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 GQA
AGFSYTD ANKNKGITWG EDTLMEYLEN PKKYIPGTKM IFAGIKKK
GE 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 GQA
VGFSYTD ANKNKGITWG E
DTLMEYLEN PKKYIPGTKM IFAGIKKK
DE R
ADLIAYLKK 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 GQA
AGFSYTD ANKNKGITWG E
DTLMEYLEN PKKYIPGTKM IFAGIKKKGE R
ADLIAYLKK 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 IFAGIKK
KGE R
EDLIAYLKK AT
NE
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
Do species change over time? 