Spliceosome U1

For an organism to make proteins necessary for life, the genes in DNA are copied to mRNA (the m before RNA stands for messinger, since there are different kinds of RNA) by a protein called RNA polymerase which I showed in a picture and previously described HERE. Once the mRNA is copied, it needs to be modified or "edited" because, for some reason not yet understood, there are unused parts between the usable parts of the gene. There are a group of special molecules which do this work called "spliceosomes." They consist of a combination of RNA and proteins. The pictures here show the beginning of the process and the first spliceosome. The ends labeled exon 1 & 2 are usable parts of the RNA that will remain, while the middle unused part, called the intron, will be removed by the molecules. The picture above is a detail of an image on Wikipedia under the heading, minor spliceosome.


The picture on the right is the first spliceosome to find a place on the RNA, called U1. The letters making up the structure (G, U, A, & C) stand for the set of molecules (made of atoms) that make up RNA--guanine, uricil, adenine, and cytosine. You can link to Wikipedia to see guanine or to my post HERE to see them all (update 2008/08). The U1 unit connects with mRNA and starts the processes needed to remove the intron. These actions are present in life in cells known as eukaryotes, which you can read about in Wikipedia HERE. They are not in prokaryotes. This means this whole set of metabolic activities would have had to develop by chance, along with many other new processes in the eukaryote, if total materialistic, naturalistic (total-natural) evolution is true.
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Update May 20, 2014: I've put in several places that I've changed from advocating Intelligent Design Theory to Direct Supernatural Creationism. I sometimes call totally materialistic, naturalistic explanations "total-natural" in contrast to "supernatural," a word already understood.

Creation and Evolution 4

The book by Stephan Horn Creation and Evolution: A Conference with Pope Benedict XVI in Castel Gandolfo (Ignatius Press, 2008), is a record of a meeting of Pope Benedict XVI with former graduate and post-graduate students in 2006. The group has been meeting annually for years to discuss various subjects, but this is the first to be presented in book form. The book was compiled by Stephan Horn, SDS, and Siegfried Wiedenhofer. This review continues from a previous entry (to see all of them, click CR-EV REVIEW label at bottom of post). The numbers in parentheses are page numbers for your reference.

The discussion starts with several questions to Professor Peter Schuster who had given one of the presentations. He is asked about the large leap organisms would have to take by evolution if totally materialistic, naturalistic evolution were true.

Schuster tells about one of the first leaps after Origin of Life that organisms would have to take--the change from simple bacteria that live without oxygen (anaerobic) to a cell that does use oxygen (aerobic). He tells about a global increase of oxygen in Earth's atmosphere. He says, "evidently a species of bacteria developed that was able to deal with oxygen, and that species made its way into our cells as mitochondria" (110).

Though there is much more content in the book, I must stop right here to comment. And, I'll add that I won't be covering the whole book, since I'd like to go on to other things. I hope I will have given enough of an overview by the end of this entry that you can decide whether it is within the scope of your own interests to read Creation and Evolution.

In his presentation, Peter Schuster did all in his power to make evolution sound easy, and even states it is adequate to explain all life (58). But he glosses over the tremendous changes needed in the organism to do so. Later in the book, Fr. Paul Erbrich brings him to task with questions and comments about the complex mechanisms needed for life (147-149). Erbrich talks about the mutational doubling of the gene, a favorite crutch of evolutionary explanation, as being inadequate to produce new information needed for things such as photosynthesis (147). He cites the complex structures of ATP as being incapable of formation by (other physical) mechanisms alone (149).

Indeed, there are many new structures and pathways needed for evolution from an anaerobe to an aerobe for which Schuster's comments are inadequate. Michael Behe, in his book The Edge of Evolution (Free Press, 2007) lists a few: "The innovations include such fundamental features as sexual reproduction (meiosis and recombination), the organization of DNA into chromatin, and the provisioning of a cellular protein 'skeleton'" (Behe, 172). All these take tremendous amounts of new information. Behe shows that Darwinian evolution is not up to the task given the amount of time in which the changes would have had to take place.

Pope Benedict XVI, who joins the discussion toward the end, reasons that evolution can’t be tested experimentally because “we cannot bring 10,000 generations into the laboratory” (162). Unfortunately, Benedict is incorrect in this assessment—a paper was just released by a group of scientists from Michigan State University that have been following the genetic activity of E. Coli for over 40,000 generations: Blount, et al, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.”, PNAS, 105, 23 (June 10, 2008): 7899-7906. Actually, Schuster had mentioned this study but he puts a different "spin" on it than Behe would have. Schuster makes evolution sound like a fact, while the scientific evidence is showing more and more information against evolution. (2019 Update: Michael Behe writes about the Michigan State study as backing his own conclusions of major limits to natural evolution HERE). Though Schuster is no doubt successful in his own scientific areas of expertise, the undercurrent of dissenting opinion from the other participants in my opinion is not well-answered by him.

