Praise God for Creating DNA

Way back in January 2013, I did a post about the make-up of a part of the cell which produces energy, a set of proteins called ATP Synthase. The post is HERE, and it includes a little video about ATP Synthase which processes protons through a membrane due to an electrical gradient set up by yet other sets of proteins. I want to re-post a picture of this sequence from KEGG database called "oxidative phosphorylation" because it is amazing (sorry if my reproduction is a little fuzzy-- a direct link for this image data is HERE). Please note that all the different-colored parts are different proteins that have different genes:

However, I did not add everything I could have to that post to make the picture complete. I showed the amino acid sequence of one of the sub-unit proteins, but I'd like to take the composition of a Beta sub-unit one step further to show the human gene sequence. This is the darker blue piece of the protein set on the right of the above picture:

Each letter in the image above stands for a molecule called a nucleotide. These in turn are a code for producing the sequence of amino acids needed to make the protein subunit. In this case there are 1590 of the DNA nucleotides. These molecules, made of atoms, exist in the ladder-like DNA helix structure which sends a code through the cell to make proteins. There are 4 letters in the chart above --c, t, g and a. Below is a picture of them (the fifth, Uracil, is in RNA, a whole other story). The N stands for nitrogen, H for hydrogen, O for oxygen, and C, carbon, is understood in the corners of the "rings" that don't have letters). The R is where they attach to the rest of the DNA molecule:

Though perhaps every amino acid (coded by the DNA nucleotides) does not have to be exactly where it is in this Beta subunit, as in all proteins, many do. The protein has to have a structure that will hold together in a certain shape, and some amino acids do better on the outside of the protein and some on the inside. Then this Beta piece along with another type of protein provide the conformations that allow the chemical change of one molecule into another (ADP to ATP). The ATP is what gives energy to our metabolism and in fact is needed to produce more DNA and proteins. The machine-like quality of the ATP Synthase is due to several specific amino acids that can accomplish this task when the ATP Synthase complex turns on an axis. There is another way to produce ATP which I won't go into: substrate-level phosphorylation. This requires its own complex sets of proteins and you can always Google the name if you are interested in learning more.

Overall, you have a chicken and egg problem: DNA is needed to code for the proteins that make ATP which is needed to make DNA. Though many want to believe that life came through natural physical laws, we have to consider at least two events: first, beginning of life; second, continuation and change of life forms (evolution). At the beginning we have to understand that the chemistry that would affect the atoms of the atmosphere is under the Law of Mass Action (Wikipedia entry HERE), where atoms and molecules move randomly but collectively act in a certain way. Even quantum physics becomes random at the Newtonian level. Though some want to dream of finding physical laws that would put DNA together "naturally," in my opinion they are literally dreaming. They accuse Creationists of not being able to acknowledge that God could create through physical laws, but what about them acknowledging that He could create directly?

In the Bible, the Apostle Paul says that God made Creation in a way that it is obvious for us to see His eternal power and divine nature (cf. Romans 1:20 NABRE). I agree with Paul.

Histones Stand Alone

The bacteria are single-celled organisms that live just about everywhere. E. coli is fairly well known because it survives in human intestinal tracts, it has been extensively studied, and it can cause food poisoning.  It has many different strains and the K12 is a common research type.  Rounding off, the K12 sub-strain MG1655 has about 4.5 million DNA base pairs (a base is one of 4 types of molecules used for the DNA code) and about 4500 genes. The sizes of bacterial cells also vary, but one organism is about 1-2 microns.  A micron is 1000th of a millimeter (which is 1000th of a meter). There are 25,000 microns in an inch. An average E. coli bacterium is therefore about 1-2 25,000th of an inch. And yet each organism has millions of DNA bases that need to be organized and compacted so the code can be copied at the right times to produce proteins, the working molecules of the cell, and other products. The proteins make energy from light sources, manufacture the cell wall, participate in reproduction, and all the other processes needed for life. Yet another job is the bending and organization of DNA.

The long DNA molecule in many bacteria is “circular.” The DNA is one loop instead of separate chromosomes as humans have.  The cells don’t have a separate chamber for the DNA as ours do.  But a lot still has to happen for the molecules to get their jobs done.  One of the ways the DNA is organized is by what is called “supercoiling.” The above picture is from Willenbrock and Ussery, "Chromatin architecture and gene expression in Escherichia coli," Genome Biology 5, 12 (Dec. 1, 2004). The full article link gives more of an explanation, including in the abstract:

Two recent genome-scale analyses underscore the importance of DNA topology [geometric properties] and chromatin structure in regulating transcription [DNA copying] in Escherichia coli.

Chromatin is shown near the middle.

The authors of the above article elaborate on the shape of the DNA, which is much more complex than pictured. They say, “DNA has sequence-dependent structures, just like proteins, and certain sequences tend to coil in three-dimensional space.” I had written in January about new research that had revealed another language in DNA beside the one which codes for proteins (the link is HERE). Though that was new research and no doubt will undergo further testing, there is no denial that DNA has the ability to communicate with the molecules that regulate its output.  But DNA has even more talents, since it has to fold and organize beyond simple mechanical compression with the help of proteins.

Besides having its variety of shapes, another way DNA is regulated is by the proteins which bend and condense it. They can move from one part to another so that a particular gene is either copied or not depending on the needs of the cell. There are several proteins which bend and regulate DNA in bacteria, one of which is HU. The second image shows two HU proteins (one silver, one gold) bending two loops of DNA (blue and purple), from NCBI entry 1P51. There can be as many as 15,000 HU proteins in one bacterial cell. These particular structures pictured each have 94 amino acids, their own subunits which have to be in correct order for the protein itself to fold and then bend the DNA.

Bacteria are known as “prokaryotes” (pronounced pro-carry-oats).  As well as not having an inner wall around the DNA (nucleus) like the cells in animals, they have other differences as well.  There is another prokaryotic domain of life known as “Archaea” (are-KEY-ah). The grouping of biological life is shifting since it became possible for scientists to learn the entire codes in the genomes of species.  The fact is that the sequences are not falling in place.  But the “Tree of Life” project Root Page (link HERE) explains:

The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly [common ancestry] of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon.

They used to think that Archaea evolved to Eubacteria (true bacteria) which evolved to Eukaryotes (true cells with an intact nucleus and other organelles as found in humans). But they found very different stories. Using as an example the proteins which bend and organize the DNA, there are none even close in bacteria to humans.  The histone they’ve found to have a similar-looking fold to humans is in Archaea (Bacterial Chromatin, Dame and Dorman, editors, [Springer, 2010]).  But this is a structural similarity, not sequential (Sandman and Reeve, "Archaeal histones and the origin of the histone fold," Current Opinion in Microbiology, 9, 5 [Oct. 2006]).  The sequences are as far from Eukaryotes as any of the others (less than 15%).  These are short proteins, so the matches or lack of them are obvious (see image below).

