Stephen Hawking's Birthday

The physicist Stephen Hawking celebrated his 70th birthday on January 8, 2012. It was a momentous occasion, since he has a disease with which many who have it do not live to this age. He is a distinguished professor and scientist, and his party was more of a symposium by other noted physicists. He wasn’t even there, but had a recording played of his thoughts. Then, as these scientists presented their discoveries, they brought him conclusions which he did not want to hear as reported by Lisa Grossman, “Why physicists can’t avoid a creation event,” New Scientist (January 11, 2012).

Physicists are known to change their minds from meeting to meeting, and the implications of the presenters are bound to be eventually argued. But whatever happens in the future, this was a milestone in the thinking of scientists who either believed or wanted to believe a multi-universe was inevitable, including Stephen Hawking. I understand he said as much on a recent PBS show about the universe (Stephen Hawking's Universe), although I admit I did not see the show (2019 Update: link to the show no longer accessible).

The reason many physicists want to think or say this is true is because they know the chance for life starting by natural means in this universe are so enormously improbable that multi-verses were their only explanation. If there were infinite universes, at least one could come up with the necessary combinations of molecules to form life.

But now several scientists have published papers that analyze the various means by which multi-verses could exist or come about. A good description is at the Uncommon Descent website HERE. All of the possible variations need a beginning. According to this new view, there is no infinite universe or multi-verse.

It is significant that one of the physicists present was Alan Guth, well known for his inflationary theory of the universe in which the Big Bang was followed by a period of extremely large inflation. For years, he had been trying to calculate the probability of production of multi-verses from quantum fluctuations. But how can you use probability to figure something that destroys the significance of probability? He was listed as an author on Borde, Guth and Vilenkin, "Inflationary Spacetimes are incomplete in past directions," Phys. Ref. Lett. 90, 151301 (April 15, 2003) which now admits that the universe had a beginning.

Many of our disciplines, including quantum physics, thermodynamics and chemistry (mass action law) rely on probabilities. Max Planck discovered quantum physics by using the probability of energy radiating from various wavelengths of light. If probabilities mean nothing in this universe, then science itself is out the window.

Many are concerned that if we think of life and the universe as created, it will stop science. That is faulty logic. There are many things to be discovered about biology, the Earth, and stars. The more the better! There are enough things to give us awe for the rest of our days, and much work needed to dispel disease, hunger and war. This is plenty to fulfill our scientific quests. But it is not quite enough to fulfill our hearts. Where that emptiness has been, some persons let fear of the lack of total knowledge take over. They don’t realize belief and love of God is the only way to give them true contentment in this life.

There are other reasons for the denial of creation. It goes hand in hand with the denial of God's existence. Many humans stubbornly cling to the desire to be their own rulers, refusing to answer to a higher power. This is not new or restricted to scientists. It's just that scientists as a whole seem to be able to guide culture, especially these days, to accept their conclusions. Scientists must be right, right?

No, Stephen Hawking, a very smart and famous physicist, is being challenged by other very smart physicists. The lesson for others is to not let scientists as a group fool you into thinking they know it all. They often speculate in the way they want things to go, then call it fact.

Think now about origin of life and evolution.

Information Theory

The past few days I've been reading and re-reading articles and books about Information Theory. William Dembski has been working with Robert J. Marks II on various aspects of Information Theory and their pertinent website is The Evolutionary Informatics Lab, found HERE. They have several papers listed under their Publications link. I read one of them which is to be published soon called, "Conservation of Information in Search." It addresses, for one thing, the use of computers to "prove" evolution by programs which pick out some final answer when a random search is used. They describe how the information in these programs is "partitioned" so that each part of the the programmed answer, such as a letter in a sentence, will stay in its place when it turns up in the random search. The outcome in these cases is dependent on information fed to the computer program.

