages can be classified differently from one another. Bears and birds for example are very different even though they both are off-shoots of the same single-cell organisms. All life is related if you go back far enough. The popular image of a tree is useful for this because it shows all branches linking together into larger branches and eventually into a single line - the trunk. The image of a shrub is considered even more appropriate.

Technically, pro-evolutionary scientists are right that their theory does not call for macro-evolution, but for simplicity of argumentation I will ask that we use this term anyway under the understanding that it is being used not to describe a type of evolution, but rather it describes just a cumulative effect of evolution over time. Macro-evolution then will refer to a series of evolutionary change leading to different species or to a new species.

Another important point is the evolutionary notion that life was created in a non-intelligent manner - that amino acids assembled themselves into proteins and that proteins assembled themselves into cells.

Also, it is important to note that sufficient time must exist for evolutionary change to create a new species or to create separate species. How much time is 'sufficient' may be up for argumentation, but it's not something that will happen overnight.

At this point I don't think I've said anything anyone will disagree with. I'm going to wait to post more until the pro-evolutionary people on this forum have had a chance to question what I've posted thus far. I'll wait until BeGood has stated that this post does not misrepresent evolution in any way before I move on.

Edited - I've changed amino acids and proteins around, and changed the verbage as follows regarding the image of a tree:

"The popular image of a tree is useful for this because it shows all branches linking together into larger branches and eventually into a single line - the trunk. The image of a shrub is considered even more appropriate."

Those edits were based on a private message. If I get more private messages I may have to make more edits.
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Post by BGoodForGoodSake »

Wall-dog wrote:BeGood,

Thank you for that very thorough synopsis!

I want to clarify right from the very beginning that I don't question most of the theory of evolution. I don't think anyone seriously questions the concept of species changing over time. What many scientists question is the notion that 1) evolutionary divergence can lead to new species, and 2) sufficient time existed for evolutionary divergence to create the initial complex species.
Actually, I will go into this in my next post.
=)
Wall-dog wrote:These scientists classified evolutionary theory into two groups. It is important to note that these groups aren't different in process - only in effect.

First we have micro-evolution. These are small changes within a species that can over time lead to variation such as different breeds of dogs or different ethnicities among humans.

Next we have macro-evolution. Macro-evolution is the notion that the changes observed in micro-evolution can, given time, create new species.
Yes and no, there is no distinction, macroevolution is microevolution given enough time. This will also be discussed in my next post on genetics and genetic analysis.
Wall-dog wrote:Pro-evolution scientists like to point out that macro-evolution doesn't really exist because at no time does one species just suddenly become another species. Rather, small changes over a vast array of time lead to different lineages and at some point the species in existence from those different lineages can be classified differently from one another. Bears and birds for example are very different even though they both are off-shoots of the same single-cell organisms. All life is related if you go back far enough. The popular image of a tree is useful for this because it shows all branches linking together into larger branches and eventually into a single line - the trunk. The image of a shrub is considered even more appropriate.

Technically, pro-evolutionary scientists are right that their theory does not call for macro-evolution, but for simplicity of argumentation I will ask that we use this term anyway under the understanding that it is being used not to describe a type of evolution, but rather it describes just a cumulative effect of evolution over time. Macro-evolution then will refer to a series of evolutionary change leading to different species or to a new species.
Correct, however the term species does not actually exist in nature, it is a construct created by the human tendancy to categorize things.
Wall-dog wrote:Another important point is the evolutionary notion that life was created in a non-intelligent manner - that amino acids assembled themselves into proteins and that proteins assembled themselves into cells.
No, evolution does not cover the origin of life. The theory only covers the diversification of life.
Wall-dog wrote:Also, it is important to note that sufficient time must exist for evolutionary change to create a new species or to create separate species. How much time is 'sufficient' may be up for argumentation, but it's not something that will happen overnight.
Actually it can happen overnight.
Wall-dog wrote:At this point I don't think I've said anything anyone will disagree with. I'm going to wait to post more until the pro-evolutionary people on this forum have had a chance to question what I've posted thus far. I'll wait until BeGood has stated that this post does not misrepresent evolution in any way before I move on.
I don't think you misrepresented evolution at all.
=)
Continue.

I will post my next to last post tomorrow morning.

Edited - I've changed amino acids and proteins around, and changed the verbage as follows regarding the image of a tree:

"The popular image of a tree is useful for this because it shows all branches linking together into larger branches and eventually into a single line - the trunk. The image of a shrub is considered even more appropriate."

