Friday, January 30, 2009

Origins 8, Second Orders

I first titled the last entry "Chemistry is not Biology." However, I realized that it might sound like I'm trying to say that chemistry doesn't work at the biological level, which is not true. The atoms and molecules in our bodies definitely work according to the rules of chemistry, physics and biology. I changed the post name to "Chemistry is not Selection." Natural selection is a property of groups of organisms, which is not the same as groups of atoms and molecules. The mathematical laws are worked out for each situation and are different.

Though Intelligent Design Theory (ID) is lumped with other Creationist theories in the minds of many detractors, ID tries to strictly follow scientific fact. The advocates are sometimes accused of not knowing the Earth is round, or that gravity is a physical law. But the point is that ID advocates know physics and chemistry very well, and there is a discontinuity between the physics and chemistry of non-living matter and that of life. The origin of biological organisms is not explained by chemical and physical laws alone.

The accusation that non-naturalistic articles concerning biological origins and evolution have not been published is untrue. One of the first articles was "Life Transcending Chemistry and Physics," by Michael Polanyi in the Chemical and Engineering News of the American Chemical Society in 1967, 45:35 pp54-66. I can't find a link to it on the Internet and ordered my copy through inter-library loan. I have a link to a commentary by Colin Duriez in the Journal of the ASA (American Scientific Affiliation) which explains Polanyi's position. He talks about "orders" of physics and chemistry. Machines, for example, are not explained by the physics and chemistry of nature alone and therefore have a second order above the movement of atoms and molecules. In this way, he believes DNA, with its informational functions, has this second order.

Next post, I want to give the definition of "Horizontal Gene Transfer," and the propositions being made as to some of the amazing findings coming out of the whole-genome sequencing that has been done for the last dozen years and will continue well into the future.

Tuesday, January 27, 2009

O7, Chemistry is not Selection

Popularizers of evolution try to sometimes ignore, sometimes mix and match, the rules of chemistry and biology. They use examples which will lead you to think that random chance does not take very long to become ordered into functional molecules and then organisms. For example, they start with a set of random letters and develop it into a sentence. They say the letters of sentences can"stop" at the correct position as other letters randomly try to fit into something intelligible. But the only way they can stop is if they "know" which sentence the experimenter wants. Such are the ways of computer simulations and games of evolution.

These persons are trying to use the principles of Population Genetics, which helps determine changes in groups of living beings through "survival of the fittest." In natural selection, animals which are more fit can survive the environment better and reproduce more, thereby passing on their "better" genes for a better species (like the random letters would pass on better sentences to become more functional). But you will never read about "survival of the fittest" in chemistry text books.

In calculating Population Genetics, the genes are already in place, and the mathematics is about the possible combinations of varieties of those genes. There may be changes over time when the gene mutates, and that is considered in mutation rates that have been experimentally discovered.

Chemistry applies different laws and we use different mathematical equations to understand and utilize them. For origins of life, the laws of chemistry apply to the atoms and molecules which would have had to react together to form life. As an example, we can think of any place where there would be a collection of atoms and molecules with potential to form life. A chemist who is an expert on DNA and RNA, Robert Shapiro, wrote an article for Scientific American in 2/12/07 called, "A Simpler Origin for Life." He described the components in the RNA/DNA world that some are saying is the way life began. The units called nucleotides are made up of about 9-10 carbon atoms, a few Nitrogen, Oxygen and Phosphorus atoms, all precisely connected in a specific 3-dimensional form. Shapiro tells us that even just this small collection of atoms can interact in thousands of different ways to form different types of nucleotides. Besides that, the same atoms could form other types of compounds which are stable enough to hang around and interact with each other. The number of types of molecules, not to mention total numbers, are in the hundreds of thousands to millions. But only FIVE TYPES (shown in picture above) are in our RNA and DNA. In natural chemistry, the "right" atoms and molecules don't hang around as they do in the sentences of writers and computer programmers. Shapiro, an expert, makes no indication that DNA in organisms is chemically favored over the other abundant possibilities.

Most Intelligent Design advocates believe the Earth is old, something like 4.5 billion years, but they do not believe that life started by naturalistic, materialistic causes. Chemistry alone cannot explain the biological origins of living beings.