It is true that not all species have been sequenced.  But these DNA-bending proteins are so greatly different that it is obvious that they could not all have come from the same source.  Even if another animal species showed up that had histone sequences half-way similar to those of a human, they could not account for the spread of differences already found. And so far, none have shown up with Archaeal-like histones (species Methanothermus fervidus), as you can see in the boxes in the image below. (This result is from a BLINK database which compares proteins from different species, run in February 2014. The query page is HERE and the Uniprot number was entered into Blink: in this case P48781). (Update 9-16-2018: When you click the given Blink link you are now re-directed to another comparative genetic database called BLAST. The Blink database was discontinued in May 2017. For more information you can read about Blink HERE.)

The "similar" Archaeal histone protein that is mentioned above is 69 amino acids long (M. fervidus). Since there are 20 biological amino acids, the possibilities for this length of chain are 20^69 (20 to the power of 69, using ^ for an exponent), or about 10^90 (a 1 with 90 zeroes after it). Contrary to simulated computer programs of mutation, there is nothing to stop the DNA from mutating the bases which cause the protein to work correctly.  Natural selection would eliminate those organisms which mutated from useful to less functional (they die or reproduce less). So even if the proteins have a small proportion of the same amino acids when compared now, say 10%, there would still have to be an average of about 10^90 tries to get from one of the structures to the other. (I want to add that as of Feb. 2014, the human histone H3 [Uniprot number P68431] entered in BLINK for matches, brings up 0 Bacteria, 0 Archaea and 0 Viruses.)

Using the volume of an E. coli and the volume of the Earth’s water to calculate the quantity limit of possible life on Earth, there could have been no more than 10^50 of these (or therefore any-sized) organisms on Earth in 4 billion years (Nelson, see reference at bottom). The bacteria only mutate less than one base per generation and not all DNA mutations cause protein changes. So even if the 10^50 number included a change in an amino acid each time, there would very, very probably not be enough of the bacteria to find the right combination to transform from one functional DNA bending protein to one of the others that we have found experimentally. In the meantime they would have had to sort through all kinds of useless proteins because after a certain number of mutations the proteins lose their ability to do their specific job. The RSCB Protein Data Bank describes histones this way: "The histone proteins are perfectly designed for their jobs...Even slight modifications can be lethal."

The last picture is a group of histones in humans (center) which wrap DNA (outer strands) in order to organize its long double helix into chromatin and chromosomes (NCBI entry 1KX5).