The Pope thinks the question of evolution belongs to philosophy, which as I wrote in the last entry is where Cardinal Schönborn puts it. Benedict, like Cardinal Schönborn, has a sense of the design of nature. A good quote from the book, I think, is from our Pope. He gives a great answer to the “God of the Gaps” argument that continues to come up in discussions between science and religion. Those who talk about God creating certain things are accused of cutting science short—that God explains a phenomenon until scientists discover the “real” reason for its existence. The Pope talks about questions that remain open, and then says, “Not as if I wanted now to cram the dear Lord into these gaps: He is too great to be able to find lodgings in such gaps” (161).

The Pope thinks that although science has discovered great things, its "findings lead to questions that reach beyond its methodological principles and cannot be answered within science itself" (163). The Pope ends in the same place as Cardinal Schönborn, with theology. He addresses the "component of terror" with which we are faced in the brutality of nature:

Here philosophy calls for something more, and faith shows us the Logos,who is creative reason and who incredibly at the same time was able to become flesh, to die and to rise again (174).

Creation and Evolution 3

The book by Stephan Horn, Creation and Evolution, A Conference with Pope Benedict XVI in Castel Gandolfo (Ignatius Press, 2008), is a record of a meeting of Pope Benedict XVI with former graduate and post-graduate students in 2006. The group has been meeting annually for years to discuss various subjects, but this is the first to be presented in book form. The book was compiled by Stephan Horn, SDS, and Siegfried Wiedenhofer. This review continues from a previous entry (to see all of them, click CR-EV REVIEW label at bottom of post). The numbers in parentheses are page numbers for your reference.

Christoph Cardinal Schönborn presented "Fides, Ratio, Scientia; the Debate about Evolution" (84). He reflects on the great scientist Isaac Newton who always saw the divine in the beauty of nature. Newton believed God actively supported the planets in their orbits and produced the great variety of natural things. The Cardinal relates the reaction to his article, Christoph Cardinal Schönborn, "Finding Design in Nature," New York Times, July 7, 2005, to the passion all humans feel about life's meaning.

Cardinal Schönborn asserts that Darwin's theory has left the level of science and become an ideology of materialism. He believes that "the decisive question...is found...on the level of natural philosophy" (91). He feels the debate is oversimplified to "creationists" vs. evolutionists. Here he defines  creationists as those who literally believe in a 6-day creation. He states that Catholics allow that the Creator could have used the instrument of evolution. However, he wonders whether "evolutionism (as an ideological concept) is compatible with belief in a Creator" (92).

The Cardinal notes that many scientists and scholars these days feel theology is either incompatible with evolution or separate from it. Many are satisfied with what is called methodological materialism, which says that scientists should experiment and theorize as though there is no supernatural element in nature. Schönborn calls this "methodological option" an "intellectual act" (93). It excludes God from nature which is antithetical to theology. Theology proclaims the Lord can be seen from what is made.

Cardinal Schönborn states, "Development of scientific theory is an intellectual process" (93). Human activity is goal-oriented, including investigations of science. And goals speak of purpose. Observation of nature sees order and design, but who recognizes it? He argues that philosophy and reason can recognize design. Using the metaphor of language, he points out that scientific objectivism "mistakes the letter for the text" (102).

He asks why, with its obvious shortcomings, evolution remains so well established. He answers, "Because so far there is no better theory." Yet evolutionary theory is a worldview (103). Anyone who thinks we were created (by God) also acknowledges a Creator who makes claims on us. We go from there to accepting ethical responsibilities.

Another reason for preference of evolution is observation of the long times and cruelties involved in our world's formation and nature. The answer here lies in accepting God's wisdom that gives meaning though we don't understand it all. His conclusion is that "The cross is the key to God's plan and counsel" (105).

I admire Cardinal Schönborn for bringing this discussion between religion and science into the open. He has been a leader of the Catholic Church and I enjoy reading his thoughts and thinking about his arguments. After this article appeared in the New York Times, he had several articles in the periodical, First Things, debating various persons, notably physicist Stephen Barr.

