Tuesday, September 30, 2008

Short History 6


In the late 1800’s and early 1900’s a large effort was being put forth by scientists to understand the atom. Many scientists even at this time rejected the concept of atoms. It was only in 1911, 2500 years after the Greek atomists, that Ernest Rutherford convincingly experimented to show that atoms exist with a negative particle encircling a positive center.

The Church’s conception of a beginning for creation has endured scientific challenge. Albert Einstein calculated his general theory of relativity with the assumption that the universe is eternal. Then in 1929, Edwin Hubble recognized that distant galaxies are moving away from each other, confirming predictions of a “Big Bang,” or initial beginning point. The “cosmological constant” with which Einstein “fudged” his numbers to agree with an eternal universe was by his own assessment his greatest mistake.[i]

It is important to note in this brief description of history that neither the church nor science is automatically right or wrong about the physical nature of the world. We must realize scientists go through many stages to get to the truth of nature. It is not wrong to use imagination to make theory—it may take years for experiments to be conducted. And our expectations should not limit our conclusions—a negative result can be as informative as a positive. In a way, every negative finding for one theory is a positive finding for a different theory. We continue to work to understand the relationships between nature and faith. Persons can use the reason God gave them to sort fact and literary metaphor in the Bible—both are there!

[i] Ronald Clark, Einstein (NY: Avon, 1971), 268-270.

Friday, September 26, 2008

Short History 5

The short history of science and religion continues:

The philosophers of the 1600’s & 1700’s promoted a movement called the “Enlightenment.” They influenced a shift in philosophy from a God-created universe to the concept that nature consists only of matter. This outlook is called philosophical naturalism.[i]

In the 18th century, a geologist named James Hutton suspected that the Earth was older than the Biblical interpretation of 6000 years. He believed that rocks slowly formed over time, a theory called uniformitarianism. Though now accepted by geologists, it was rejected by science at the time.

William Paley in 1802 wrote Natural Theology in which he saw the wonder of design in nature. Much of his book describes anatomy, but it also includes the famous “watchmaker” argument. If someone were walking over a heath and saw a watch on a stone, he says, they would immediately recognize the timepiece as made by a designer. When Paley finds intricate marvels with important functions, such as the mechanical muscular system in animals, he concludes they could only be made by a designer with intelligence. One could appreciate nature yet see it as God’s design.

Then in 1859, Charles Darwin introduced The Origin of Species which described his theory of evolution. He believed all species derived from one or a few original organisms. The following generations of offspring changed through the combination of random variation and natural selection. The laws of genetic inheritance had not yet been worked out.

These laws were presented in 1865 by a monk, Gregor Mendel, who had discovered them by careful observation in generations of plants. They were not accepted by the scientific community for some time but are now known to be true.

The 1920’s many persons worked to blend Darwin’s theory with Mendel’s genetic laws. The names of Morgan, Mayr and Dobzhansky are prominent in the formation of what is now called neo-Darwinism. This new synthesis, however, was taken by some to be more than a scientific theory. It has been used as a reason to reject any possibility of supernatural intervention.

[i] Del Ratzsch, Science and its Limits (Downers Grove, IL: InterVarsity Press, 2000), 180, footnote 10 from page 122.

Tuesday, September 23, 2008

Short History 4

We continue our (very) short history of the relationships between science and religion.

After Christ's life on Earth, Christianity spread throughout Europe, Africa and Asia Minor. Other world religions thrived: Hinduism, Confucianism, Buddhism. Mohammed, originator of Islam, was born in 570 AD.