These comparisons are just for histones.  Even if human histones are compared to other proteins to find a supposed source, many of the thousands of proteins in animals and plants are much longer than histones and/or have no obvious ancestors. They would have to undergo much greater evolutionary transformations. Many scientists and the media do not bring these types of things to attention.  They seem to want you to think evolution is easy.  I guess it is wishful thinking on their part, but why do they wish these things are by chance?  Life is better when you increasingly appreciate the Creator of all.

~~~~~~~~~~~~~~

Nelson, Fred.  "Needed: A New Vocabulary for Understanding Evolution." Perspectives on Science and Christian Faith 58, 1 (Mar. 2006): 31. The link HERE goes to a PDF file of the article.

Images 2 and 5 are from NCBI:

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. "MMDB: 3D structures and macromolecular interactions." Nucleic Acids Res. 2012 Jan; 40(Database issue):D461-4

Shifting Paradigms

An interesting article has come out by Philip Ball, "Celebrate the Unknowns," Nature 496 (April 24, 2013): 419-420.  The author marks the 60th anniversary of the discovery of the structure of DNA (our cellular source of genes) by Watson and Crick. He basically says scientists don’t understand molecular evolution, which means they don’t understand evolution period.  Ball in turn quotes another biologist, Patrick Phillips, who said, "[P]rojects such as ENCODE are showing scientists that they don't really understand how genotypes map into phenotypes, or how exactly evolutionary forces shape any given genome." The genotype is the makeup of the gene and the phenotype is the physical structure of the individual organism. 

It’s intriguing that Nature would produce such an article, since they are the ones who published the Consortium Project collection, "ENCODE,". Nature (Sept. 5, 2012). A summary of the findings can be seen in another article by Brendan Maher, "ENCODE: The human encyclopaedia," Nature 489 (Sept. 5, 2012).  Basically ENCODE found that at least 80% of DNA is functional, which totally eliminates chance as the fundamental cause of life and speciation.  This research has falsified Darwinian evolution, but many scientists still won’t admit it.  To deny that only chance was involved, they’ve claimed natural selection has moved life and evolution along.  However, that was based on nature being able to select individuals with genes which formed by chance into something useful.  And that depended on a DNA molecule that was mostly "junk," supposedly giving room for the chance formation of useful genes to be selected. ENCODE has eliminated the "junk" hypothesis.

The high functionality of DNA defies the “billions of years” modifier used in the past to explain materialistic evolution.  Billions of years is a drop in the bucket for the millions of regulatory switches found by the ENCODE research.  There is just no way these could have randomly gathered and been able to function in the fine-tuned world of the biological organism.  Anyone familiar with probabilities will know the truth of that.  It is time for a change in our paradigm.

In my blog, I’ve been trying to show that human beings can’t be here from simple chance of nature.  I know there is still a long way for some of you to go in your understanding, but I hope you are starting to see how true it is that we are made by a Genius Whom we know as God.  The next step for those who are just starting to accept that neo-Darwinian theory is defunct is to determine Who this God is.

My approach is in contrast to what the advocates of Intelligent Design Theory (ID) say about biological design being separate from religion.  They seem to think that is a valid approach and are not the only ones who make distinct categories.  The biologist Stephen Jay Gould felt they were different spheres.  But Creationists have long combined the two, and their concept of biological Creation is independent of the age of the Earth, though many believe in a Young Earth.  In other words, a Creationist does not have to believe in 6 literal 24-hour days of creation to believe that God made people and/or species directly. And when Christians believe that biological life was made by a Designer, there should be no question to them of Who that is.  That is the Triune God of the Bible: Father, Son and Holy Spirit.

ID advocates insist that they are not secretly promoting religion, describing the designer only as intelligent.  They define a quality of the designer but not the identity.  But once we see the complexity of biology it is natural to ask the “Who” as well as the “How.”  This is where the ID people ignore a portion of the population as much as materialistic scientists do. Creationists see all questions as valid, even if some of the answers will always be beyond our understanding.

So I ask those of you who are starting to see the validity of what Creationists have said all along to keep on your journey.  When I was searching for answers to spiritual questions, I prayed for the Truth.  Even if you don’t know Who God may be, He will hear you.  I prayed in this way and found Christianity.  I now believe this religion to be True and am joyful to have discovered fulfillment such that I never could have previously imagined. 

It’s not that unusual to fear new territory and yet when we allow ourselves to experience it we often find the opposite from what we expect.  Seekers may think Christianity is limiting, but it is expanding.  They may think it will confine them if they embrace it, but it frees them.  But like a foreign country, you can’t really know what Christianity is like until you go there.

Cell Biology

When you start learning biology, there are new terms. With computers, your job, and/or your school, you learn new things all the time, so you are already acquainted with the activity. So I hope you will be open to learning about cell biology. It is a fascinating subject, and well worth the time. Perhaps you already know biology, but I hope you will still look at what I have here.

There are an estimated 75 trillion cells in the human body (and trillions of atoms in each cell). From bacteria to humans the cell is the basic unit of biology, and its activities are called “metabolism.” The cell absorbs and stores food, then breaks it down and converts it into energy. It uses energy to reproduce DNA (genes) and assemble proteins among other things. The DNA is used as a code for the proteins  which in turn do the work of the cell and the body. For example, your muscles have muscle cells which contain muscle proteins that contract and relax. They are called by specific terms, but we don’t have to name everything to get the overall perspective.

One of the basic parts of the ongoing process of metabolism is where several groups of proteins are embedded in a membrane of of the cell. The membranes are in folds, and in humans the folds are parts of what are called mitochondria (mite-oh-CON-dree-ah). First I have a short video (less than 4 minutes) for you to see how one of the groups works to form the energy molecule called ATP. ATP has chemical qualities that give it the ability to use a chemical bond for activity needed in the cell as I described above. It changes to ADP when used up, then is re-cycled back to ATP by this complex. You may hear some terms you don’t understand, but just try to get the concept of this series of steps going on in most of your body’s cells.

The video is done by North Dakota State University which has done other animations you can see HERE if you want to learn more. As interesting as the above video is, the protein complexes are drawn rather simply. Below is a more detailed picture of a series of complexes needed to make the last one, ATP Synthase (SIN-thase), work. They are needed to produce the electrical gradient which is described in the video. The mitochondrial membrane is pictured between the complexes, with ATP Synthase at the far right.

The image (link HERE) comes from a database called Kyoto Encyclopedia of Genes and Genomes (KEGG). The boxes in the picture give information for various parts of the complex when you click on them at the KEGG website.