Friday, January 23, 2009

Origins 6, ATPase

All living organisms have in common certain mechanisms for producing energy to supply for their metabolic needs. One of the sets of molecules is called ATP Synthase, or ATPase. This picture is from the Research Collaboratory for Structural Bioinformatics. It shows the "machine" that puts a high-energy piece onto a lower-energy molecule (ADP). The energetic ATP then supports various chemical reactions. It is necessary for the reproduction of DNA and the production of proteins.

This molecule has over 60,000 atoms. (I added up the amino acids of all the parts of the bacterial E. coli ATPase and got over 6,400 amino acids.) There are thousands of these machines in each cell of every organism, and they are assumed to be little changed through evolution.

The second picture shows some aspects of the mechanism. There are hydrogen protons (hydrogen atoms without their electron) on the outside of the membrane to which the molecules are attached. The protons have been pumped outside the membrane, so there is a gradient of postive to negative charges. The protons are attracted to the negative charges and lower concentrations of protons inside the membrane. They come back through the ATP Synthase molecule, which turns it. The mechanism attaches ADP and a separate molecule to it and combines the two to form ATP. This in turn has the high energy needed for cell metabolism.

So, we have three domains with some pretty major differences, just a few of which I mentioned in previous posts. They have large percentages of different proteins with structures in the thousands of atoms. But they all have this super-complex energy machine. That pretty effectively eliminates separate "chance" formations of each of the three domains. So that is why the Last Unknown Common Ancestor (LUCA) has been proposed. This would be a single organism that could give rise to all the others.

The other possibility, say some, is that molecules floated around loosely, having their own lives, and then "mixed and matched" as they formed into each of the Domains. For the ATP Synthase, this seems pretty unlikely, since it needs the membrane and concentration gradient of ions in order to work. It comes under the heading named by Michael Behe of "Irreducibly Complex."

Materialistic evolutionists argue that proteins have "other jobs" before they get to the functions that we see and study today. But ATP synthase is needed by the cell for the energy to break down food and make DNA, RNA, proteins and other molecules of the cell. Though there are sources of energy like the sun and oceanic thermal vents, the energy must be controlled and directed. A river can't make cars. However the energy from a river can be harnessed to create electricity and thereby run the factory that makes cars. Lightening is very powerful, but does not construct delicate arrangements of atoms and molecules. Without cellular conversion of energy to bring a steady supply of building blocks and small energy packets to the assembly lines of cells, there are no "other jobs" for proteins.

Tuesday, January 20, 2009

Origins 5, DNA

The Three Domains of Life are divided as to cell types. The Archaea and Bacteria do not have the well-defined nucleus of the Eukaryotic (true) cell or many other organelles. They are therefore often lumped into the category called Prokaryotes (from Greek meaning "kernel"). The first picture shows a sketch of a Prokaryote. The DNA is organized in structures called Chromosomes . In Prokaryotes, it sits loosely in the middle and is usually Circular DNA. It is reproduced by proteins which copy it from one point to the another along the single strand.

The Eukaryote has a nuclear membrane which holds its DNA. The DNA is reproduced in a different way, called Mitosis. The second picture shows DNA in pairs which are lined up and divide along lines made of specialized tubules. This is a much more complex set-up than the Prokaryotes. So, one would think that the group of proteins which copy the DNA in the Prokaryotes, Bacteria and Archaea, would be similar to each other and be different in Eukaryotes.

However, this is not the case! The proteins were found to be similar in Archaea and Eukaryotes, and different in Bacteria! This is reported by Edgell and Doolittle in "Archaea and the Origin(s) of DNA Replication Proteins," Cell, June 27, 1997 (in the link, it is easier to see the chart which compares proteins if you bring up the PDF file option shown above the title). There is almost no primary sequence similarity between the bacteria and archaea/eukaryotes. I have pictured two proteins which copy DNA, one each from Archaea and Bacteria, in a previous post. As it tells you there, they each are made of hundreds of amino acids in specific orders to give them the shape needed for their jobs. Though various combinations of amino acids can produce similar protein functions, there are more combinations which do different jobs within the cell and vastly more which do not function at all.