Roger Bacon (c.1214-1292) was a British Franciscan (friar of the order of St. Francis) who is credited with the grounding of science in experiment. He conducted some experiments of his own and promoted optics, mathematics and language as keys to the sciences. Persons in the church, however, became suspicious of him and he was imprisoned for a time.[i]

Also in the 1200’s, Thomas Aquinas took a new look at Aristotle. Europe had seemed to lose interest in him, but Aristotle was preserved in the Arab world and now was being revived in Europe. Aquinas wrote the famous Summa Theologica. His first premise was that humans need both reason and revelation from God for full knowledge.[ii]

Nicolaus Copernicus (1473-1543) was both a scientist and churchman. His belief in the heliocentric (sun-centered) solar system was reinforced by Galileo (1564-1642). Many know of Galileo’s clash with religious authority of his day. He was condemned two times by the Catholic Church, but later exonerated by other scientists. In 1992, Pope John Paul II apologized on behalf of the Church.[iii]

Francis Bacon (1561-1626) encouraged the “inductive” method of science. He said science should be conducted only through observation and experiment. He was reacting against the mixture of knowledge of nature with spiritual speculation of the day. For example, investigators of chemistry often included alchemy and magic in their reasoning.

[i] New Catholic Encyclopedia, Second ed., s.v. “Roger Bacon.”
[ii] Thomas Aquinas, Summa Theologica Part I, Question 1, Article 1.
[iii] Smith, A. Mark, “Galileo,” 11/15/06, http://www.nasa.gov/worldbook/galileo_worldbook.html#wbtop .

Friday, September 19, 2008

Short History 3

From Old Testament times, prophets predicted a Messiah for the Jewish people. They expected a political liberator who would bring in a new age where Israel would be triumphant and rule over enemies.


Jesus Christ was born about 4 BC According to the Christian religion, Jesus was and is the Messiah, but His leadership was not what the Jews were expecting. Christians believe He is the Son of God and came to redeem and free the human race from sin. He died around 30 AD (the exact year can only be approximated).[i]

Shortly afterward Paul, a disciple of Jesus, wrote regarding knowledge of God through nature: “For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made…so that they are without excuse” (Rom. 1:20).

In 30 AD, Galen, a Greek physician, was born. He wrote books which influenced the way medicine was practiced for about 1500 years, even though it was very limited. For example, he did not know that blood circulated in the body.

Also, Ptolemy, an Egyptian (probably Greek immigrant parents) living at 100 AD, drew an elaborate planetary system in which the Earth was center. It agreed with Aristotle’s view and continued to be accepted in the Middle East and Europe.

St. Augustine, a great theologian, lived in about 400 AD. In “The Literal Meaning of Genesis,” he warned Christians that unbelievers know facts about physical elements of earth and sky. If Christians try to teach Scripture in terms of false facts, they would detract from the true spiritual messages.[ii] However, Augustine himself did not hesitate to proclaim that the initial Creation is God’s handiwork.[iii]

This short history of relationships between science and religion will be continued.

[i] New Catholic Encyclopedia, Second ed., s.v. “Jesus Christ.”
[ii] Cf. St. Augustine, the Literal Meaning of Genesis Sec. 38-39, Ancient Christian Writers. trans. John Hammond Taylor (NY: Paulist, 1982), search “augustine-genesis” at: http://www.holycross.edu/search.html .
[iii] Cf. St. Augustine, City of God, Book XI, Ch. 1-8,

Tuesday, September 16, 2008

Short History 2

Continuing in the historical relationship between religion and science, Abraham lived at about 2000 BC. He believed in one God, and that God promised he would be very fruitful, the ancestor of kings and nations (cf. Gen. 17:4). He was the great-grandfather of the twelve tribes of Israel and is listed in the genealogy of Jesus Christ.

Various groups of peoples lived in the Americas from the times before Christ. The Olmecs were developing calendars and language in Mexico. They were polytheistic, worshipping, for example, gods of sun and rain.
[i]

Ancient Greeks worked on understanding nature. Pythagoras (circa 582-507) wove ideas about mathematics and philosophy. Around 500 BC, “atomists” believed in tiny building blocks for the structure of nature. Anaxagoras, himself an atomist, thought a cosmic “Mind” had intervened to bring order from chaos, thereby perhaps anticipating Intelligent Design Theory (picture from Wikipedia s.v. Anaxagoras).