My impression of the Cardinal's arguments at that time have been reinforced by his presentation in this book. He presents the tensions between the modern science mindset and religion in general as one of philosophy. My opinion is that these differences stem from theology and I believe the Cardinal himself mixes theology in with his arguments. It can be hard to separate them, since philosophy relates to reason. How do we correctly evaluate and describe faith without an effort of reason? But the Cardinal's presentation in the end appeals to the cross, resurrection and God's wisdom as answers to the ultimate questions--those of meaning and purpose. This is theology, and what he can't reach with his philosophy arguments is that the problem is really about faith. For example, in the Intelligent Design movement there are many people who see design but do not accept God as the Creator. They think another intelligence or aliens of some different makeup than ours (they themselves being naturalistically evolved) have designed us. Can Aristotle or Plato change the minds of these people? Perhaps if all of us saw things as the Cardinal would wish to teach, but I'm afraid in our era he would (and does) meet minds closed to his arguments.

As for the appearance of life as we know it, there is a much better fit with the facts than naturalistic evolotion: that we were created directly in a supernatural way. This is called "special creationism." It's just that evolution is the only naturalistic theory to which non-believers can cling.

I will review the discussion part of the book in the next entry.

Creation and Evolution 2

The book by Stephan Horn, Creation and Evolution: A Conference with Pope Benedict XVI in Castel Gandolfo (Ignatius Press, 2008), is a record of a meeting of Pope Benedict XVI with former graduate and post-graduate students in 2006. The group has been meeting annually for years to discuss various subjects, but this is the first to be presented in book form. The book was compiled by Stephan Horn, SDS, and Siegfried Wiedenhofer. This review continues from a previous entry (to see all of them, click CR-EV REVIEW label at bottom of post). The numbers in parentheses are page numbers for your reference.

The next speaker to be presented in the book is Robert Spaeman (61). He talks about the differences between the natural sciences and philosophy. He seems to take evolution for granted (not all the participants do). Spaeman uses the metaphor of double codes in one of Bach’s Sonatas to infer that the code of biological evolution can be accompanied by a more purposeful code—that of human self-awareness (68).

Fr. Paul Erbrich, SJ, calls his presentation “The Problem of Creation and Evolution” (70). He distinguishes between ideas of “chance” held by biologists vs. those held by the critics of evolution. For biologists, evolution is by chance alone. The critics see evolution as “goal-oriented," and materialistic explanations are not sufficient for the “innovations that must come about in some other way” (72). I think he refers to the many genes in DNA that are in specific molecular order so that they can produce the organs and cellular functions of the body.

Fr. Erbrich also discusses the term, “mechanism.” He asserts that scientists of disciplines which can’t be explained totally by mathematics, such as biology, use this term to express causality. The term and its implied meaning keep the discipline separated from exploration into mental causality and the body-soul problem (77). To the materialists, bodies are simply a conglomeration of mechanisms.

When it comes to explaining the origin of the innovations needed for life, some biologists say complex systems can self-organize. Erbrich shows we cannot have the self composing itself. The beginning of an original totality must be a creation from nothing by God (82-83).

I would add here that theories of self-organization are about all the biologists have at present as a resort for their own resistance against supernatural creation. The probability that molecules of life have formed by chance is amazingly remote. Of course, scientists seem to hope for a spectacular experiment or discovery of a physical law which would explain everything and make the possibility of creation go away. They have thought in times past they have had it, such as the 1952 experiment by Stanley Miller which was to prove that lightning in the "primordial soup" created life. Over 50 years later, much has been discovered to deflate the hopes of that particular experiment, including the probable atmosphere of Earth at the time and the lack of molecules of the necessary complexity. Also, any recourse to self-organizing physical laws would need the same explanations as the fine-tuning laws of the universe collectively known as the "anthropic principle."

Next entry: the presentation by Christoph Cardinal Schönborn.

Creation and Evolution 1

The book by Stephan Horn, Creation and Evolution: A Conference with Pope Benedict XVI in Castel Gandolfo (Ignatius Press, 2008), is a record of a meeting of Pope Benedict XVI with former graduate and post-graduate students in 2006. The group has been meeting annually for years to discuss various subjects, but this is the first to be presented in book form. The book was compiled by Stephan Horn, SDS, and Siegfried Wiedenhofer. I will give a review in my next few entries (to see all of them, click CR-EV REVIEW label at bottom of post). The numbers in parentheses are page numbers for your reference.

