Important Research

Many people seem swayed to believe in totally materialistic evolution for various reasons. But if you are going to be "scientific," you have to be willing to look at all the evidence. What many are missing are the huge differences in the species that greatly overwhelm the similarities.

It has been 30 years since a very significant scientific article about proteins was published by researchers. One of the scientists is Robert T. Sauer, Salvador E. Luria Professor of Biology at MIT. He has a BA from Amherst in biophysics and a PhD from Harvard. The paper and the findings are technical, but I will attempt to explain, so I hope you will try to read through. The paper is by JF Reidhaar-Olson and RT Sauer, "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor," Proteins, 7, 4 (1990): 306-16. From here I will refer to the article as RO&S, and the abstract can be found in the paper title link at the NCBI PubMed website. NCBI stands for National Center for Biotechnology Information.

The Lambda phage is a virus that infects bacteria, in this case E. coli., and it has a protein called repressor. I have included an image of repressor (purple) next to a DNA strand, from Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). More information on this protein is at RCSB PDB entry 3BDN.  Citation for RCSB PDB: Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne, "The Protein Data Bank," Nucleic Acids Research 28, 1 (Jan. 1, 2000): 235–242.

Proteins are made within the cell, the basic unit of biology, of every living organism. DNA codes for proteins, which do much of the work of the specific cells. The alpha helical regions to which the RO&S paper refer are among the particular parts of proteins that give them their function. The lambda repressor was the protein they were researching, although they used just part of the protein for the experiments. The substitutions in the title refer to the subunits of proteins, called amino acids. There are 20 kinds of these in most proteins and each is made of a certain set of atoms. The researchers wanted to see how many amino acids could be interchanged with the parts of the protein still remaining functional. They used an experimental method to make random substitutions in these subunits within the repressor protein. The amino acids are numbered and they used two sets: 8-23 and 75-83 (Using 1-92 amino acids of a 237 amino acid protein).

I will use the term "permutation" here, meaning the evaluation of proteins must include specific order of amino acids and their repetition, unlike "combination" which does not require a specific order. (I am saying here, though will elaborate in another post, protein probabilities are not evaluated like card games.) RO&S reveals that though there are a large number of subunit permutations which can make working protein folds similar to the particular one they studied, the proportion of functional ones of possible permutations are only about 1 in 10^63. 10^63 is the number 1 with 63 0's following it. (I like to use a caret ^ when writing what are called exponents because it is easier but (for example in this case) the number can be written 10⁶³ . The first or lower number is the base and the second or upper one is the exponent. The exponent tells you how many times to multiply the base times itself to get to the final number it describes.)  1 in 10^63 is a very, very small proportion of permutations that work. Relating to evolution, the less proportion of functional choices there are, the less the probability you will get one to form by chance. There has to be something to choose from (coming from mutations) in order to get any selection!

The authors of the RO&S paper claim the gist of this research was supposed to show the admittedly large number of possibilities for the amino acid subunit combinations to make protein folds (the term “degeneracy” they speak about in abstract). However, the paper showed something way more significant, the proportion of non-functional to functional as already described. To give the researchers credit, they do talk about the limitations of content of proteins in the abstract, but not the specific findings. A reader has to follow the paper to the second last paragraph of the article to find it, and the paper is behind a paywall!

If you are at all interested in reading the whole RO&S article, the abstract page from my link has a link you can follow to get access to the paper. But it is through Readcube and there is a charge and as far as I know you can't get it free online. If anyone knows it is available online, please let me know. However, I got my copy of the entire paper through inter-library loan for free a few years ago. Inter-library loan is still available, although I don’t know if it always provides the whole paper. Or, you may live close to a University which allows access to their journals. I was able to read several other articles in this way. Fortunately, there are some research articles which are available online in complete form, and I have an important one here with a link (Fredric P. Nelson) which I discuss below.

Another significant fact about the RO&S research was that, although they used different methods than some theoretical work done earlier by Hubert Yockey who applied Information Theory, their work closely backed his. Yockey's research was done in the 1970s and gave indications then that proteins are very rare. I have a previous post about this work. He used a protein involved in respiration, Cytochrome C, and compared it in different species. An image of it is included here from Uniprot entry P99999. Citation for Uniprot is Uniprot Consortium, "UniProt: a worldwide hub of protein knowledge," Nucleic Acids Research 47, D1 (Jan. 8, 2019): D506-D515.

