Thursday, January 31, 2013

Beneath the Surface

I am adding another post to my blog about the subject of biology. This is not to confuse you but to hope you appreciate the vastly complicated interactions that must take place in order for life to occur and proceed. Evolutionists talk about fossils and bones, but beneath the surface of individual bacteria, plants and animals is a vast interacting world which must function in order to get life going and continuing.  I have a few pictures below to give you an idea of these activities.

Did the organized biochemistry of life happen by totally materialistic, naturalistic means through chance? On one hand, the current theory, called “neo-Darwinism” claims that natural selection, known as “survival of fittest,” is not by chance, but comes about by competition of those who reproduce. But on the other hand according to the same neo-Darwinism, any superiority of individuals depends on random mutation of their genes. They can't get away from the fact that materialistic evolution is ultimately based on chance.

Neo-Darwinism is not better and is actually less logical than the belief that God made species directly. I wonder sometimes what evolutionists are thinking. In fact, I’ve got to believe there are many scientists out there who are not saying much publicly but must seriously doubt whether totally materialistic, naturalistic evolution can be true.

That is why I am taking the time to show you some of the facts. Though I’m not an expert in cell biology, I have a background in biology (I graduated from two universities with a BS in animal science and a VMD in veterinary medicine). I have spent a lot of time reading scientific research on genetics, biochemistry and cell biology.

My last post was about the complexity of the cell’s energy-making system. But, it was actually only a part of that system. Another part is needed to process food we eat in order to get pieces of it to feed into this system. In humans, the process is known by a few names, one being the citrate cycle .

Chemical interactions between molecules are the underpinning of biological function. The molecules are made of atoms, with which most of us are familiar. The air we breathe is made of various atoms, including oxygen. These combinations of atoms are often described with terms we don’t recognize unless we study them, but we can still understand some concepts without knowing all the names of the molecules. There are more and more databases of information about biology and other disciplines available. Scientists add to this data from their discoveries and use it for further research. A lot of the information is accessible by Internet, which is a wonderful service to scientists and anyone else who wants to learn.

One of these databases is called Kegg, for Kyoto Encyclopedia of Genes and Genomes. I had a picture of part of the energy system from Kegg in my last post. Here I will show an overview map (picture 1) of the biochemical activities of cells which they have put in their database. (You don’t have to go to the website since I have a picture here of what you would find, but if you want to go, you can click on the "overview map" link.  You can also click on the picture here to get a larger view.) The paths contain biochemical reactions for various species.  For example, it describes how the body processes things like fats and proteins that we eat. These chemicals must have precise coordination of molecules for fitting together and producing the desired outcome in each species.

The map does not nearly cover all the biochemcial reactions that exist. In fact, the current estimate for the number of species on Earth is over 11 million. The National Institutes of Health did a 2008 study on the single-cell organisms of bacteria and what are called archaea (are-KEY-ah). They found that “remarkable biochemical diversity is a hallmark of bacterial and archaeal biology.” So you can be sure there is much out there that is not yet on this map. These are the chemical data that the people who do the map know about and have inserted.

The citrate cycle is a small portion of biological metabolism. In the overall map, the cycle is named inside the small round blue line in about the middle near the bottom. If you go to the Kegg site and click on the “citrate cycle” name, it will bring you to a chart of the chemical reactions that happen in the cycle. I have a picture of the human citrate cycle here (picture 2). The green boxes are links to further information about the human biochemical reactions. They show facts about the proteins called enzymes (EN-zimes) that work to change molecules within the cycle so they produce the necessary segments for energy production.

Don’t be concerned if these terms sound foreign to you. I’d just like you to get an idea of what goes on in our bodies. One of the green boxes shows the number 4.2.1.3. This is a protein enzyme called aconitate hydratase (ah-CON-ih-tate HI-drah-tase). If you click the box at the Kegg website, you get information, with more links, about aconitate hydratase.  The rectangular box here is what you would see (pic. 3).

The box contains a picture of the protein. I want to show you a similar, larger picture from another database of the aconitate hydratase protein as they use it in models. The last picture here (picture 4) is from Swiss Model Repository, which is a database that shows the 3 dimensional models of proteins. The swirls and arrows show the types of folds that the amino acids make in order to form the protein so it does a specific job. This protein is made up of 780 amino acids which must be in a particular order (if you are interested in more details of the protein, you can get them at yet another database, Uniprot ). At the bottom of the third picture, there is a list of amino acids that make up the enzyme that we are talking about. (For information on amino acids, go here.)  For purposes of saving space, I did not add the bottom section of the box, which lists the specific order of the DNA of the protein's gene.

If you have gotten this far, I appreciate that you have been interested enough to read about the complexity of cell biology. It is important because of what I’ve been talking about concerning the question of neo-Darwinian evolution and whether it actually happened. Though you may hear some scientists or their spokespersons say evolution is a fact, the possibility and reality of it is something you have to decide for yourself.

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