Those edits were based on a private message. If I get more private messages I may have to make more edits.[/quote]
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Post by Wall-dog »

BeGood,

I apologize! I thought you were done...

I don't want to interfere with you at all until you have had ample time to fully illustrate the scientific method of evolution. I'll wait for you to finish.
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Post by August »

No, evolution does not cover the origin of life. The theory only covers the diversification of life.
What is Macroevolution?

* The process by which new species are produced from earlier species (speciation). It also involves processes leading to the extinction of species.

* Occurs at the level of the species or above.

* Such changes often span long periods of time (but can also happen rapidly).

* Examples of macroevolution include: the origin of all life; the origin of humans; the origin of eukaryotic cells; and extinction of the dinosaurs.
http://www.life.uiuc.edu/bio100/lecture ... macro.html

Seems those stupid professors at the University of Illinois have got it wrong then...
Acts 17:24-25 (NIV)
"The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by hands. [25] And he is not served by human hands, as if he needed anything, because he himself gives all men life and breath and everything else."

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Post by BGoodForGoodSake »

August wrote:
No, evolution does not cover the origin of life. The theory only covers the diversification of life.
What is Macroevolution?

* The process by which new species are produced from earlier species (speciation). It also involves processes leading to the extinction of species.

* Occurs at the level of the species or above.

* Such changes often span long periods of time (but can also happen rapidly).

* Examples of macroevolution include: the origin of all life; the origin of humans; the origin of eukaryotic cells; and extinction of the dinosaurs.
http://www.life.uiuc.edu/bio100/lecture ... macro.html

Seems those stupid professors at the University of Illinois have got it wrong then...
This does not refer to the origin of the first life but rather the origin of all the diversity.

The origin of all life != origin of life.

Perhaps they need to clarify this website, it's a bit poorly done.
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Post by August »

BGoodForGoodSake wrote:
August wrote:
No, evolution does not cover the origin of life. The theory only covers the diversification of life.
What is Macroevolution?

* The process by which new species are produced from earlier species (speciation). It also involves processes leading to the extinction of species.

* Occurs at the level of the species or above.

* Such changes often span long periods of time (but can also happen rapidly).

* Examples of macroevolution include: the origin of all life; the origin of humans; the origin of eukaryotic cells; and extinction of the dinosaurs.
http://www.life.uiuc.edu/bio100/lecture ... macro.html

Seems those stupid professors at the University of Illinois have got it wrong then...
This does not refer to the origin of the first life but rather the origin of all the diversity.

The origin of all life != origin of life.

Perhaps they need to clarify this website, it's a bit poorly done.
How can the origin of ALL life not include the origin of the first life? Was the first life not part of all life?
Acts 17:24-25 (NIV)
"The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by hands. [25] And he is not served by human hands, as if he needed anything, because he himself gives all men life and breath and everything else."

//www.omnipotentgrace.org
//christianskepticism.blogspot.com
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Post by BGoodForGoodSake »

August wrote:
This does not refer to the origin of the first life but rather the origin of all the diversity.

The origin of all life != origin of life.

Perhaps they need to clarify this website, it's a bit poorly done.
How can the origin of ALL life not include the origin of the first life? Was the first life not part of all life?
=)
Language is not as exact as one some may think.

Perhaps you can email them and have them clarify for you.
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Post by August »

BGoodForGoodSake wrote:
August wrote:
This does not refer to the origin of the first life but rather the origin of all the diversity.

The origin of all life != origin of life.

Perhaps they need to clarify this website, it's a bit poorly done.
How can the origin of ALL life not include the origin of the first life? Was the first life not part of all life?
=)
Language is not as exact as one some may think.

Perhaps you can email them and have them clarify for you.
It contradicts your statement, and you should deal with it.
Acts 17:24-25 (NIV)
"The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by hands. [25] And he is not served by human hands, as if he needed anything, because he himself gives all men life and breath and everything else."

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Post by BGoodForGoodSake »

August wrote: It contradicts your statement, and you should deal with it.
I see how you can interpret it that way.

I will send them an email, in the mean time I stand by my statement.

Evolution deals with the origin of diversity of life not the origin of the first form of life.
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Post by August »

BGoodForGoodSake wrote:
August wrote: It contradicts your statement, and you should deal with it.
I see how you can interpret it that way.

I will send them an email, in the mean time I stand by my statement.

