Bacterial Origin of Certain Eukaryotic Organelles - Evidence for Evolution

The theory of an endosymbiotic relationship forming the origin of
certain organelles (cellular compartments) in eukaryotic cells is
pretty cool and the evidence is just too good to dismiss. This theory
was formally proposed in 1905 by a Russian botanist familiar with the
work of another botanist who noticed in 1883 that chloroplasts, the
organelle in plant cells that carries out photosynthesis, divide in a
manner strikingly similar to free-living cyanobacteria. This idea was
extended to include the mitochondria (the energy factories of our
cells) of all eukaryotic cells in the 1920s. Of course this idea was
not widely accepted at first, as is true with most scientific advances.
Newer microscopic technology revealed great structural similarity
between chloroplasts and cyanobacteria in the 1960s and the idea was
resurrected.
What is the current evidence supporting the idea that, at an ancient
date, one cell engulfed a bacteria and that the bacteria survived
inside that cell and was adapted over time to serve a specific and
unique, but vital, function inside the engulfing cell?
1) New mitochondria and chloroplasts are formed only by a process
similar to bacterial binary fission
2) These organelles are surrounded by 2 membranes; the inner membrane
shows differences in composition compared to other membranes of the
cell and it contains a peptidoglycan wall similar to a bacterial cell
3) Mitochondria and chloroplasts contain their own DNA (that's right
not all of your DNA is in the nucleus) that is similar to bacterial DNA
in its size and shape - ie nuclear DNA is straight, mitochondrial DNA
is circular like bacterial DNA
4) The ribosomes (important in protein manufacturing) of mitochondria
have biochemical properties resembling bacterial ribosomes rather than
the ribosomes of the cell
5) The amino acid that initiates protein synthesis for mitochondrial
proteins is the same as that used by bacterial cells which is not the
same amino acid as the cell uses to initiate protein synthesis.
There is more but those are the most convincing. This idea that at one
time our cell's ancestors were host to free-living bacteria is not
surprising. There are protists today that contain free-living bacteria
in their cytoplasm and the two get along quite nicely together. I think
it's an elegant illustration of symbiosis that has evolved to be
beneficial, even necessary, for the development of more complex
organisms. Adapting a bacterial cell to be our energy producers is an
ingenious detail of creation.

As Promised

Here is the first installment of my noble attempts to educate you sufficient to refute common arguments against the theory of evolution by natural selection. Remember (Ammon) that my purpose here is not to convince skeptics that current evolutionary theory is the final word, I merely wish to correct common misconceptions about evolution. In this way, as you continue to think about the validity of these theories you won't be encumbered by a false understanding of what the theory actually states.

Oh, and I won't cover all 10 of the previosly stated misconceptions in this post for the sake of time. I'll do 5 now and 5 later.

1 - "Evolution is just a theory" - The implication here is that evolution hasn't been proven, that it's just an unsubstantiated guess. People who say this are most likely to be people who don't know what Darwin actually theorized and are too lazy to look into it so they just dismiss it out of hand. They're like agnostics; they prefer to remain ignorant. But let's analyze the actual statement. While it's true that evolution is a theory, the use of the word "JUST" reveals a fundamental inability to comprehend what a scientific theory is. Well, first of all a simple definition of evolution is "a change in allele (ie - some variant of a gene) frequency over time" and is thus an undisputed fact. The informal usage of the word "theory" is very different than the scientific use of the term. In science, a theory is a collection of proposals to explain some observed phenomena. The proposals are supported and substantiated by alot of evidence over time. Often, some will claim that evolution is not a scientific law. Well, it's not a chain of progression. Scientific theories don't graduate to the status of law given a sufficient amount of evidence. Theories remain theories. These theories continue to accumulate evidence in support of them, or new evidence arises which causes the community to tweak the theory a bit. The theory of evolution by natural selection continues to be supported by all available evidence across all fields of biology (genetics, embryology, anatomy, microbiology, paleontology, behavioral science, molecular biology, etc.)

2 - There are no transitional fossils - A transitional fossil would be one that represents an intermediate between two species. Thus, it would have certain features representative of species A and others that are representative of species B. Well, first of all this is just false. Secondly, the fossil is record is imperfect and always will be given that the conditions for fossilization to occur are very stringent and the occurrence of fossil formation is the rare exception to the rule. However, we do have transitional fossils found in different strata of the earth documenting dramatic progressive changes in features of ancient animals. This, of course, all supports the idea of descent with modification.

3 - If we all evolved from apes, why are there still apes running around? - Well the first problem with this is that the asker doesn't understand that the theory of evolution doesn't claim that we evolved from modern apes. Modern apes and humans share a common ancestor that no longer exists. An ancestral species doesn't have to give rise to just one descendant. There can be parallel evolution where different species evolve differently (based on the available gene alleles and environmental conditions) from the common ancestor. This is apparently what happened. But either way, just because a new lineage begins to split off doesn't mean that an ancestral species HAS to go extinct. So even if we descended from modern apes, that doesn't mean modern apes would have to go extinct in order for us to exist.

The explanation for this one is a bit more subtle and I fear I'm having trouble explaining it but inside this statement is a fundamental misunderstanding about the theory of evolution so don't ever be foolish enought to say that evolution can't be true because there are still apes on the earth. On a personal note, if you've ever spent time really staring at an ape in the zoo you can't honestly tell me that there isn't something "more" there. Looking, really looking, into the eyes of an ape is worlds different that looking at a bird or even an elephant or giraffe. There's a closer relationship there, there's alot more commonality and it is very evident. It's quite an experience.

4 - Natural selection always leads to greater complexity (organisms are always "getting better") - Simply false. Selection is blind to anything except whether or not an organism can reproduce. In nature, good enough is good enough.

5 - Evolution promotes the survival of species - Evolution can take place at the level of a gene and what promotes the survival of a particular gene doesn't always lead to great reproductive fitness for a population. For example there are parasitic DNA elements that can spread through a population but cause disease. Hemophilia is caused by such a DNA element and this certainly doesn't promote survival. Varying mutation rates can affect survival as well. A mutation rate that is too high can be very detrimental to a species because nature doesn't have time to weed out the "bad" mutations before they spread too widely. For example, HIV exists on a very narrow error threshold. HIV mutates so rapidly that it is precariously close to destroying itself because many of the mutations create unviable virus.