Proteins are the machinery of living tissue that builds the structures and carries out the chemical reactions necessary for life.
As can be seen even by this limited number of examples proteins carry out amazingly diverse functions.
Thus it seemed to Haeckel that such simple life could easily be produced from inanimate material.
In Darwin's time all of biology was a black box: not only the cell, or the eye, or digestion, or immunity, but every biological structure and function because, ultimately, no one could explain how biological processes occurred.
This fact immediately suggested a singular event - that at some time in the distant past the universe began expanding from an extremely small size. To many people this inference was loaded with overtones of a supernatural event - the creation, the beginning of the universe.
It is often said that science must avoid any conclusions which smack of the supernatural.
Although Darwin was able to persuade much of the world that a modern eye could be produced gradually from a much simpler structure, he did not even attempt to explain how the simple light sensitive spot that was his starting point actually worked.
In the 19th century the anatomy of the eye was known in great detail and the sophisticated mechanisms it employs to deliver an accurate picture of the outside world astounded everyone who was familiar with them.
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.
The point here is that physics followed the data where it seemed to lead, even though some thought the model gave aid and comfort to religion.
In many biological structures proteins are simply components of larger molecular machines.
In order to say that some function is understood, every relevant step in the process must be elucidated.
The basic structure of proteins is quite simple: they are formed by hooking together in a chain discrete subunits called amino acids.
Biology has progressed tremendously due to the model that Darwin put forth. But the black boxes Darwin accepted are now being opened, and our view of the world is again being shaken.
Science is not a game in which arbitrary rules are used to decide what explanations are to be permitted.
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