An introduction was given by Christoph Cardinal Schönborn  (7). He is among the former students of Pope Benedict and is well known as editor of the most recent Catholic Catechism. The Cardinal started an international discussion, as is reported on the book jacket, by his Opinion article, Christoph Cardinal Schönborn, "Finding Design in Nature," New York Times, July 7, 2005, about creation and evolution. He seems very interested in the current design arguments, as do other participants in the symposium. The introduction (forward) extensively quotes previous statements by Pope Benedict about the nature of human "being" that is special because we are made to know God. The spirit is of first importance with the material as its support. The human is special as soon as s/he has an idea of God, whether we are "made" from direct molding or evolutionary descent (15). The details of the material are left to natural science (8).

Pope Benedict points out the dangers of evolutionary philosophy, in which naturalistic, materialistic evolution is claimed by some to answer all of life's questions (9-10). He believes it is of utmost importance for Christians to frame a proper discourse to address this matter. That is one of the main goals of their conference with its presentations and discussions presented in this book.

The first speaker was Professor Peter Schuster of the Institute of Theoretical Chemistry of the University of Vienna (27). He uses charts and pictures to give some scientific background to his talk, but does not complete his presentation with actual proof of molecular evolution. His conclusion that evolution can now be explained by material, naturalistic means (58) is therefore not convincing. Perhaps he feels it is too complicated to present to laypersons.

I must here point out there are many scientific articles which paint a different story. They have much more detail and demonstrate that there are still many hurdles yet to be overcome to explain how life could have evolved by chance. One is by a leading origin-of-life proponent, Leslie Orgel, "The Implausibility of Metabolic Cycles on the Prebiotic Earth," PLOS Biol. 6, 1 (Jan. 22 2008).  This is just one example of problems of life starting with random atomic movements.

I will continue this review in the next (chronological) entry.

Population Genetics

Population Genetics has been used as a tool for figuring out how genes express themselves in populations. The Britons R.A. Fisher and J.B.S. Haldane and the American Sewall Wright founded this discipline and others have added to it. It is part of a model called the Modern Evolutionary Synthesis. Many evolutionary scientists, including Richard Dawkins, are relying on its principles to explain evolution.

The model explains genes within breeding populations using observation, graphs for data and mathematics. It uses genetic material that already exists to examine the variation that can take place in a species. For example, a moth can change color over a period of time if the change helps to protect it from predators. The population geneticists can look at the genes for color and track how they change.

The main premise was worked out before structures in DNA and proteins were discovered. The Modern Synthesis scientists have incorporated new genetic information into their theories. They have been successful in applying mathematics to some biological phenomena. However, they have had problems in giving the details of how evolution has worked in the large jumps it has supposedly made at certain times. These large jumps include the origin of life, the development from what is called a prokaryotic cell (e.g. bacteria) to a eukaryotic cell (literally a true cell), and multicellular, multisystem animals. In these large jumps, new genetic material is needed, not just pre-existing DNA. ID advocates ask when and how the new material was generated.

So, some people look at proteins and their amino acid and DNA sequences and see material which can be used in other ways for proteins so that they can evolve into other structures. These generally are the Population Genetics crowd. Others look at the sequences and want to know how exactly such complex structures could have gotten to the point they are at. The ID advocates belong to the latter group, because when they apply the numbers to probabilities for new genetic information, they see probabilities that are minute in the extreme. The improbability is not the only factor, however. It is the fact that these improbable products are also functional. That is known as specified complexity.

This is a difference in perspective that should be kept in mind when evaluating what scientists tell us about evolution.

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The book Creation and Evolution, compiled by Stephen Horn and Siefgried Wiedenhofer (Ignatius Press, 2008), became available May 28. I hope to give you a review next week. The book is about a group that has met with Pope Benedict XVI for many years. They are former students of his at the Universities of Bonn, Münster and meet with him annually in summer to discuss theology and related issues. They sometimes have invited guest speakers. This book is the first to give a summary of their meetings, and covers their speeches and discussions about creation and evolution.

Transcription Factors

Scientists have discovered that many factors play on DNA and RNA in the process of protein production. I have shown you a picture of the protein, RNA polymerase, that copies DNA to RNA (May 26 2008) and here is a picture of what is called a transcription factor. You can click on the picture at right to see the fine print.

As an example, the amino acid sequence for one of the fruit fly muscle transcription factors is at the Uniprot site entry  P22816 HERE. It has 332 amino acids. The transcription factor is a protein that has to be made by separate DNA so it can combine with the muscle gene DNA at the right place when the fly embryo forms. The organism needs muscles that are formed with the correct attachments so the fly will be able move. It gets the RNA polymerase working (seen on the May 26 post linked above) which copies the DNA to RNA. The picture in this post is not this fruit fly P22816 factor specifically, but it shows a transcription factor at work on the DNA.