Evolution deals with the origin of diversity of life not the origin of the first form of life.
While you are at it, are you going to ask these guys too?
Welcome to BIOL 471
EVOLUTION

BIOL 471 is a course in three parts: (1) Phylogenetic reconstruction (classification, historical evolution, origin of life theory and fossil record); (2) microevolution (genetic variation, population genetics, molecular evolution); and (3) selection and adaptation (selection, modes of reproduction, species recognition, speciation). Available to juniors or seniors who have taken BIOL 311 or a college course in genetics.

The objective of this course is for students: (1) to appreciate the scope of modern evolutionary biology and genetics; (2) to become familiar with the professional literature in evolutionary biology; (3) to communicate evolution concepts to the public by means of written reports, posters and/or presentations; (4) to hear research reports presented by evolutionary biologists.
http://mason.gmu.edu/~jlawrey/biol471/

I didn't mean to bog down the discussion between you and Wall-dog, but your statement, which I believe to be generally correct, does not seem to be consistently applied across the teaching of evolutionary theory. I have seen at least 10 more college curricula that teach origin of life theories as part of evolutionary biology. The distinction may not be as clear-cut as you think. Can you maybe comment as to why the origin of life was excluded from evolutionary theory, since Darwin did include it in his writings?
Acts 17:24-25 (NIV)
"The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by hands. [25] And he is not served by human hands, as if he needed anything, because he himself gives all men life and breath and everything else."

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//christianskepticism.blogspot.com
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Post by BGoodForGoodSake »

August wrote:
BGoodForGoodSake wrote:
August wrote: It contradicts your statement, and you should deal with it.
I see how you can interpret it that way.

I will send them an email, in the mean time I stand by my statement.

Evolution deals with the origin of diversity of life not the origin of the first form of life.
While you are at it, are you going to ask these guys too?
Welcome to BIOL 471
EVOLUTION

BIOL 471 is a course in three parts: (1) Phylogenetic reconstruction (classification, historical evolution, origin of life theory and fossil record); (2) microevolution (genetic variation, population genetics, molecular evolution); and (3) selection and adaptation (selection, modes of reproduction, species recognition, speciation). Available to juniors or seniors who have taken BIOL 311 or a college course in genetics.

The objective of this course is for students: (1) to appreciate the scope of modern evolutionary biology and genetics; (2) to become familiar with the professional literature in evolutionary biology; (3) to communicate evolution concepts to the public by means of written reports, posters and/or presentations; (4) to hear research reports presented by evolutionary biologists.
http://mason.gmu.edu/~jlawrey/biol471/
No need,

The origin of life theory is a separate theory.

When discussing the variety of life one naturally asks where did it all begin.
The theory is related but not needed to study evolution.

There is another thread on science's lack of information for the origin of life here.
http://discussions.godandscience.org/about1733-0.html
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Post by August »

BGoodForGoodSake wrote:
August wrote:
BGoodForGoodSake wrote:
August wrote: It contradicts your statement, and you should deal with it.
I see how you can interpret it that way.

I will send them an email, in the mean time I stand by my statement.

Evolution deals with the origin of diversity of life not the origin of the first form of life.
While you are at it, are you going to ask these guys too?
Welcome to BIOL 471
EVOLUTION

BIOL 471 is a course in three parts: (1) Phylogenetic reconstruction (classification, historical evolution, origin of life theory and fossil record); (2) microevolution (genetic variation, population genetics, molecular evolution); and (3) selection and adaptation (selection, modes of reproduction, species recognition, speciation). Available to juniors or seniors who have taken BIOL 311 or a college course in genetics.

The objective of this course is for students: (1) to appreciate the scope of modern evolutionary biology and genetics; (2) to become familiar with the professional literature in evolutionary biology; (3) to communicate evolution concepts to the public by means of written reports, posters and/or presentations; (4) to hear research reports presented by evolutionary biologists.
http://mason.gmu.edu/~jlawrey/biol471/
No need,

The origin of life theory is a separate theory.

When discussing the variety of life one naturally asks where did it all begin.
The theory is related but not needed to study evolution.

There is another thread on science's lack of information for the origin of life here.
http://discussions.godandscience.org/about1733-0.html
While that is debateable, (the name of the course and the course objectives show that origin theory forms part of evolutionary theory), I will let you and Wall-dog get on with your discussion. We can return to this topic later.
Acts 17:24-25 (NIV)
"The God who made the world and everything in it is the Lord of heaven and earth and does not live in temples built by hands. [25] And he is not served by human hands, as if he needed anything, because he himself gives all men life and breath and everything else."

//www.omnipotentgrace.org
//christianskepticism.blogspot.com
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Post by BGoodForGoodSake »

In the previous post we answered some of the question, but by answering them new questions were brought up.