A link is here to the abstract of the paper by Hubert P. Yockey, "A calculation of the probability of spontaneous biogenesis by information theory," Journal of Theoretical Biology 67, 3 (August 7, 1977): 377-398. He included a few more chemical factors and estimated a chance in the range of 1 in 10^65 for nature to select a Cytochrome C sequence randomly.

Then other experiments were done and numbers proved to be again similar. An important scientist has researched at University of Cambridge. The Abstract in one of his papers is from Douglas Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology 341, 5 (Aug 27, 2004): 1295-1315. It shows a 1 in 10^64 proportion for a low-function domain and 1 in 10^77 for overall short protein function. Perhaps a general number of 1 in 10^70 could be used for simple proteins, but many are much more complex and therefore would be even more rare. The numbers compare to 10^65 atoms in our galaxy to 1^90 particles in the universe.

The Darwinian claim is to take the fact that DNA randomly mutates (or changes) as time goes by and conclude that the resulting proteins, which are a little different from previous ones, will lead to new species. The fittest, or best, of these changes in particular individuals allows them to survive and leads to fitter organisms.  Evolutionists say the 4 billion years of the Earth's habitable environment allowed for enough changes for humans to emerge. But organisms change only a little at a time. Bacteria do not even have one change per generation.

There may be some small, natural neo-Darwinian evolution in life, but there are other considerations. We must include large differences between some proteins as well as small ones. Some resemble each other and are functional and may have come from random mutations of DNA down the generations. Maybe even a protein that is slightly broken from a mutation may stop an antibiotic from binding to a bacteria's wall thereby making it resistant to the antibiotic. But there are many critically necessary proteins that are not even close to others in terms of their subunit arrangements and could never have evolved one from another, in a Darwinian sense, even in four billion years.

Fredric P. Nelson calculated the maximum number of organisms that could have existed on the Earth by water volume in 4 billion years at about 10^50. You would not have enough organisms in 4 billion years to try for proteins that are only available at the rate of 1 in 10^70. Fortunately, this whole paper is available online. Page 31 and the footnotes are especially interesting since his calculations are there. The link is here for Fredric P. Nelson, “Needed: A New Vocabulary for Understanding Evolution,”  Perspectives on Science and Christian Faith 58, 1 (March 2006): 28-36.

We need to look at a few more discoveries. As scientists discover the DNA (and thereby protein) codes of more and more species, they are finding a certain percentage of each, around 10% to 30%, are not related to any other species. These as a group are known, among other names, as orphan, or ORFan genes (a gene being defined as a protein-coding part of the DNA chain). Among the many scientific papers that have been reporting this finding is by Arendsee, Li, and Wurtele, "Coming of age: orphan genes in plants," Trends in Plant Science 19, 11 (Nov. 2014): 698-708. This finding is related to the limit of numbers of organisms that have been available to mutate for "tries" for functional proteins just mentioned.

Concerning life's origin, a minimal, natural free-living organism (not a lab creature which is given nutrients) has been estimated to need around 1000 proteins to survive by NCBI researchers Koonin and Wolf, "Geneomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 2008): 6688-6719. Even if some were closely related, the independent probability of only 10%, or 100, functional proteins is about 1 in 10^7,000. 

Pertaining to both origin and evolution, N. Tokuriki and D. Tawfik researched protein stability in terms of thermodynamics and kinetics. They found only a few substitutions could be tolerated before the proteins became severely impeded in their function. Though there can be compensation, this severely limits any ease of evolution. The article is N. Tokuriki and D. Tawfik, "Stability effects of mutations and protein evolvability," Current Opinion in Structural Biology 19, 5 (Oct. 2009): 596-604.

So no, these numbers are not wiped away by the Darwinian duo of random mutation and selection of the fittest. We must keep in mind that for evolution,  the first step, random mutation, must happen first inside the organisms in their reproductive cells in order to form any new proteins that could be selected. This vast improbability of functional proteins overwhelms even the number of organisms that existed on Earth. No mutation rate could bring about new proteins on a viable level.

Also, I don't believe quantum physics either explains or explains away proteins. QP is real and admittedly very strange, but chemistry is also real and is described by its own physical rules. If that were not true, we'd all be constantly slipping in and out of reality (granted, some think this is exactly what happens).