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I have just bought the book Creation and Evolution compiled by Stephen Horn and Siegfried Wiednenhofer. It is the result of Pope Benedict's conference with former students in 2006 at his summer retreat, Castel Gandolfo. Christoph Cardinal Schönborn is one of the participants. He had written an article in the New York Times in July 2005 about evolution and design which made quite a stir. I'm about 2/3's through and would like to do a review on my blog when I'm finished--should be soon.

Randomness

The best part of the movie Expelled, in my opinion, was near the end when Ben Stein asked Richard Dawkins, the famous evolutionist from Oxford University, how life came about. Dawkins said that nobody knows. When Stein pressed him for details, the biologist said the first organism could have come from aliens.

Stein did us all a great service in that interview. It seems that among laypeople there is the feeling that scientists either know or are on the verge of knowing how life has formed. This interview exposed the truth. They don’t and aren’t. Why do people think they do? Scientists may give that impression themselves (to generalize).

Though Origin of Life and evolution are two different phenomena, they are somewhat related since they evaluate DNA, RNA, proteins and other cell activity. If Dawkins were to be truthful, he could have just as well said that nobody knows how evolution works. There are teachers and media involved in transporting information to the public. They come right out and say that evolution is a fact. How can it be a fact when we don’t even know where life came from? How can it be a fact when we have not evaluated fully all the implications of all the new microbiological information that is coming out from experiments?

I remember reading in one of Dawkins' books that the numbers of galaxies and star systems are in the billions and trillions, and that’s good enough for him to cover the probability that life started by chance. That sounds pretty scientific, right?

The study of probabilities is a discipline that is complicated and I am no expert. However, some aspects of probability are not too hard to understand, and the chance occurrence of life can first be considered under “independent probability.” This means that each molecule of amino acid or DNA could randomly connect to another. We can at least start here.

Professor of Theology and Science William Dembski, in his book, The Design Inference (Cambridge University Press, 1998), has shown that the limit of the number events in this universe are at 10^150. This is a very important limit to know, because we can compare it with the number of tries it would take to get life.

To start with a simple example, the probability of getting 3 heads with 8 sets-of-3 coin throws is 1 in 8 (see image).  This example can be classified under independent probability because one coin toss does not affect another. You’d have to do the 3 coin-flips at a time for 8 times to get a good chance of 3 heads. The probability of 1 in 8 comes from 2^3 (2 cubed or 2 the third power—see exponent link on right for more info). The base is 2 because of 2 possible outcomes for every throw (heads or tails) and the exponent is 3 because the set of 3 throws at a time gives a certain number of total possible outcome combinations (8). You still might not get the 3 heads in 8 tries or you may get them twice. But as the numbers of times you throw a set-of-3 go up, you are likely to fall pretty close to the probabilities that the possible options give you. If you have enough time, eventually you are pretty sure to get 3 heads in a 3-coin-toss. If you only get one set-of-3 toss, though, you have a 7 in 8 chance you won't get 3 heads.

However, to change the example, if you flip one coin one hundred times and want one hundred heads in a row, you will have 1 chance in 2^100, which is about 1 in 10^30. That number is a 1 with 30 zeroes after it. To compare that number to another, the number of seconds so far in the universe if it is 14 billion years old is about 4.4 x 10^17. If you could toss a coin every second for your whole life of 70 years, it would amount to about 2.2 x 10^9 (2.2 billion) tosses. Your chances are very small of getting 100 heads in a row even if you toss all your life. Beyond that, you can wish to get a trillion (10^12) heads in a row, but you simply don't have the time to even toss that number of coins, much less get a specific outcome.

In past posts I have put lists of the sub-unit codes for DNA and proteins. Douglas Axe, a researcher in protein function, put the proportion of specific to general functional proteins between 1 in 10^63 to 1 in 10^77 (link to article abstract HERE). To get total probabilities in independent probability, you multiply each probability. (With exponents, you add the exponents keeping the base the same: you can see more HERE.) The smallest number of proteins of a living bacteria found so far is ~1100, and bacteria are the simplest free-living organisms. When you take in account the types of bonds of the amino acids and the specific positions they need to have in order to function and the DNA which codes for them, you can compare that to the number of particles in the universe, which is estimated at about 10^90. The chances are much smaller for functional proteins in one living bacteria compared to all the particles in the universe.