We will continue the discussion with comparative genetics.

We know now that a proteins function is dependant on it's shape. It's shape in turn is determined by the properties of the individual amino acids which comprise the polypeptide(amino acid chain).
http://www.friedli.com/herbs/phytochem/proteins.html

Proteins have what is known as an active site. This is the area of the protein which interacts with other substances. The rest of the protein is only support. Due to the complex way a protein folds.
[url]ttp://folding.stanford.edu/science.html[/url]

Now sometimes changing the sequence will dramatically alter the shape of the protein due to the way it folds.
Other times the resulting change only slightly modifies the active site. And at other times there is no effect to the active site at all. We will cover more on this later in the summary, but for now lets focus on the last example.

The cytochrome C experiment.

The active site of a specific protein is essential to the function of this protein, changes made here could have deleterious impact on an organism. Any changes made to an active site on an essential protein will most likely be removed from the process of evolution because the resulting organisms will die. The rest of the protein is arbitrary, as long as it does not impact the way the polypeptide folds any sequence is ok.

How do we know this? We replaced in a yeast cell the human equivalent.
http://www.pnas.org/cgi/reprint/91/25/11978.pdf
This metabolic pathway exists for all Eukaryotic(~non bacterial) Organisms.
So why is there an interest in the arbitrary sections of this particular protein?

The sequence for this section of the gene could have been any number of a random sequence of nucleic acids. However the gene which encodes for this protein does not show an arbitrary sequence when genetic analysis is done.

In other words animals thought to have shared a common ancestor have more similarities than those which are less related.

When populations which have been separated for some time are genetically analyzed clear differences in the gene pools between populations can be found.
http://www.blackwell-synergy.com/links/ ... 09040753.x

The following is a series of genetic sequences each letter represents an amino acid which in turn is coded in the DNA by triplets of nucleic acid.

For example.
Arabian Camel
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAVGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAVGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
Llama

A Camel and a LLama have the exact same sequence.

So do a Mouse and a Norway Rat
Mouse
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAAGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAAGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
Norway Rat

A Rabbit is different from the Rat by only two letters.
Rabbit
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAVGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKDE RADLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAAGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
Norway Rat

Sheep, Cow, Burro's, Zebra's all have the same sequence.
Orangutan, Chimpanzee's, and Gorillas also all have the same sequence for this particular protein.

By comparing differences we reach the same conclusion that scientist have reached using phylogenic comparisons. That animal species have a genetic relationship to each other.

For example after having shown that all rats share the same sequence here while having variations elsewhere.
And showing that rats share a genetic similarity to mice.
Then we show how mice are similar to rabbits.
And how rabbits are similar to sheep, there is a difference of three letters here.
Rabbit
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAVGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKDE RADLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKGE REDLIAYLKK ATNE
Sheep

Lets also look at sheep and rats.
Norway Rat
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAAGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKKGE RADLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKGE REDLIAYLKK ATNE
Sheep

Now looking at the amino acid sequence for just this gene one can surmise that perhaps sheep and rabbits had a common ancestor which possessed 2 or three of the same mutation, and then through diversion picked up one in the case of the rabbit and perhaps 2 in the case of the sheep more mutations.


...................------------------------------Rat,Mouse
Ancestor 1<................................-------Rabbit
...................---------Ancestor 2<
..................................................-------Sheep,Zebra,Cow,Burro

Now lets throw in the dog

Sheep
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKKGE REDLIAYLKK ATNE
GDVEKGKKIF VQKCAQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGFSYTD ANKNKGITWG EETLMEYLEN PKKYIPGTKM IFAGIKKTGE RADLIAYLKK ATKE
Dog

It shares 2 of the three mutations in relation to the rat and has additional mutations of its own in comparison to the sheep. So now we can draw the following.

...................----------------------------------------------Rat,Mouse
Ancestor 1<.........................--------------------------Rabbit
...................----Ancestor 2<................................----Sheep,Zebra,Cow,Burro
...........................................--- Ancestor 3-----<
..........................................................................----Dogs

After additional analysis we can see that it is the rat in relation to the dog and the rabbit which underwent changes in its sequence so we end up with the following cladogram.

..............................................................................----Rat,Mouse
..............................................--- Ancestor 3a-----<
...................----Ancestor 2a<................................----Rabbit
Ancestor 1<
...................----Ancestor 2b<................................----Sheep,Zebra,Cow,Burro
..............................................--- Ancestor 3b-----<
.............................................................................----Dogs

Of course we have thousands of genes and billions of non-coding sections we can compare as well!