Now, please stick with me a little longer to get more of the perspective of how complicated this series is. In the picture, the last group of proteins on the right is ATP Synthase. On the bottom part, there are blue-colored sections. The darker blue have a β on them for beta subunit (beta is Greek for “B”). Proteins are made of yet smaller units called amino acids (ah-ME-no acids, Wikipedia entry HERE). These are repeating groups of atoms, including carbon, oxygen, nitrogen and hydrogen (C, O, N and H). Here is a picture of one of the 20 types of amino acids found in biology, called alanine (AL-ah-neen):

Carbon is also understood to be in the angles of the molecule image. The types of amino acids need to be in correct order, according to their size, electrical charge and other factors, so the proteins can fold into the shapes in which they function. It is similar to machine parts which need to have the right shapes to fit and move together. Now I have just one more picture. It is the list of amino acids in this one part of the whole complex, the beta (B) subunit of ATP Synthase as pictured above. This particular one (human) has 529 amino acids, as listed in another database called Uniprot, entry P06576. Each letter stands for an amino acid, such as A for alanine (letters can stand for different things depending on their context):

All the proteins parts of this entire complex are made of various arrangements of the amino acids. Many are at least 100 amino acids and some are many more, as you have seen. These need to be constructed and put together within most of the cells that we have. There are many such complexes within each cell.

Thank you for bearing with me to learn about this part of cell metabolism. Remember, this is only a very small fraction of the complexity in the cells. Even small organisms need energy systems such as these to put together their own genes and proteins. Please think about whether this could have come about by chance, no matter what the time frame. After all, a computer would not form on its own, no matter how many billions years pass, and that is not nearly as complicated as we are.

Cosmological Model

Picture from Hubble Space Craft, NASA.

Dr. Eugene Koonin of the National Center for Biotechnology Information (NCBI) wrote several articles published last year. One is "The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life," Biology Direct, 2007; 2: 15, full text found at the link in the title. Koonin takes unsolved aspects of evolution to a higher level. The numbers of combinations that atoms can make randomly show us that biological life by random chance is improbable to the extreme. Genes are claimed to flow, drift, move horizontally or vertically or double, triple or quadruple but how did they form out of the so-called pre-biotic elements? And how did they change into new functional forms? Though scientists are trying to find chemistry which produces the present organization, they haven't found a set of answers which can explain the complexity of life.

What has been found on the cosmological level is an anthropic fine-tuning of physical laws that had to be as they are to make the universe livable for humans (anthropic). So Koonin blends the high improbabilities of life into the anthropic principle. He says, "In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable."

Koonin says that in this scenario, the RNA world may never have existed. The universe we live in is, in this theory, fine-tuned not only for physical laws but biological origin and evolution. It has only become that way, however, by chance because an infinite number of universes would cover everything.

This is a scientific article published by a scientific journal. Yet many believe evolution is a fact, not a theory.

The infinite universe theory is as un-falsifiable as they accuse Intelligent Design of being. It seems to me that if the multiverse wipes out biological probabilities, it would wipe out physical ones as well--the ones used to understand quantum physics in the first place. It is quantum physics that underlies the multiverse claim--a quantum fluctuation somewhere in space (see references in Koonin article for more information). And quantum physics was first described by Max Planck based on probabilities of energy radiating from light at various frequencies.

New microbiological scientific data does not coincide with past evolutionary data and theory. If new facts fell into the expected place, it would be different. Scientists should evaluate where we are now no matter what they hope for the future. It is important for citizens such as judges and school board members to know the truth. As of now, though there may be micro-evolution where species can make small changes, macro-evolution of all species, one from another, is not a fact.

I talked a while ago about doing some posts on the history of science and religion. I haven't gotten very far but will try to do more shortly.

Exaptation

The number of possible combinations of amino acids in proteins is directly related to the number of combinations of sections of DNA called "nucleotides." The central rungs of the "ladder" in DNA as seen in the picture on left and the August 19, 2008 post are composed of a sub-unit called a nitrogenous base. Every set of three of these rungs is coded for one of the 20 amino acids used in proteins. So you need the right order of 4 possible nucleotides to get the right order of amino acids in the protein. The four nucleotides contain cytosine, thymine, guanine and adenine, designated c, t, g or a. It seems a little easier to talk about 20 amino acids than the codes of 3 nucleotides from combinations of 4. In the last post I said it is estimated that about 1 in 10^65 short proteins are specifically functional. This was estimated for proteins of about 100 amino acids in length. Therefore, 300 nucleotides would have to be in correct order for the proteins to have 100 amino acids in correct order. It gets a little complicated because some sets of nucleotides can code for the same amino acid. But this gives us at least an idea of the numbers we are talking about.

I put all this in to comment on the theory of the "RNA world" that many are touting as the answer to origin of life. It wasn't protein, they say, that had to form by chance, but RNA. Well, RNA still has to overcome the numbers just like protein. The RNA nucleotides have to be in the right place to do the work it is supposed to and to "evolve" to the right molecules that we find in the bacteria and archaea. (RNA has one different nitrogenous base from DNA--uracil for thymine).

Another concept that some scientists insist is the answer to all our questions about evolution is "exaptation." So what if the flagellum of the bacteria is a complicated machine made of about 25 types of proteins? All we have to do is realize that these proteins had other jobs on their way to evolving a flagellum. The Cyanobacteria DNA polymerase protein has over 900 amino acids. That is a total of 10^1200 possible combinations of 20 amino acids for the molecule. How long before it falls into the configuration that copies Cyanobacteria DNA? What about the other 3,100 or so proteins of Cyanobacteria (as reported by Kaneko et al.)? And what about the hundreds of amino acids that are not found in protein?

With information theory, Hubert Yockey gives us the number of 1 in 10^65 amino acid combinations (of the 20 biological amino acids) is functional for a specific job. That's a 1 with 65 zeroes after it. With the kinds of numbers of intermediates, exaptation means little. Who can think of all the other functions these proteins would need to take on the way to becoming what they are? What would carry on the work of replication while we waited? And many of the "one in 10^65" combinations for DNA polymerase would not even have folds which proteins need for function. These unfolded proteins as well as folded on their way to the right use would be hanging around looking for a place to work like the jobless at an employment agency.