I talked in the previous entry (June 3) about the true meaning of the word RANDOM. Lee Strobel, a journalist who wrote a great investigative book called The Case for a Creator, (Zondervan, 2004) about the prevailing attitudes in public perceptions of “modern science,” science education and what is really true. He interviewed Stephen Meyer concerning probabilities that life may have started by chance (p. 228-30). Meyer commented that origin-of-life experts have rejected the possibility of chance. In other words, they must look for a law of nature other than the ones we already know that would somehow cause life to form if they are to prove life came about by RANDOM nature alone.

Cardinal Schonborn, Design

As I mentioned in the previous entry, the article by Christoph Cardinal Schönborn, "Finding Design in Nature," New York Times, July 7, 2005, pointed out differences between the idea that evolution has occurred  totally random and unguided and an “overwhelming evidence for design in biology.” He brings up Pope John Paul II’s teachings concerning the directionality of nature which leads to the conclusion that a Mind has created it. It is worth reading Cardinal Schönborn’s short article (link in the title above).

The letter created quite a stir after publication. It prompted the article by George Coyne which is discussed in my May 30 entry. Many Christians like Coyne feel that God created the world through the randomness of nature. They present to us the best of both worlds—we happily join the ranks of modern science while we wink knowingly that God did it. They defend the theory of evolution and some chastise those who think otherwise. Perhaps, like Coyne, they add some "fertility of the universe" ingredient which he declared to be scientific but is much less so than the design he denigrated.

Perhaps they are worried that if we say "God did it" and it is proven otherwise, we look ignorant to the rest of the world and deflate others in the hope there really is a God. They keep bringing up Newton, who said God adjusted planets' orbits, and then later came Laplace who proved the planets could orbit on their own by physical law. As I've written before, Newton is still considered one of the greatest scientists in history and not everyone stopped believing in God after Laplace. What's more, the new discoveries of the fine-tuning of the universe (see link on right to Anthropic Principle) have brought full circle our appreciation of God's handiwork in the heavens. So, new discoveries don't always answer all the questions--they can bring on more of them.

But in my opinion a major problem here is that the concept of randomness is misunderstood, or at least understood differently by different people. This is a pervasive problem and I have seen evidence of it throughout the ranks of scientists such as physicists and geneticists, much less philosophers and theologians. I concede it is a difficult problem to overcome because science is complicated and so is God. Who is to give the final word on what is true? Yet, undaunted, I would like to try to find common understanding so everyone can communicate and think as clearly as possible about the complex questions we face in biology and elsewhere. So, I use here the meaning of "random" as a term understood by laypersons as "happening by chance."

I will capitalize the word RANDOM and make bold some other words along the way for emphasis.

1. I am going to assume atoms and molecules do not have minds of their own as to what other atoms and molecules they attach to in chemical reactions. There are those who would not even agree to that, but I think most people do and that at least gives us a start.

2. Since atoms and molecules don't have minds of their own, they move and react with other atoms and molecules according to physical and chemical laws. They have energy, motion, and their reactions depend on and/or cause energy exchanges, but all these movements and combinations so far, I hope we agree, are RANDOM.

3. Our first wrench in the machine is quantum physics (don't give up here--you don't have to know quantum physics to read this). In quantum physics, subatomic particles act in a way we did not expect. Surprisingly they react differently when measured (observed). However, scientists have worked out new ways to understand and expect their movements. Even in quantum physics, particles act in certain ways that can be predicted to behave within certain limits. Their movements can be predicted and understood under physical laws. Quantum mechanics itself was discovered from principles of probability and is in part based on it. If particles consistently appear or react outside certain limits, we no longer have findings that agree with current physical laws. Even if we observe and measure particles, chemistry is still chemistry. Once subatomic particles reduce to the classical level of our world, they react under the chemical law of mass action.

Many refer to the mysteries of quantum physics and Heisenberg's Uncertainty Principle as their proof that there can be randomness in nature and yet non-randomness by God at the same time. But quantum physics does not change the overall randomness of atom and molecule movements and their reactions with each other. We are still dealing with RANDOM. If God intervenes at chemical (biological) levels to make certain atoms connect with others or certain specific molecules to react and stay bonded with others, the structure is NO LONGER RANDOM.

4. So, when we talk about DNA or proteins being in specific order, we can still talk about probabilities that atoms or molecules will connect in these specific orders. The subject of probability will be in my next entry.