This dramatic finding shows a lack of logical progression from supposedly simple organisms to complex. In the next post I will talk about one similarity of all three domains before going into the chemistry of pre-life origins.

Friday, January 16, 2009

Origins 4, Domains

Biological life used to be divided into Kingdoms, known as Plant, Animal and Monera (one-celled organisms). Now one of the most common ways, as I said in a previous post, is to divide life into three Domains: Archaea, Bacteria, and Eukaryota.

The reason organisms are divided in this way is that there are 3 very distinct cell structures. The structure is more important in this categorization than the number of cells (which is why some scientists disagree with this system). The Archaea and Bacteria are one-celled, but the Eukaryotes can be one-celled or multi-celled, as in trees and humans. The cell structure of Eukaryotes remains basically the same, although can be specialized (I just read that humans have 210 cell types).

I'll show you a few differences today and next week. For one, the Bacteria make a cell wall outside of the regular cell membrane. The membrane is the outer part of the cell, but it can be covered with the wall and other layers. The wall has a distinct chemical makeup, called peptidoglycans, which link together. The structure is shown at right. The letters stand for atoms (oxygen, nitrogen, hydrogen, carbon). Almost all Bacteria, and only Bacteria, have the wall.

Another difference is between Archaea and the other two Domains. All cell membranes have what are called phospholipids. They keep many of the cell molecules inside and let only certain things go through either direction. The arrangement of atoms are distinctly different in the Archaea, as seen in the picture at left. (Again, the letters stand for atoms, and a clearer picture can be found at the Wikipedia entry "Archaea"). The phospholipid layer is made by cell machinery (proteins called enzymes). Three of the enzymes which make the different link in Archaea are reported by Koga et al. in Microbiology and Molecular Biology Reviews to be different from any known enzymes, meaning their structure is unique.

Next week I will show you other differences between the 3 Domains. These are important, because they are the reason that many scientists have concluded that they are not ancestors to each other. It was thought that archaea evolved to bacteria which in turn evolved to eukaryotes, but because they are so different, it would not be mathematically possible for the different proteins to have developed by this route. Instead they all need a previous ancestor to make the case that there was only one organism which formed by random movements of atoms and molecules.

Tuesday, January 13, 2009

Origins 3, Perspectives

We are talking about origins of life. Since biological life is so complex, it’s a little hard to know where to start. As I was thinking about it, I realized an over-all perspective is important. Many of the arguments that support totally naturalist, materialistic evolution seem to focus on the ability of biological life to “fix” properties (bring about traits that are beneficial to itself) through natural selection. And this is true. For example, if a bacteria has a mutation in its gene and becomes resistant to drugs, it is more likely to survive than its neighbors and therefore reproduce more progeny with this modification. Therefore, the random mutation will be selected and live on in ancestors. But we must remember this fixation is within an already working organism and its progeny, which already have all the cell processes present and in working order. Each cell is protected by specialized membranes which keeps most of the outer environment outside of consideration. The mutations come as a result of copying of genes. The cell already has the equipment to do the copying and use what is produced. Most are copied correctly. However, the mutation itself IS random, and when drugs are withdrawn, as is described in Michael Behe’s book, Edge of Evolution, the progeny of drug-resistant organisms may go right back to being killed by drugs. The mutation itself has no knowledge of whether it helped the bacteria or not.

An especially important application of the random process is before life began. Here, atoms and molecules are affected in different ways, with no limiting factor of the specialized cell membrane. There are many circumstances which affect them. For one, a tremendous variety of atoms and molecule combinations come into contact with each other in an open ocean, atmosphere or other large medium. Though they have varying attractions to each other, they are susceptible to forces which break them up as well as put them together. In this case, nothing is "set" and even if several molecules combine, they can just as easily fall apart. Another factor is their concentrations in relation to the water or air in which they float. This will have an affect on their chemical equilibrium.