Biological Big Bang

It is an exciting time in biology. Last year, several articles about origin of life (OOL) and evolution by Eugene Koonin from the National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, were published. Though I don't agree with his theories, Koonin does the best job in summarizing the state of OOL and evolution that I have seen. One article was called "The Biological Big Bang model for the major transitions in evolution," Biology Direct, 2007; 2: 21, published online August 20, 2007. Koonin discusses the areas in biology that show "the sudden emergence of diverse forms at a new level of complexity." These areas typically co-exist with the old forms rather than replace them as is predicted in Darwin's theory.

Koonin lists six areas of transition that are unexplained: Origin of protein folds; Origin of Viruses; Origin of cells; Origin of the major branches (phyla) of bacteria and archaea; Origin of the major branches (supergroups) of eukaryotes (true cells); Origin of animal phyla.

Several very interesting facts emerge from the text. One is that two of the principle cell types that exits, bacteria and archaea (one-celled organisms) have, among other things, "non-homologous core DNA replication enzymes." This means that the proteins of bacteria are distinctly different from another group of simple cells, the archaea (to see examples, scroll down or hit DNA label below or on right under topics). Some scientists had expected the archaea to be the evolutionary precursors of the bacteria, but they are not. The DNA polymerase molecule of a bacteria, Cyanobacteria, (Uniprot  Q2JWV2 ) which has over 900 amino acids is different than the DNA polymerase in one of the archaea species (Uniprot Q7SIG7 ) which has 773 amino acids.

Now, this does show that different molecules can do the same thing. But, as Koonin says, "This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria..." Two different molecules with the same specific job came from a tremendously large pool of possible combinations. After all, I've shown you molecules that do very different jobs within the cells, so the amino acid sequence is crucial to function.

Hubert Yockey used Information Theory to estimate that with a short protein of 100 amino acids, only about 1 in 10^65 are functional for a specific job. A longer protein would have even less chance to be functional enough to replicate DNA in conjunction with other equally complex molecules.

Koonin proposes alternate solutions, still hoping for that common ancestor. But for Cyanobacteria, just one long protein, the DNA polymerase, has about 10^1200 combinations of 20 specific amino acids. The number of events (including chemical reactions) in the universe, if it is about 14 billion years old, has been less than 10^150. This number of events in the universe leaves very little probability that even one long protein formed by chance.

2019 Update: Koonin's full article can be found online at the link in the title of the article above.

DNA Polymerase

In the picture of DNA replication from August 19, we skip to the left a few molecules along the top and find "DNA polymerase." This is the molecule which is necessary for copies of genes (DNA) to be made. DNA replicates in order to produce the next generation of organisms and, in plants and animals, for cell reproduction. We are talking now about Archaea and Cyanobacteria since they were among the first organisms on Earth. The DNA polymerase (pronounced po-LIM-er-ace) has a complex job and we will not go into all the details. I want to show you the pictures of those from one species of Archaea and one of Cyanobacteria. At the top is a computer structure from Swiss Model Repository DNA polymerase from Archea. Details are reported at Swiss Model Repository P26811 and Uniprot P26811. It has over 800 amino acids.

The Cyanobacteria DNA polymerase pictured above has 928 amino acids as reported at Uniprot Q2JWV2. It is shaped in a way that it can work on the DNA molecule to manipulate the chemical reactions needed. Different organisms have variations, but many have a DNA polymerase which consists of several parts that fit together in order to function.

I could go on with showing you the rest of the molecules that are pictured on the DNA replication picture as well as some which are not. There are sub-units of DNA polymerase which repair DNA when it is broken. There are some which attach short molecules at first that have to be replaced later for the DNA replication to be complete. I think, however, that by now you see the vast complexity of even the very simplest of organisms.

There is much to be said about this complexity and I will discuss implications in posts to come. I want to link you to some articles from mainstream scientific journals that help us see that this complexity is a very significant obstacle to the notion of random, materialistic origin of life and total random, materialistic evolution (total-natural evolution) to explain all life.

DNA Primase

Organisms called Archaea were discovered in fossils dating, according to accepted radiometric methods, from about 3.5 billion years ago (bya), with certain of their chemical products in rocks even older. I've shown some of the molecules from the first of bacteria, found in fossils from 2 bya, Cyanobacteria (and will show one of Archaea soon). Another molecule to add to the Cyanobacteria list is "DNA primase" which you can read about in the link to Wikipedia HERE. The primase helps the helicase make the DNA ready for replication. A picture of one is here.


The image was accessed from the Internet in August 2008. This protien molecule has 646 amino acids as reported by Uniprot Q2JLC5. This is a different protein than the helicase and topoisomerase which also are needed to replicate DNA. The molecules are each shaped uniquely to give them the ability to do specific jobs, just like a toaster and coffee-maker are shaped differently, with different shapes and arrangements of parts.

2019 Update: Unfortunately this image is no longer accessible at Swiss Model Repository under the given code of Q2JLC5 but I'm glad I could get it when I did under the address shown in the image.

Helicase

The DNA molecule as seen in my previous entry HERE (and at DNA label below) is undergoing reproduction. There I showed a molecule which affects the DNA to prepare it for the process of replication. Now we come to another molecule, called a "helicase," further described HERE. These take apart the pairs of nucleotide units which make up the DNA. Above is the chemical activity of a helicase molecule (not shown) from a Cyanobacterial species. The image and other details of this molecule are in Uniprot Reference Q8DG65. This molecule is made of 773 amino acids, as reported in the same link (HERE). To remind you, there are 20 types of amino acids in proteins, as opposed to hundreds found throughout nature. I am adding pictures of the 20. They are made of atoms like Oxygen, hydrogen and nitrogen. The corners of the lines are understood to have the atom Carbon. The Creationwiki Amino Acid link HERE takes you to a better view if you want it.

These are the units which make up the proteins. There were over 900 amino acids in the first molecule we needed to loosen up the DNA so it would be ready to replicate. This molecule with over 700 amino acids is needed to take apart the DNA so it can be copied to make more cells and organisms. The amino acids have to be in enough of a specific order to allow for the protein to form the way it should. Some of the amino acids may be substituted by a limited amount of others, since there are several groups which have similar properties. But experimentally, some amino acid placements have been found to be absolutely necessary or a protein will not work. Just one difference will completely leave the protein without function.

Topoisomerase

Every cell that has DNA needs a set of tools for copying it so the cell can reproduce. We turn over most cells in our bodies, so new ones have to be made. Also, when the organism reproduces, DNA must be replicated.