The "father" of Information Theory is considered to be Claude Shannon. He used statistical information about language to improve methods of communications. I can follow a lot of the explanations, and some of it is easy to understand, but other parts are complicated. The link to "Information Theory" in Wikipedia HERE has some mathematical explanations and other references for those of you who are interested and mathematically-minded.


Another man, physicist Hubert Yockey, applied Information Theory to biological systems. I've re-read some of his papers from the 1970's and 1980's. One of them is "A Calculation of the Probability of Spontaneous Biogenesis by Information Theory," Journal of Theoretical Biology 67, 3 (Aug 7, 1977): 377-398. (The link in the title goes to an abstract. You can either get it online by association with an accepted institution or payment, but I got this and other full articles by him through inter-library loan). He used data previously worked out by Grantham in 1974 on a particular molecule in most species called cytochrome c. He compared 101 amino acids which make up cytochrome c in the categories of composition, volume and polarity (electric charges). Yockey worked on the number of molecules which could function as cytochrome c compared to the number of molecules that couldn't, using the 20 amino acids that make up protein. Though he found a tremendous number that could function as cytochrome c (about 4 x 10^61), the probability that the 20 amino acids would form any of them by chance is only about 1 in 10^65 (10^65 being a 1 with 65 zero's after it).

Yockey's calculations with information theory were reinforced by more direct experiments with proteins, which is very significant. I plan to write about these in times to come. These scientific investigations refute the prevailing theories of evolutionary pre-life formation by showing how improbable are the events that would lead from random molecules to formation of functional proteins and/or genomes. They eliminate even the possibility of life forming at any time in the universe on any available planet. However, it is interesting how materialistic pre-life theories persist even today.

One personal note: it's my husband's birthday. Happy birthday, Tom, and may you have many more!!

Also, Thursday is Lincoln's birthday and Washington's is to come soon. Tom and I watched several shows on slavery and the Civil Rights movement Sunday on PBS. It was interesting how the former slaves adjusted to freedom very soon after the end of the civil war. They became a part of government very quickly, but then were attacked by the persons who remained prejudice and unwilling to follow the new laws. The African-Americans were again oppressed. If Lincoln had lived longer, perhaps permanent changes for the good would not have taken so long.

Origins 10, Molecules

Since, as we have seen, the smallest free-living organism is too large to have begun by chance (needing about 1 million DNA nucleotide molecules in sufficient order to function), some say that smaller entities could have built up to the whole organism. They use terms such as "selfish cooperator" and "gene pool" and "pre- or proto-biont."

These pre-bionts (meaning molecules waiting to be living things) would have to be composed of thousands of atoms in enough order to carry on specific chemical reactions under the laws of physics and chemistry. Let's look at just one very simple molecule made of 3 atoms, Water. As we see in the 1st picture, to the left, it is composed of 2 hydrogen atoms (white) and 1 oxygen atom (red) in a certain configuration. You can click on these images to see them more clearly. The charts on this page and much more information are provided at the Wikipedia entry "Properties of Water" HERE.

Don't be turned away if you don't understand all the terminology of the "Information and Properties" below the picture. I would just like you to see for yourself the complexity of a simple molecule of water. Most people know that water freezes and thaws and boils at certain temperatures. These temperatures are listed below the first picture and called melting point and boiling point. There are many other physical and chemical properties of water which affect how it stays together, comes apart, or reacts with other molecules. The Wikipedia link above is brimming with information about this one little molecule (excuse the pun), such as the two charts on the right.

I do not understand all the terms myself, but I am amazed when I look at all the details of just one little molecule of three atoms. Often, the longer the molecule in a solution is, the slower the reactions to make it longer and the more likely it is to come apart (unless real physical effects like pressure might compress them into things like rocks). Many reactions need help from other atoms or molecules just to take place within a short enough time period to be useful biologically. The chemistry of water does not depend on what this molecule is supposed to become. Life's organisms are full of water molecules, but a water molecule outside of living organisms is not called a "pre-biont." It is a water molecule.

