Friday, August 29, 2008

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 a species of Archaea and Cyanobacteria. At the top is a computer structure from Swiss Model RepositoryDNA polymerase from Archea. Details are reported at Uniprot P26811. It has 882 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. It is made by other molecules which can carry out reactions that copy the DNA genes and transform the code of the DNA to proteins. One of those molecules is RNA polymerase, which is pictured in the right column of the blog.

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 first 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.

Tuesday, August 26, 2008

DNA Primase

Organisms called Archaea were discovered in fossils dating, according to accepted radiometric methods, from about 3.8 billion years ago (bya). 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 list is DNA Primase which you can read about in the link to Wikipedia. The primase helps the helicase make the DNA ready for replication. A picture of one is here.


This protien molecule has 646 amino acids as reported by UniprotKB/trEMBL here. The amino acids are shown and described in the previous post. This is a different protein than the helicase and topoisomerase which I showed in previous pictures (use DNA link under topics and label or scroll down). 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.

Friday, August 22, 2008

Helicase


The DNA molecule as seen in my previous entry (and at DNA label below) is undergoing reproduction. There I showed the first molecule which affects the DNA to prepare it for the process of replication. Now we come to another molecule, called a helicase. These take apart the pairs of nucleotide units which make up the DNA. Above and at the link is a picture of one from Swiss-Model Repository from a Cyanobacterial species. This molecule is made of 773 amino acids, as reported in the research reference in Uniprot Q8DG65. 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 Amino Acid--Creationwiki link at right 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.

Tuesday, August 19, 2008

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 at the right in the top picture is called "topoisomerase." 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. 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. It is less than 1 event in all the events of the universe so far, including chemical reactions (which is 10^150). But we have many more molecules to go to show the extent to which Cyanobacteria had probably already developed.

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.
Added 8/9/2010: 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.

Friday, August 15, 2008

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 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. from "DNA Research" tells us a certain strain of Cyanobacteria have 3.5 million base pairs in their 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. (The molecules on the right 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. from "Research in Microbiology" has shown that at least 1000 genes are needed for life to exist independently.

Tuesday, August 12, 2008

Book Finally Finished

It finally happened! I'm finished writing my book! That doesn't mean I'm done with the work. There are many things yet to do, including the type-setting, getting the bar code, proof-reading, etc. But with the possible exception of a little more editing, the writing part is finished!

Perhaps there are people who find creative writing easy, but not my husband and I. Do you see all the technical entries about Intelligent Design Theory in this blog? They were EASY to accomplish compared to creative writing. Perhaps ID is the greatest distraction I had in getting this book done. Every day, I wanted to read and write about ID first. Maybe I was partially avoiding the creative writing, but more because I truly enjoy ID and find it fascinating. I will feel more free now to pursue speaking and teaching opportunities in ID now that the book is done.

ID is a difficult subject and not everyone is that interested in it. But I think it is up & coming and is getting more publicity. I have found that people are quite amazed by what I tell them about it. It especially helps to show slides--you know what a picture can be worth. And though there are getting to be many good websites about ID, there is no substitute for personal instruction.

Here I am again, moving from the subject of my book to ID. My book contains Catholic themes, and situations which I think would be interesting to anyone concerned about problems in today's world. As time goes on I'll talk more about the plot and eventually give you an excerpt.

Friday, August 8, 2008

Biologic Anthropic Principle

In the previous entry I talked about the theories and discovery of the atom. Though the atom seems commonplace knowledge today, it was only proven to exist in 1909. Stormy disagreements among prominent scientists occured before the atom was accepted.

Disagreements abound today about evolution of life. Some say it is fact, some say it never happened. One of the arguments is that evolution can partially happen in a natural way without supernatural intervention, but some aspects are not possible by nature alone.

Recently discovered scientific facts are contrary to previously held beliefs. The biology of the cell does not always support the theory of evolution by natural means. Other facts point to organisms' ability to chage by DNA mutation and natural selection. Will a definitive answer be found in the future?

Biological evolution can't be separated from the theological implications lurking behind the theories, try as some might to do so. If evolution can't be explained by natural laws, then supernatural ones should be considered. The problem is that some people are not accepting even the possibility of a supernatural cause even though it may very well turn out to be true.

Not only is the implication of creation showing up in biology, but cosmology as well. The Anthropic Principle notes that the universe is fine-tuned for life. Many physical phenomena had to be balanced in amazing proportions to form atoms, planets and all else the universe now offers.

It is not a far stretch to proclaim a Biologic Anthropic Principle. The physical and chemical qualities that make up life are beyond totally naturalistic, materialist explanation. Even if some biological self-organizing physical law were found, as some artificial life computer programmers think is needed, that law would have to be analyzed under the anthropic umbrella.

Some prominent scientists who are Christians seem to think it is OK for God to create the universe in a pre-packaged plan, but must not be allowed to touch His own creation after the Big Bang. There is still very much to be learned about science and we must remember it took 2500 years to prove the atom. However, I would like to remind these scientists that God came in the flesh about 2000 years ago, and touched his creation in a profound way. He also performed miracles that defied our presently known scientific laws.

I quote the beginning of chapter 38 of Job, from Gospelcom, NIV. We may all do well to read from this chapter to the end of the book (and eventually the whole book):

The LORD Speaks
1 Then the LORD answered Job out of the storm. He said:
2 "Who is this that darkens my counsel with words without knowledge?
3 Brace yourself like a man; I will question you, and you shall answer me.
4 "Where were you when I laid the earth's foundation? Tell me, if you understand.
5 Who marked off its dimensions? Surely you know! Who stretched a measuring line across it?
6 On what were its footings set, or who laid its cornerstone-
7 while the morning stars sang together and all the angels shouted for joy?
8 "Who shut up the sea behind doors when it burst forth from the womb,
9 when I made the clouds its garment and wrapped it in thick darkness,
10 when I fixed limits for it and set its doors and bars in place,
11 when I said, 'This far you may come and no farther; here is where your proud waves halt'?