Last time I talked about Archaea and Cyanobacteria, since they are some of the first organisms to be seen in fossilized form on the Earth. We will see some of the microscopic tools these ancient organisms must have had from the start. To begin, they needed the DNA itself, shown at top. In my previous post I had a picture of the molecules which make up the rungs and sides of the DNA (which is shaped like a twisted ladder). Though scientists speculate that molecules evolved from RNA, these organisms all need DNA. Some of the DNA is stored in circular form, but it needs to be copied for reproduction and production of cell products, the proteins.

The molecule in the top picture at the right (green ring) is called "topoisomerase," pronounced toe-poe-aye-som-er-ace and described in Wikipedia HERE. This molecule is necessary in the process of copying DNA. In circular DNA, it loosens the DNA which is packed tightly. A picture of a topoisomerase acting on a DNA strand is at left, from PDB-101 Molecule of the Month, seen HERE. The molecule in one species of Cyanobacteria has 933 amino acids, as shown in Uniprot Q2JJ84. The atoms of this molecule have to be arranged in an order that will do the job of systematically working on the DNA to prepare it for reproduction.

Each of the 933 amino acids themselves must be in correct order of atoms, since the order determines the arrangement of charges which hold the topoisomerase molecule together. The 933 amino acids first are connected in a straight line, but then they must attract each other in just a way to make folds that make a working machine.

The probability that 933 amino acids formed by chance 3.8 billion years ago so that the DNA of a Cyanobacteria could be copied is, as you might guess, infinitesimally small. But this is only one of many proteins which Cyanobacteria needs in order to function.

Many scientists think there was some way that these molecules could form naturally, such as following a law which caused arrangements that could perform these tasks. The scientists insist life started without supernatural help from God. In the meantime, though they are far from finding the supposed way it happened, they are incensed when others are reluctant to believe a non-established theory that life somehow started by materialistic, naturalistic means.

Even many scientists who are Christian insist that it is unreasonable to look to direct supernatural intervention to explain life. Are they worried that children will not grow up with curiosity in science? I think curiosity is a human trait that comes from and through all circumstances. No one will stop wondering about science just because of Intelligent Design Theory. Some fear Intelligent Design Theory will suppress the pursuit of knowledge. I hope my blog shows that the more one pursues knowledge, the more the wonders of the biological world reveal earmarks of design.

2010 Update: I have moved from using the term "Intelligent Design Theory" to "Creationism" to describe my own stance. Though ID theory has done much to show the science of biology, the theological attitude is that the designer could be anyone. I do not agree with this. If you are a Christian, you believe that God is the creator and designer. Science cannot be separated from theology for a Christian in the way the ID advocates say.

Archaea, Cyanobacteria

The Archaea are considered one of the first forms of life. They were found in rocks that were judged by radiometric dating (r.d.) to be 3.5 billion years old. Traces of one of their molecules they contain (a lipid, which is a fat), were found in west Greenland and r.d. to 3.8 billion years ago. These organisms were found at extreme temperature environments at first, but since then have been found in almost any kind of environment.

Archaea were supposed at first to be variations of the bacteria, but were eventually found to be so different from bacteria that they were classified in a different kingdom, or domain, from bacteria and the other type of cell (eukaryote, or true cell). And so, it became apparent that the original organism that Darwinists look for had to be a common ancestor of both the archaea and bacteria. The search for this Last Unknown Common Ancestor, known as LUCA, is what is going on now in Origin of Life studies. Here's the rub: the fossils for the Archaea appear almost as soon as the Earth, after being bombarded by meteors, was cool enough to allow any life at all .

The cyanobacteria were formerly called bluegreen algae but now are considered bacteria. They have made hardened structures called Stromatolites, seen HERE, which scientists use to date bacteria as far back as 2 billion years.
So, because the proteins of the prokaryotes such as cyanobacteria do not match closely to the proteins of the archaea, scientists are looking for a last previous common ancestor. They are running out of pre-organism time, because the structures of functional molecules in each of these types of organisms alone would take not millions or billions but trillions upon trillions of years to happen by chance. Any laws of physics or chemistry that would cause them to organize like the molecules I will be showing you would themselves be non-random laws (and therefore lead to a biologic anthropic principle). One study by Kaneko et al., "Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. strain PCC6803," DNA Research, 8-1-1995, tells us a certain strain of Cyanobacteria has 3.5 million base pairs in its DNA. It also estimates a total of over 3000 genes. The following picture shows a unit of the DNA. These units alone are hard to find in nature, much less put together in a way that is functional. They are made of atoms, such as oxygen, hydrogen, nitrogen and carbon which are arranged in a specific way. The unit on the left is the "backbone" of the DNA, the part that looks like the long sides of a ladder. The molecules on the right are attached where it says "Base" to the backbone. Each pairs to another, thus the name "base pairs" for description of DNA. A short one connects to a long one, always in the same A-T or C-G pairing. The Uracil is used in RNA instead of Thymine. These base pairs form the rungs of the ladder and make a genetic code that can be read to form proteins. The picture is from Wikipedia s.v. nucleotide, seen HERE. (The molecules on the right, excluding thymine, are also the components of spliceosomes I've had in recent posts).

Cyanobacteria are free-living because they have a system for photosynthesis, which allows them to convert light energy into a source for chemical energy (ATP). Kaneko et al. estimates 128 genes are needed for photosynthesis alone. The organisms can then make all the molecules they need for structure and metabolism. Their genes, made of the DNA, allow them to reproduce by themselves. The structures that have been suggested by some scientists as original life, such as ribozymes, have been manufactured in the laboratory and cannot do these necessary things, and cannot sustain themselves. One study 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, Epub 12-19-2005, has shown that at least 1000 genes are needed for life to exist independently.

FF 5, Embryo 2

The concentration of molecules in the fruit fly embryo determines the "switch" of the DNA to produce specific proteins at specific places that will become the adult parts of the body. There are 4 major molecules from the mother which start the process. The book Developmental Biology, by Scott Gilbert (Sinaur, 6th ed.), describes it in Chapter 9, Sec. 2. (The site only allows searches for the book, but you can enter the term "anterior-posterior polarity" to get where you want.) These molecules in turn produce four proteins which continue the process. The molecules of RNA start from the mother cells in the front of the embryo and diffuse toward the back. The diffusion rate of the molecules is critical to the development of the embryo. The DNA of the new embryo can discriminate the concentration of the molecules of protein made from these mother RNA molecules. It does this by the code in the DNA in sets of genes that detect strong and weaker concentrations. A link to the fruit fly embryo picture HERE is from the book mentioned above.