Yet many biologists and those doing computer simulations try to impose the "fixations" by natural selection at these levels. As an analogy, they want to tell us random letters will stay put in a sentence once they are "correct." The same for atoms and molecules floating around in the primordial ocean. One of the physical laws for fluid movement and the molecules therein is the Law of Mass Action, which is concerned with equilibrium in chemical reactions. This has no power to put atoms and molecules in particular orders for life to begin.

Now, if there were a law that brought random molecules together to form life, I think I would have heard of it. We will keep this division in perspective as we explore possibilities for the beginning of life.

Friday, January 9, 2009

Origins 2

The first entire genome sequence of an organism was done in 1995 on the bacterium Haemophilus influenzae by the Institute for Genomic Research. This means that the entire DNA of the organism became known. From that time, a great many organisms have been sequenced, including humans.

It also means that these organisms for the first time can be compared on a molecular basis. The DNA is made of atoms arranged in specific orders. These atoms form molecules, which are then arranged in patterns. The patterns then can be compared, organism to organism.

Darwin's theory predicted patterns have changed throughout life just a little bit from one organism to the next. However, the genome sequencing has shown otherwise. In fact, there are areas where intermediate species are absent, both in the fossil record and in the sequences that would represent slow change. This has been reported by the National Center for Biotechnology Information (NCBI), as in the article, "Biological Big Bang Model for the Major Transitions in Evolution" by Eugene Koonin.

For a while it was thought that archaea were ancestors to bacteria, since traces have been found in rocks that are thought to be about 3.8-3.85 billion years old. But when they were sequenced, starting in 1996, it was realized that they were too different to be direct ancestors. So, it was proposed that both archaea and bacteria had a single previous common ancestor, known as LUCA (last unknown common ancestor).

Several scientific teams, using computers, have worked on the composition of what LUCA would have had to be. One paper published in Research in Microbiology by Ouzounis, et al. in 2006 reported that the organism would need between 1006 and 1189 gene families to mathematically satisfy the requirements for producing both archaea and bacteria. If the eukaryotes are considered (see my previous post for description), LUCA would need between 1344 and 1529 families (depending on underlying hypothetical development).

We will see what that means in terms of random chance for the origin of life in coming posts.

Tuesday, January 6, 2009

Hello 2009, Origins 1

The new year is a good time to start looking at the beginning of life, which we call Origin of Life studies, or OOL. There are several ways to classify the structures of living organisms. We will use the 3-domain system here, which divides into organisms of these types: Archaea, Bacteria and Eukaryotes. Pictures of these three are on this page.

The archaea (pronounced are-KEY-a) can make their own food, reproduce and create their own energy. These are single-celled organisms which were thought to be ancestors to bacteria. But when their entire genome was first sequenced in 1996, it was found they were not directly related to bacteria. So, they were put in a different domain of life. Some scientists think these archaea were present on Earth at 3.8 to 3.85 billion years ago.

I think everyone knows what bacteria are. They live everywhere and can cause diseases of different sorts. We will use the example of Cyanobacteria, since they are considered the first known bacteria on the Earth. Cyanobacteria are able to live on their own, unlike some bacteria which are known as parasites and can't make their own food. We use these because we can determine what is necessary for life to appear and then have a steady supply of food made from photosynthesis, which takes sunlight and water to create sugar and building supplies for the organism.

The last is called a Eukaryote (pronounced you-CARry-oat) and is what is known as a "true cell." The others are cells too, but they don't have as many of the complex organs that the eukaryote has. There are some single-celled organisms that are eukaryotes, such as the one that causes malaria, called Plasmodium. Also, the multi-celled plants and animals, including humans, are made of these eukaryotic cells.

These three types of cells are the earliest that we know, since they are still living on the planet. Scientists used to think these three domains were part of the evolutionary progress from simple to complex. For example, they thought at one time that bacteria were first, then over millions of years became slowly more complex and eventually gave rise to eukaryotes. But because the molecular structue is so different from each other, it was determined that they did not start with one and lead to another by Darwinian processes (small change and selection). These discoveries can be read here in a paper by the National Center of Biotechnical Information (NCBI).

Some believe the three domains had a common ancestor. If so, that ancestor would have had to have certain qualities. The ancestor is known as LUCA (last unknown common ancestor). I will get into more details in upcoming posts.