Water is not "selfish." Nor are any other molecules.

Water may occupy the nooks and crannies of the bottom of the ocean, but the heat of the thermal vents is sure to keep it moving. In fact, it is estimated that the entire water of the ocean is filtered through the thermal vents every 10 million years, which some believe limits the origin of life to that amount of time, such as Lascano and Miller, "The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World and Time," Cell, 85, 6, (1996): 793-798. That is because the molecules of life are pulled through and torn apart in that extreme heat.

Water molecules have followed the laws of physics and chemistry, which is the point. It is not that Special Creationists and Intelligent Design advocates deny the laws of physics and chemistry. We are saying they are discontinuous with the existence of biological life.

Origins 9, First Cells

The three domains of life are divided into Bacteria, Archaea and Eukaryotes. Every organism has a set of genes which is used as a pattern for building the organism itself and passing along the pattern to the organism's offspring. The collection of genes in an animal is called the "genome" (Wikipedia HERE). Scientists have been able to do what is called full-genome sequencing, determining the entire make-up of these genes within individual organisms, since 1995. The genes are made of DNA or RNA, molecules made up of atoms in specific orders. An article which compares bacteria and archaea, which are mostly one-celled organisms, was written by Koonin and Wolf, of the National Center for Biotechnology Information. It is called, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36: 21 (Dec. 1, 2008): 6688-6719.

Though only a small percentage of species have been sequenced, the introduction to the article explains that the researchers feel the work done so far is representative enough to survey patterns. One of the purposes of whole-genome sequencing is to compare the make-up of the genes and see if the orders of the molecules matched what scientists expected according to evolution theory (including the order in which organisms may have appeared on Earth).

Perhaps you have heard already, in the news or elsewhere, that the pattern of organism genomes has not produced a "tree of life" as Darwin predicted. At first, the term "web of life" was used as a substitute to tree. But now, Eugene Koonin, one of the authors of this article, asserts that web is even too clear a term for the genetic patterns. If you look up the article, you can see a picture on page 6708 which represents the new dynamic view of the genetic pattern for life. It is a group of circles representing genomes with lines connecting them every which way (Figure 17).

One of the reasons for this lack of clear, Darwinian progress is believed to be "Horizontal Gene Transfer," or HGT, as described in this article by Koonin, Makarova and Aravind, "Horizontal Gene Transfer in Prokaryotes: Quantification and Classification," Annual Review of Microbiology 55 (Oct 2001): 709-742. Bacteria and archaea are able to switch genes from one adult to the another by a few different mechanisms. Therefore, the patterns of adult to offspring are not closed or caused by internal mutation. Genes (parts of the genome which produce proteins) are present when they shouldn't be and not present when they should be, according to what is expected. Many genes are found only in one or two organisms, never to be seen again. Considering the complex protein products they make, the sudden appearance and disappearance does not sound like slow, random change predicted by Charles Darwin.

There are limits to HGT and how much it can explain. The closer the organisms are in type and location of growth, the closer the genes to each other. Also, we are talking here of one-celled organisms. Multi-celled would not be so easily affected by HGT. The article states that HGT is still controversial, unable to explain all the differences. And, most obvious, there have to be genes in the first place in order for them to be exchanged. I had talked about LUCA, the last common unknown organism, in a previous post. Because the archaea and bacteria cells are so different, there would have had to be a great variety of genes in a single organism that existed previously that can be figured to be the original organism. The computer program came up with a cell with at least 1000 different genes, probably much more. Koonin, in the "Genomics" article mentioned above, interestingly points out that a free-living cell would need a minimum of about 1000 genes.

Genes are an average length of 1000 nucleotides (Wikipedia HERE). A free-living cell would need at the least about one million nucleotides of DNA in specific, functioning order to survive well enough to reproduce. Though not all those would have to be in one exact order, a large percentage would have to be in specific sequence to make functional proteins. As you might guess, this is far beyond what we would expect from the random movements of atoms, which themselves follow certain laws of chemistry.