One of the greatest philosophers, Aristotle, was born in 384 BC. He believed in a God who sustained an infinite universe, with the Earth in the center. He thought God had little to do personally with human beings. Aristotle classified nature as he observed it and developed formal logic.

The theory that the Earth was the center of the universe, therefore, was not just from the Bible. In ancient times, philosophy, science and theology were intertwined in various forms. Philosophy literally meant a “pursuit of wisdom” which in that day included knowledge of the natural world.

To be continued.

[i]
World Book Encyclopedia, 2006 ed., s.v. “Mexico.”

Friday, September 12, 2008

Short History 1

People throughout the ages have had both a yearning for God and a curiosity about nature. It may be helpful to look at a very short summary of science and religion history to give perspective for today's comparisons.

Many civilizations of the Earth in these early times believed in multiple gods. The Sumerians by 2500 BC worshipped Mother Goddess Innin and son Tammuz. Egypt in 2000 BC had Isis (picture from Wikipedia s.v. Isis) and Osiris.[i]

The vast times of history before 2000 BC are dim. But in one of the earliest scientific endeavors, Egyptians developed a 300-day calendar with 12 30-day months, then eventually one with 365 days regulated by the sun, moon and stars.[ii]

Also before 2000 BC, Sumerians (who lived in present-day Iraq) were writing on clay tablets with pictograph signs. Egyptians and Sumerians were using copper alloys.[iii]

The Old Testament of the Bible is in part a history of the Jewish people. The book of Genesis proclaims the creation of Heaven and Earth and the first people, Adam and Eve. A man named Tubalcain was the seventh generation after Adam. He was “an instructor of every artificer in brass and iron” (Gen. 4:22, KJV).

To be continued.

[i] Bernard Grun, The Timetables of History, New third rev. ed. (NY: Simon and Schuster, 1991), 2.
[ii] Grun, 3.
[iii] Grun, 2.

Tuesday, September 9, 2008

Cosmological Model

Picture from Hubble Space Craft, NASA.


Another of Eugene Koonin's articles published last year, "The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life," 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 so improbable as to be impossible. Genes can flow, drift, move horizontally or vertically or double, triple or quadruple but they just can't overcome these probability numbers. That is because the extreme improbability encompasses all the movements and chemical reactions of the so-called pre-biotic elements. 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.

Friday, September 5, 2008

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 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 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 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.

Tuesday, September 2, 2008

Biological Big Bang

It is an exciting time in biology. Last year, several articles about origin of life (OOL) and evolution were published by Eugene Koonin from the National Center f0r Biotechnology Information, National Institutes of Health, Bethesda, MD. 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." It 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 the Cyanobacteria which has over 900 amino acids is different than the molecule that replicates DNA in one of the archaea species which has 882 amino acids as reported in Uniprot (Q2JWV2 and P26811).

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. Koonin proposes alternate solutions, still hoping for that common ancestor. But let's look at the numbers. For Cyanobacteria, just one 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 discrepency is obvious.

Hubert Yockey used Information Theory to estimate that in a protein of 100 amino acids, only about 1 in 10^65 are functional for a specific job. I can imagine that a longer protein would have even less chance to be functional enough to replicate DNA in conjunction with other equally complex molecules. To determine the exact proportion of functional combinations would be a great project for proponents of Intelligent Design (it has not yet been done that I know). That area of study is being stifled in universities, as reported in various places such as Discovery Institute (link on right column of this blog). It is the subject of the movie "Expelled" with Ben Stein that was shown over the summer.

Assuming reactions between potential proteins, with 1 in 10^65 proteins being specifically functional, the probability that 3 functional ones would meet together would be about 1 in 10^195. Less than one chance in all the events of the universe for the combination of 3 proteins to function as they need. And even 3 specific, functional proteins are not enough for DNA replication for one organism.