The bicoid gene in the fruit fly is involved in the development of the embryo. The sequencing of bicoid has been done and I obtained it on the FlyBase website as well as the graph below:



This graph tells where the gene is on the chromosome. The DNA lines up on separate strands in the organism, and the fruit fly has 4 pairs of these, while humans have 23 pairs. In the next entry I will show the sequence of the gene.

2019 Update: I found the graph at the time of my post, but the link and visuals are a little different. However, you can get to the newer one HERE.

Fruit Fly 2

This is a picture of DNA from the National Human Genome Research Institute website. Don't worry if you can't understand the technical words. Just realize this is the way organisms carry genes--the features which are passed onto offspring. The DNA also is what is used to make the protein. It acts as a code. The bars in the middle come apart and they are "read" by another molecule, the RNA, to produce a mirror-image template. This template moves on to another part of the cell to eventually be read again. This time, the reading leads to new proteins.

The bars in the middle of the DNA are known as "base pairs." DNA has four different molecules that can be used as base pairs--two linked to each other along the rungs of the ladder. The reading is done by splitting DNA the long way and translating code of the four molecules in combinations of three that run along the length of the template. A new molecule of RNA is made and that is further processed to make protein. For example, a CGA will eventually be read as the amino acid "Arginine." That will be a part of the protein which is made by putting the amino acids together in correct order.The fruit fly has 180 million base pairs. After division and recombination through egg and sperm, they are passed along to individuals of the next generation which will once again have 180 million base pairs.

The fruit fly has two life forms, the larva and the adult. There are also developments through embryo and pupa stages. The larva gets a shell around it as it metamorphosizes to the adult. The micro-processes by which it develops are being discovered. They are important and fit in with the discoveries of the genes and how they work.

It was previously thought that each gene translates into one protein in the organism. To remind you very briefly, sections of the DNA are divided into specific genes. The great surprise from the Human Genome Project is there are less genes than proteins. For example, there are only about 25-30 thousand genes in humans. There are around 100 thousand proteins, and these have further modifications done to them in the cell so that there may be one million types of proteins in the human body.

The modifications to proteins in organisms come both before and after these proteins are made. There are differences between species, and I'll be talking about a variety of species, not just the fruit fly.

You have probably heard in the media that human and monkey DNA are very similar (varying reports of 95-99%). However, humans and monkeys are not 95% similar. A great deal of the differences are now being discovered in the regulatory levels of the genes. There are areas in DNA which had been called "junk DNA." These are between the genes and were thought to have little activity. Now they are thought to have regulatory affects on protein production.

As for the fruit fly, it is going to be an interesting study in how all these factors work together in an amazingly complex way.

Muscle, Probability

This is another protein from the fruitfly. This protein, called myogenic-determination protein, is needed just to get the DNA started in a cell so that the cell becomes a muscle cell. It is entry P22816 at UniProt where you can find the sequence, the people who did the work to find the sequence, and other infomation about it, like what it does. Remember, the letters stand for amino acids which are the sub-units of proteins.

10 20 30 40 50 60
MTKYNSGSSE MPAAQTIKQE YHNGYGQPTH PGYGFSAYSQ QNPIAHPGQN PHQTLQNFFS

70 80 90 100 110 120
RFNAVGDASA GNGGAASISA NGSGSSCNYS HANHHPAELD KPLGMNMTPS PIYTTDYDDE

130 140 150 160 170 180
NSSLSSEEHV LAPLVCSSAQ SSRPCLTWAC KACKKKSVTV DRRKAATMRE RRRLRKVNEA

190 200 210 220 230 240
FEILKRRTSS NPNQRLPKVE ILRNAIEYIE SLEDLLQESS TTRDGDNLAP SLSGKSCQSD

250 260 270 280 290 300
YLSSYAGAYL EDKLSFYNKH MEKYGQFTDF DGNANGSSLD CLNLIVQSIN KSTTSPIQNK

310 320 330
ATPSASDTQS PPSSGATAPT SLHVNFKRKC ST


Before you can have a muscle, you need the cells of the embryo to differentiate and each become one of the hundreds of specialized cells of the body. The embryo starts to form in a certain pattern, then some parts of the embyro outside the cell give signals that get to the inside of the cell so that the cell then starts with producing proteins called transcription factors that bind to DNA. The DNA will then produce other proteins, like one of the muscle proteins that is in another entry in my blog (March 27). The cell therefore becomes a muscle cell with muscle fibers inside that contract when the muscle is moved. Of course, you need other proteins called enzymes to help get the process working, like the ones that copy the DNA, called RNA polymerase. That would be this one:

10 20 30 40 50 60
MPKEQFRASA LNKKISHVQF GISGADEIQQ EALVRIISKN LYQAQRQPVP YGVLDRRMGI

70 80 90 100 110 120
STKDAMCETC GQGLNECIGH FGYLDLALPV FHIGHFRSTI NILQMICKVC AHVMLKPEDR

130 140 150 160 170 180
QLYEKKLHNP NFSYLGKKAL HVQMLAKAKK VTKCPHCGSP NGGVKKGPGL LKILHDPYKG

190 200 210 220 230 240
RKMDSLFTSN MNEMLRSTQT NRDLNSTLGN YSTAEELTPL MVLDLFEQIP QRDVALLGMC

250 260 270 280 290 300
SHDAHPKHLI VTRVFVPPAC IRPSVLSEVK AGTTEDDLTM KQSEILLIND VIQRHMATGG

310 320 330 340 350 360
KIELIHEDWD FLQLHVALYF HSEISGIPIN MAPKKTTRGI VQRLKGKQGR FRCNLSGKRV

370 380 390 400 410 420
DFSGRTVISP DPNLMINQVG VPVRVAKILT YPERVNPANI RHMRELVRNG PSMHPGANYV

430 440 450 460 470 480
QQRGSSFKKY LAYGNREKVA QELKCGDVVE RHLRDGDIVL FNRQPSLHKM SIMCHRAKVQ

490 500 510 520 530 540
PQRTFRFNEC ACTPYNADFD GDEMNLHLPQ TEEARAEALI LMGNQSNLVT PKNGEILIAA

550 560 570 580 590 600
TQDFITGGYL LTQKEVFLTK EEAMQLAACF LANEDSTMHI KLPPPALLKP RRLWTGKQMF

610 620 630 640 650 660
SLLMRPNDDS QVRLNMVNKG RNYTRNKDLC SNDSWIHIRN SELMCGVMDK ATMGSGTKQC

670 680 690 700 710 720
IFYLLLRDFG ESHATKAMWR LARNRGFSFG ISDVTPSKKL LQHKELLLNN GYAKCNEYIE

730 740 750 760 770 780
LLKAGTLQCQ PGCTPEETLE SVMLRELSAI REQAAKTCFA ELHPTNSALI MALSGSKGSN

790 800 810 820 830 840
INISQMIACV GQQAISGKRV PNGFENRALP HFERHSAIPA ARGFVQNSFY SGLTPTEFFF

850 860 870 880 890 900
HTMAGREGLV DTAVKTAETG YLQRRLVKCL EDLVVHYDGT VRNAVNEMVD TIYGGDGLDP

910 920 930 940 950 960
VSMETRNKPV DLVHQYDNLR AQHPQGKDRP LNAEEMSEAL ETLLRTPEFA EARDDFKLDV

970 980 990 1000 1010 1020
RNHINTVSKR IGQLQKRYEK CIDLCHQIEC LTTEQLLQFV RRINDRYNRA VTEPGTAVGA

1030 1040 1050 1060 1070 1080
IAAQSIGEPG TQMTLKTFHF AGVASMNITQ GVPRIVEIIN ATKTISTPII TAELENCHSM

1090 1100 1110 1120 1130 1140
EFARQVKARI EKTTLAELSS YVEVVCGPYS CYLAIGVDMA RIKLLGLHID LDTIVFSILK

1150 1160 1170 1180 1190 1200
SRMRVKPTQV EVVASQSRIV VRVEATRTST INAELARLAL SLQNVVVAGL PNINRAVIAV

1210 1220 1230 1240 1250 1260
DDARQPPTYK LCIEGYGLRD VIATYGVVGK RTRSNNICEI YQTLGIEAAR TIIMSEITEV

1270 1280 1290 1300 1310 1320
MEGHGMSVDW RHIMLLASQM TARGEVLGIT RHGLAKMRES VFNLASFEKT ADHLFDAAYY

1330 1340 1350 1360 1370
GQTDAINGVS ERIILGMPAC IGTGIFKLLQ QHEDKQVPPI EPTICSSLNL LPSKTT


This is actually a sub-unit that is called the beta chain of the RNA polymerase. There are other parts. The entry is A8JUY3 at UniProt.

Let's talk about probability that life could have happened by chance. A well-known metaphor for chance is the image of one million monkeys sitting at a million typewriters. If given enough time, some say, they will type out by chance the works of Shakespeare. However, the mathematics of probability shows that even for the old-Earthers, the 14 billion years of the universe so far has not been nearly enough time for this to happen. For one million monkeys on keyboards with all the letters, a space and period keys (a total of 28 units) typing continuously at 60 words per minute, it would take seconds to type any 31-unit string. But to cover all possibilities except duplications (or on-average), they would need about 7 thousand trillion trillion trillion years to write the specific 31-unit string: It was a dark and stormy night.