That leads us to the post "Origins 10," where we will take a look at smaller organisms than cells--the viruses--and see if their genome patterns lead us to any knowledge of how life began.

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. (This is not to detract from Special Creationism, the belief in direct supernatural creation. We also are aware of the same things ID advocates know.)

The accusation that non-naturalistic articles concerning biological origins and evolution have not been published is untrue. One of the first articles was by Michael Polanyi, "Life Transcending Chemistry and Physics," Chemical and Engineering News, 45, 35 (1967): 54-69. This journal is published by the American Chemical Society. Polanyi writes 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.

O7, Chemistry is not Selection

Popularizers of evolution try to sometimes ignore, sometimes mix and match, the rules of chemistry and biology (respectively described in Wikipedia HERE and HERE). 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 (Wikipedia HERE), 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 generations 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 "A Simpler Origin for Life,"  Scientific American (Feb. 12, 2007). He described the components in the RNA/DNA world that some are saying is the way life began. The units, called nucleotides (Wikipedia HERE), 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 OF NUCLEOTIDES (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.

Many Intelligent Design advocates and even Special Creationists (direct supernatural creation of life) 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.

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, Wikipedia entry HERE. 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 (Wikipedia HERE) then supports various chemical reactions. It is necessary for the reproduction of DNA and the production of proteins.

This molecule would have at least 100,000 atoms. (I added up the amino acids of all the parts of the bacterial E. coli ATPase and got over 6,400 amino acids, with an average of 20 atoms per amino acid.) 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 positive 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 (click origins label at bottom of post for the others). 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.

Origins 5, DNA

The Three Domains of Life, described more fully HERE, are divided as to cell types. (The "HERE" entries in this post are from Wikipedia). 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, also described HERE. The DNA is organized in structures called Chromosomes, seen HERE. In Prokaryotes, DNA 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, HERE, has a nuclear membrane which holds its DNA. The DNA is reproduced in a different way, called Mitosis HERE. 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, "Archaea and the Origin(s) of DNA Replication Proteins," Cell 89, 7 (June 27, 1997). There is almost no primary sequence similarity between the bacteria and archaea / eukaryotes. (The article uses the term, "Clade," which is the supposed lineage of organisms from common ancestors. It is described more HERE.)

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.

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, Wikipedian entry HERE, 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, Wikipedia HERE. 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 entr Archea HERE. The phospholipid layer is made by cell machinery (proteins called enzymes HERE). Three of the enzymes which make the different link in Archaea are reported to be different from any known enzymes, meaning their structure is unique, by Koga and Morii, "Biosynthesis of Ether-Type Polar Lipds in Archaea and Evolutionary Considerations," Microbiology and Molecular Biology Reviews  DOI: 10.1128/MMBR.00033-06 .

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. That is due to the number of generations possible and the mutation rates of the various species. 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.

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," described in Wikipedia HERE, which is concerned with equilibrium in chemical reactions. Despite various theories, this natural law has no known power to put atoms and molecules in particular orders for life to begin.

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

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 by Eugene Koonin, "Biological Big Bang Model for the Major Transitions in Evolution," Biology Direct 2: 21 (2007).

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 by Ouzounis, et al., "A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective," Research in Microbiology 157, 1 (Jan-Feb 2006): 57-68, reported that the organism would need between 1006 and 1189 "gene families," sets of similar genes supposedly derived from single genes, described in Wikipedia HERE, 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). The authors saw this as so impossible under Darwinian terms as to talk about planetary exploration to find an original organism (see abstract).

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

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-ah) 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 structure 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 are described in an article by Eugene Koonin of the National Center of Biotechnical Information (NCBI). called, "The Biological Big Bang model for the major transitions of evolution," Biology Direct  2; 21 (2007), which can be found HERE .

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.