The rarity of functional protein folds is one of the features that convinced a well-known Yale computer expert and professor to recently exclaim Darwin’s theory proven false. His essay is David Gelernter, "Giving up Darwin," Claremont Review of Books, XIX, 2 (Spring 2019): 104-109.

There are admittedly many, many things to learn about proteins and DNA. That is important for creationists to keep in mind. However, for scientists to insist on totally naturalistic evolution by random chance, they deny what is true once again. In Darwin's day, they said the cells were blobs which had little to no internal activity. Then scientists denied DNA and proteins were rare due to specificity, which is proving to be wrong. They claimed DNA was filled with junk which is now being revealed as useful. All their false concepts delay scientific progress, yet they claim the creationists are the ones who are detrimental to it. Thankfully there are individuals who do not stop investigating when the consensus resists change. 

One book about Catholics and evolution is by Fr. Michael Chaberek, OP, Aquinas and Evolution (Chartwell Press, 2007). Chaberek asserts that at the end of the nineteenth century, "Thomists universally rejected the Darwinian theory of origins" (p. 10). He lays out his thesis that Aquinas was not an evolutionist and today's science would not change his mind. In the Forward to the book, Logan Gage, PhD, Chair of the Philosophy Dept. at Franciscan University of Steubenville, writes, "Culturally it has been easy to dismiss worries about Darwinian evolution as a 'fundamentalists' Protestant problem. Additionally, we Catholics have a 'Galileo Complex.'"

Some Christians insist that God would only create life in a certain materialistic way. I remind everyone that God does as He sees fit, and many Christians look at the living wonders of the world and think God made at least some of them in original species through Special Creation. New scientific discoveries are actually supporting our view.

For us, science is the study of created physical things. We need to show the world it is not only reasonable to be a believer, it adds the vital meaning to our lives. Let us praise the Lord, through Jesus Christ, for His Creation.

Creation Biology

It is another First Friday and I am posting this time about Creation Biology, my new booklet. It is now available from this post's link in the name and from the picture in the right column of womanatwell. I have put it on the blog for the primary reason that I’d like all persons to be able to understand the controversy over evolution.

To some degree the booklet is a work in progress. I’ve re-done it already and will probably continue to edit it if I think of ways to explain the facts better. It also has direct links to references.

I do not think the media or most science "popularizers" give the whole story about evolution. Therefore many people are arguing from stances that are not fully informed. There are strong feelings each way about evolution. Did species evolve in a totally natural way or did God create different types directly and supernaturally (called Special Creation)? Did God partially direct biological diversity in a supernatural way? Or did He move in a way we humans understand as random?

A person may wonder if it really matters how we came to be. I think if you consider the facts and see how unlikely it is that we came about by chance, it will bring a new appreciation of God's creative power. And yes, the Darwinian Theory is based on chance—the part about Natural Selection does not change that. First you need working parts before any selection can be made. That is one of the things I explain in Creation Biology.

Ever since the Church’s early 17th century experience with Galileo, through whom the worldview of Earth-centered changed to Sun-centered, people have been wary of religious explanations for physical matters. But the Big Bang Theory was introduced in the 1930's by a Belgian Priest, Georges Lemaître, when Albert Einstein backed the eternal universe view.

Some things don’t change, such as the Christian doctrine of the redemptive death and resurrection of Jesus Christ. But other ideas we have may not hold up to closer scrutiny. A worldview we may consider unshakable actually can fall under the weight of new discoveries. We must all be willing to continue to learn, because science changes and study is a life-long pursuit. And to see the continuing discoveries of cell complexity brings the sacredness of life into fuller focus than we may have previously contemplated.

I hope you will take a little time from your busy life to read the Creation Biology booklet, which can be downloaded from the page.

For this emotion-charged subject, you need to see for yourself if you really know what others are talking about. Then like a juror, you can judge for yourself what rings true.

Total-Natural Evolution

I have written much about the vast improbabilities of whether DNA and proteins could have formed for the origin of life and changed in a functional way for the diversity we observe. There are other major scientific developments that relate to the Darwinian Theory of Evolution that go beyond these probabilities. I won’t go into a lot of detail, but will try to give a clear summary and have some references to read if you are interested. Then I want to mention a new group of scientists who have rejected the current Darwinian Theory of Evolution  (also known with a few variations such as neo-Darwinism), and who have collectively put up a new website called The Third Way. I'll conclude by addressing the title of this blog post: Total-Natural Evolution.