After thorough analysis we get something like the following.
http://www.biomedcentral.com/1741-7007/2/19/figure/F5
The data is here
http://www.biomedcentral.com/1741-7007/2/19

Now is all life really related?
Well lets take a look from another perspective.
One can divide life into two groups.
Prokaryotic and eukaryotic life.
Prokaryotic cells are bacteria and archaeobacteria. They are very simple and tiny. Their DNA comes as a single ring shaped molecule.
Eukaryotic cells are what we are made of. They are about a thousand times larger than bacteria. What is it's organization? Well that can be the subject of another long post. But one interesting thing to note is that it appears to be a collection of smaller parts cooperating together. Sort of like how the body itself is a collection of cells working together as one.

Inside all Eukaryotic cells is an organelle called a mitocondria.
It reproduces on it's own and has its own genetic code. And like prokaryotes the DNA is in a ring formation not clustered into chromosomes like in the nucleus. There are more similarities to bacteria.
http://users.rcn.com/jkimball.ma.ultran ... iosis.html

It is theorized that the first eukaryotic life forms somewhere along the line formed a symbiotic relationship with mitochondrial bacteria precursors. This is known as the theory of endosymbiosis.

Does this still occur today?
http://www.sciencemag.org/cgi/content/s ... 0/5746/287

Because of the unlikelyhood of this occuring more than once, and the similarities between a yeast, plant and animal cell, all eukaryotic life is thought to have a common ancestor.

So the relationship of species is shown by analysis from several different angles.
Phylogenic trees can be developed by grouping animals into broader and broader categories.
Phylogenic comparisons allow the categorization of bats as mammals for example.
Or the layout of bones in all higher vertebrates allows one to see a relationshipo between a whale and a bird.(five digits on each hand, even though a whale uses it's to swim and a bird to fly.

Genetic studies examine the similarities and differences in the genes themselves.

The interaction of proteins makes it difficult to predict the results of a mutation. Many as we have seen above have no significant impact on the well being of an organism. Others can effect an organisms systemically causing wide spreading altercations, these are rarely harmless. And others just add more variety to the gene pool. These results are from the painstaking and numerous experiments on fruit flies and rats.

Development involves environmental and complex chemical signals. These chemical signals are, you guessed it, proteins encoded in the DNA.http://arjournals.annualreviews.org/doi ... e=pharmtox
In a way an organism is a colony of cells which communicate with each other through these developmental signals.

From develemental studies one discovers that many of the changes between species arises in the development of an organism. It can be shown that development of many organisms is parallel in many respects up until a diversion point. So a common ancestor must have had all the common development aspects and must act as a precursor to both.

Animals which are as diverse as dogs and horses share much of this development and only show distinctions in the later stages of development.

The degrees of relation can be determined in this manor. The genetic evidence supports the results, and phenotypic evidence supports this as well to a degree.

Now back to where it all started, the fossils.
Can we use fossils to prove evolution? No, but we can use fossils to point us in the right direction and as supplemental evidence. As we have seen before the fossil record led many to speculate multiple creation events. There are long periods of stasis and then sudden appearence of new species and diversity. This would seem counter to darwins idea of gradual change. Over time the new forms diversify, but not at the initial pace.

We will cover this in the final post.

So in summary we began with the following questions.

How do we go from one form to another? How does a new species form?
Species form from isolation.

Is all life related?
Phylogenic and genetic analysis point to this conclusion.
The theory of endosymbiosis has strong evidence that mitochondria is a result of symbiotic relationship and that all multicellular life is related to an original form.

Is evolution gradual?
It would appear that the evolution does not show gradual evolution but rather long periods of stasis followed by rapid evolution of new forms.

How do mutations actually work to add traits?
Mutations cause minor to major changes in proteins in which they encode, which can have minor to drastic results in the final form of the organism(cellular colony).

This adds to the list more questions.
How are changes in the genetic code supported by organisms which require specific proteins to survive. As we discussed earlier changes in a protein can radically alter its shape. If this occurs this new protein is added to the mix of existing proteins within a cell and interact with other elements according to the laws of chemistry which are based on the laws of nature. Because sexually reproducing are diploid this allows some changes to occur which may not effect the survivability of an individual. Sexually reproducing organisms are diploid, they have two copies of each gene. In the last post we will address gene duplication and other mechanisms which allow new features to arise.

Why is evolution not gradual?
Why do some species go unchanged for long periods?
Why does life go through periods of rapid evolution?
It is not length of life, but depth of life. -- Ralph Waldo Emerson
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