A really good book about probability of life is by John Lennox, a teacher of mathematics at Oxford University. It's published by Lion and called God's Undertaker: Has Science Buried God? He shows the vast improbability both of random beginnings of life and evolution.

Some say that possibly billions of planets exist in the universe and so life was inevitable. William Dembski has shown that the maximum possible events, including chemical reactions, in the universe is about 10 to the 150th (I'm going to use the caret, ^ , for the exponent from now on--10^150 in this case). Billions of planets (10^9 or so), are not enough for a random start to life.

The simplest bacteria I've seen so far has 1100 proteins. Cyanobacteria, which can make all their own energy and reproduce, unlike virus or mitochondria, have about 3.5 million DNA base pairs. E. coli bacteria have over 4000 proteins. The odds for these structures starting by chance even in the whole universe are related to the overwhelming number of combinations that are possible in amino acids.

Even evolution, where you supposedly have a start in DNA and proteins which can change by mutation over generations, cannot overcome the numbers when it comes to combinations needed for regulatory signals and feedback mechanisms.

Muscle Protein

Previously I discussed what proteins and amino acids and DNA look like, I'd like to start putting into my blog some of the amazing discoveries in biology of the last few years. First, we'll start with the fruit fly. That's a critter that has been researched extensively. It has muscle proteins, just as many animals do, including humans. It uses muscles to move in various ways. See the set of muscles HERE. The muscles are made of different components which are pictured HERE. One part of the muscle fiber, myosin, is made of 3 sets of proteins: 2 heavy chains of myosin and 4 light ones. Below is the amino acid sequence for the heavy chain. I got this from the UniProt website. I have a link to their home page HERE. I also have a link HERE to muscle in Wikipedia if you want more information on muscle. Click the pictures there to see bigger versions.

The letters each stand for an amino acid. For example, M is for methionine and P stands for proline. The numbers tell you how many there are (they are more spread out on UniProt). You can look this one up from the UniProt site by going to the QUERY BOX at the top of the page and putting in the code for this one which happens to be P05661 (the 0 is a zero) or just click HERE. The file you get shows you the protein sequence, the people who did the work on it, and some information about it. It's fascinating.

10 20 30 40 50 60
MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV

70 80 90 100 110 120
SVGLQGGEVR DIKSEKVEKV NPPKFEKIED MADMTVLNTP CVLHNLRQRY YAKLIYTYSG

130 140 150 160 170 180
LFCVAINPYK RYPVYTNRCA KMYRGKRRNE VPPHIFAISD GAYVDMLTNH VNQSMLITGE

190 200 210 220 230 240
SGAGKTENTK KVIAYFATVG ASKKTDEAAK SKGSLEDQVV QTNPVLEAFG NAKTVRNDNS

250 260 270 280 290 300
SRFGKFIRIH FGPTGKLAGA DIETYLLEKA RVISQQSLER SYHIFYQIMS GSVPGVKDIC

310 320 330 340 350 360
LLTDNIYDYH IVSQGKVTVA SIDDAEEFSL TDQAFDILGF TKQEKEDVYR ITAAVMHMGG

370 380 390 400 410 420
MKFKQRGREE QAEQDGEEEG GRVSKLFGCD TAELYKNLLK PRIKVGNEFV TQGRNVQQVT

430 440 450 460 470 480
NSIGALCKGV FDRLFKWLVK KCNETLDTQQ KRQHFIGVLD IAGFEIFEYN GFEQLCINFT

490 500 510 520 530 540
NEKLQQFFNH IMFVMEQEEY KKEGINWDFI DFGMDLLACI DLIEKPMGIL SILEEESMFP

550 560 570 580 590 600
KATDQTFSEK LTNTHLGKSA PFQKPKPPKP GQQAAHFAIA HYAGCVSYNI TGWLEKNKDP

610 620 630 640 650 660
LNDTVVDQFK KSQNKLLIEI FADHAGQSGG GEQAKGGRGK KGGGFATVSS AYKEQLNSLM

670 680 690 700 710 720
TTLRSTQPHF VRCIIPNEMK QPGVVDAHLV MHQLTCNGVL EGIRICRKGF PNRMMYPDFK

730 740 750 760 770 780
MRYQILNPRG IKDLDCPKKA SKVLIESTEL NEDLYRLGHT KVFFRAGVLG QMEEFRDERL

790 800 810 820 830 840
GKIMSWMQAW ARGYLSRKGF KKLQEQRVAL KVVQRNLRKY LQLRTWPWYK LWQKVKPLLN

850 860 870 880 890 900
VSRIEDEIAR LEEKAKKAEE LHAAEVKVRK ELEALNAKLL AEKTALLDSL SGEKGALQDY

910 920 930 940 950 960
QERNAKLTAQ KNDLENQLRD IQERLTQEED ARNQLFQQKK KADQEISGLK KDIEDLELNV

970 980 990 1000 1010 1020
QKAEQDKATK DHQIRNLNDE IAHQDELINK LNKEKKMQGE TNQKTGEELQ AAEDKINHLN

1030 1040 1050 1060 1070 1080
KVKAKLEQTL DELEDSLERE KKVRGDVEKS KRKVEGDLKL TQEAVADLER NKKELEQTIQ

1090 1100 1110 1120 1130 1140
RKDKELSSIT AKLEDEQVVV LKHQRQIKEL QARIEELEEE VEAERQARAK AEKQRADLAR

1150 1160 1170 1180 1190 1200
ELEELGERLE EAGGATSAQI ELNKKREAEL SKLRRDLEEA NIQHESTLAN LRKKHNDAVA

1210 1220 1230 1240 1250 1260
EMAEQVDQLN KLKAKAEHDR QTCHNELNQT RTACDQLGRD KAAQEKIAKQ LQHTLNEVQS

1270 1280 1290 1300 1310 1320
KLDETNRTLN DFDASKKKLS IENSDLLRQL EEAESQVSQL SKIKISLTTQ LEDTKRLADE

1330 1340 1350 1360 1370 1380
ESRERATLLG KFRNLEHDLD NLREQVEEEA EGKADLQRQL SKANAEAQVW RSKYESDGVA

1390 1400 1410 1420 1430 1440
RSEELEEAKR KLQARLAEAE ETIESLNQKC IGLEKTKQRL STEVEDLQLE VDRANAIANA

1450 1460 1470 1480 1490 1500
AEKKQKAFDK IIGEWKLKVD DLAAELDASQ KECRNYSTEL FRLKGAYEEG QEQLEAVRRE

1510 1520 1530 1540 1550 1560
NKNLADEVKD LLDQIGEGGR NIHEIEKARK RLEAEKDELQ AALEEAEAAL EQEENKVLRA

1570 1580 1590 1600 1610 1620
QLELSQVRQE IDRRIQEKEE EFENTRKNHQ RALDSMQASL EAEAKGKAEA LRMKKKLEAD

1630 1640 1650 1660 1670 1680
INELEIALDH ANKANAEAQK NIKRYQQQLK DIQTALEEEQ RARDDAREQL GISERRANAL

1690 1700 1710 1720 1730 1740
QNELEESRTL LEQADRGRRQ AEQELADAHE QLNEVSAQNA SISAAKRKLE SELQTLHSDL

1750 1760 1770 1780 1790 1800
DELLNEAKNS EEKAKKAMVD AARLADELRA EQDHAQTQEK LRKALEQQIK ELQVRLDEAE

1810 1820 1830 1840 1850 1860
ANALKGGKKA IQKLEQRVRE LENELDGEQR RHADAQKNLR KSERRVKELS FQSEEDRKNH

1870 1880 1890 1900 1910 1920
ERMQDLVDKL QQKIKTYKRQ IEEAEEIAAL NLAKFRKAQQ ELEEAEERAD LAEQAISKFR

1930 1940 1950 1960
AKGRAGSVGR GASPAPRATS VRPQFDGLAF PPRFDLAPEN EF

You may wonder why I put the sequences of part of a muscle fiber of a fruitfly on my blog. I want to show you the type of information that is used in Intelligent Design Theory. This fiber has over 1900 amino acids in a row (called a sequence). There are 20 kinds of amino acids in an order that works only for this muscle fiber. That is called a specified order. It is also called complex because of all of the amino acids needed. In Intelligent Design Theory (ID), the biology of living systems is believed to be Irreducibly Complex. In other words, you can't get the muscle of the fruitfly to work if it doesn't have all or at least most of these amino acids. ID also says that biological machines such as muscle are of Specified Complexity. The amino acids have to be specifically where they are to work. These two components of ID have been written about by Michael Behe in Darwin's Black Box (Simon and Schuster, 1996) and William Dembski in Intelligent Design (InterVarsity Press, 1999).

Update 1/21/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species separately and directly. Much of the biological science in ID is similar to Special Creationism.

DNA, RNA and Genes

An overview of the cell, the basic unit of biology is at the link HERE. The link describes the two basic types of living cells (prokaryotes and eukaryotes) and gives descriptions and further links to the contents such as DNA and protein.

DNA and RNA make amino acids into protein (click HERE for picture in Wikipedia). The letters in the Wikipedia picture stand for subunits of DNA, RNA and proteins, which I will get to later. DNA is divided into genes and has other areas that don't make genes directly.

The Human Genome Project found that humans have about 20-30 thousand genes. This was a surprise, since many thought there would be at least 100,000. The genes are used as a code to make protein. However, many proteins can be modified so that there are about 1 million variations of proteins. Now scientists are discovering that proteins themselves and RNA, which copies the DNA, are involved in regulating types and amounts of protein. We will get into details later.