My hope is that all of us may quest for knowledge in a humble way and respect each others' opinions. I ask this of everyone, but especially of Christians.

Tuesday, August 5, 2008

Discovery of Atom


The story of the scientific discovery of the atom is quite interesting. Anaxagoras, a philosopher who lived in Athens about 2500 years ago, believed that an initial chaos was brought into form by a Mind (Nous). He suspected tiny particles to be the building blocks of nature but believed they were mixed together in unlike forms. He thought the Mind separated and organized the units.

Let us zoom now to the early 1800's. Scientists were studying gases and their properties linked with pressure, volume, temperature, etc. An Englishman named John Dalton discovered properties that led him to believe gas was made of atoms. He published his work in 1803.

But in 1900, scientists still did not agree on whether or not atoms exist! Chemists were becoming more convinced, due to Dalton's work. But physicists working on the study of heat, work and energy exchange of substances, called thermodynamics, were not convinced of atoms. They were thinking more in terms of fluid movement and, 100 years after Dalton, atoms did not fit their theories or expectations.


Enter Ludwig Boltzmann into the mix. He was a brilliant Austrian physicist, who taught at several universities. He came up with the idea that gasses may behave in a statistical way, dependent on probabilities that could be analyzed mathematically. Only if gas is made of atoms could this be true.

But, many physicists of the day would not hear of it. They would not publish Boltzmann's work as he wrote it and made interpretations of it to their own liking which took away his main points. He moved away from one university because of a rival who had a prominent name and position, and only returned when that rival retired. Sadly, in 1906, Boltzmann committed suicide.

In 1909, Earnest Rutherford's lab experimentally proved the existence of the atom with what was called the "gold foil experiement" (you can read details at the link). The experiment also led to the true structure of the atom, with positive charge in the inner area and negative charges surrounding it.

Boltzmann's analysis that gas can be understood statistically stands today, and has been used to build further knowledge.

Friday, August 1, 2008

Introns

It's an exciting time in biology. New knowledge is coming forth and reported in scientific articles. And, what's more, many do not support totally materialistic, naturalistic evolution (total-natural evolution). The authors of these articles, however, may not be willing to agree that their findings do not support Darwin. On one hand, we should realize that a huge amount of new information has become available from microbiological research and more will be coming. Many scientists look to the future for confirmation of materialistic evolution. On the other hand, scientists should be willing to express where we stand now. And when you look at the math, total Darwin doesn't add up.

One of these articles is (don't give up--you don't have to understand the jargon) "Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach." It is in Molecular Biology and Evolution under Oxford Journals and written by Miklós Csürös, et al., published online Feb. 21, 2008. You can link to the article abstract by clicking on the title.

To understand the significance, you need to know that there are different types of cells. Two major types are Prokaryotes and Eukaryotes. Eukaryotes (pronounced you-carry-oats) are the cells humans and multi-celled animals have. Prokaryotes (pro-carry-oats) are the type that many (not all) single-celled organisms have, such as bacteria. There is much more detail about the differences at Wikipedia under Cell (biology) . A few of the differences are: 1) DNA in the eukaryote is structured and divides different than the prokaryote; 2) the eukaryote has a type of skeleton in the cell but not the prokaryote; 3) the eukaryote has INTRONS and the prokaryote does not. The introns are what I have been talking about in the last few posts. They are "extra" parts of the DNA which are copied to RNA and are removed before RNA makes the protein. You can see the mechnism and parts needed for it in the previous posts (scroll or click spliceosome link below).

So the research reported by the article above was to use mathematical tools to find out how many introns were in the ancestors of selected living eukaryotes. The abstract, or short description of the paper, admits that the outcome was unexpected. The ancestors of several subgroups of organisms they studied had much higher levels of introns than one might predict if one expected Darwinian evolution. In fact, one subgroup had a higher intron density than humans!

Now, look at my previous entries about spliceosomes (you can click here to see them or on the spliceosome link below). These show that five spliceosomes are used in the splicing process to remove introns. There has to be genetic codes in DNA to make each of the RNA-protein units (U1, U2, U4-6). The units also must have work done to form them into the shapes they need to do specific jobs (just like hammers and screwdrivers need to be certain shapes to do their jobs). Below is a picture from Swiss Model Repository of a protein molecule that changes RNA structure, called a pseudouridine synthase. It is from an organism known as Pseudomonas aeruginosa. It works on a different RNA, called tRNA (not all proteins have yet been modeled), but it gives you an idea of the type of molecule needed to change the shapes of RNA into what you have seen on my posts about spliceosomes. (I have added the link to ExPASy at the right side of the blog screen. When you get to that page, you can access Swiss Model Repository which computes these models.)



The findings in the article to me imply that the ancestors of eukaryotes must have had these complex mechanisms from the start. The theory that these cells and the bacterial prokaryote cells had a common ancestor is wearing thin. As Hugh Ross and others have explained, findings in geology have shown that not much time lapsed between the cooling of the earth and the start of biological life. The spliceosomes and the DNA and proteins needed to form them have thousands of atoms in specific positions to allow them to do specific activities. These atoms have astronomical numbers of potential combinations, but only extremely rare combinations will work. As I said, it's an exciting time in biology.