Protein stability and Epistasis:

Proteins work through their physical makeup of their sub-parts, called amino acids. These have various shapes and charges, and with the help of other proteins, chains of amino acids often fold into a larger, specific shape for the over-all protein.  The chains may fit together with other proteins to do the specific job. So the total protein machine may have thousands of amino acids.

Darwinian evolution theory depends on chance changes to genes that code for these amino acids, and therefore to chance changes of amino acids. At first, scientists did not know how many changes in amino acids would affect the ability for these proteins to fold and work as they should. Many believed the proteins could run through all kinds of differences in order to find new functions. But in the last few years, experiments have shown that it takes only a few of these changes to ruin the internal energy balance needed for the protein to fold properly. It might tolerate 2 or 3 changes, but after that, the internal stability usually plummets dramatically. It not only can't find new functions, it can't do its own work. I refer to a research paper by Tokuriki and Tawfik, "Stability effects of mutations and protein evolvability," Current Opinion in Structural Biology 19, 5 (Oct. 2009): 596-604.

In further work on this issue, researchers compared organisms. The scientists found that if they had changes of amino acids that experimentally ruined a protein, the changes could be found in various organisms, but were “compensated” by other specific amino acid changes that balanced the internal energy (and therefore stability) of the protein. However, this was not good evolutionary news after all. They believe these compensations kept the “bad” amino acid change from reverting back to the original, which turns out to have better function, and therefore evolution is limited.

These findings were for studies on one protein at a time, but other researchers have realized that there is a diminishing return on most cumulative protein changes. The term used is “epistasis” and often two or more newly changed proteins will not work together as well as the original ones, or a second change will not be as effective after the first change. These results have implications for protein function in various species, in that the changes do not allow transfer of function from one species to another. You can read an abstract of the research by Breen et al., "Epistasis as the primary factor in molecular evolution," Nature 490 (Oct. 14, 2012): 535-538. "Don't let the word "evolution" fool you because this is about lack of it.

Proteome discoveries:

“Extensive Cataloging of Human Proteins Uncovers 193 Never Known to Exist,” Johns Hopkins Medicine News Archive, May 28, 2014, reported that researchers have found almost 200 new human proteins. Because of the circumstances, the scientists expect many more new proteins to be found. That is because they were found in areas that were not normally considered “protein-coding” regions. A professor at Johns Hopkins, Akhilesh Pandey, stated, “the human proteome is so extensive and complex that researchers’ catalog of it will never be fully complete, but this work provides a solid foundation that others can reliably build upon.” Kind of boggles the imagination.

The research paper is Min-Sik Kim, et al., "A draft map of the human proteome," Nature 509 (May 28, 2014): 575-581. Though on the Internet you have to pay for the article, I’ve requested it through inter-library loan.

The Third Way:

There is now a website, The Third Way, in which a group of scientists is openly claiming that the currently held Darwinian Theory of Evolution is no longer to be considered true. Here are the introductory words:

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations. 

I don’t know how the findings about Creationism are inconsistent with empirical evidence, since God is able to do all things. But that discussion is perhaps for another time. The point here is that they are claiming Charles Darwin’s Theory of Evolution is false. In scientific terms, it is falsified.

James Shapiro, the first scientist listed on The Third Way website under “People,” is a prominent microbiologist teaching at the University of Chicago. He has been telling folks that Darwin is dead for over a decade. Shapiro proposes the Third Way in a theory called “Natural Genetic Engineering.” The only problem is, he is still trying to make a case in another way for totally naturalistic causes. 

Also claiming that Darwin's theory is wrong is Eugene Koonin, listed further down the People page. He is the Senior Investigator and the leader of the Evolutionary Genomics Group in the Computational Biology Branch of the National Center for Biotechnology Information (NCBI). This is the headquarters for comparative genomics, the field now possible through the whole gene sequencing of living organisms since 1995. As their data grows, they can see that these genes do not take the routes predicted by Darwinian evolution, and Koonin has clearly written about it. In the linked 2008 article he says the "Tree of Life" concept is undermined and a new conceptual framework needed. Yet he has been summarily ignored by the press and so-called science promoters and even “real” scientists.

If you read the papers and books listed on The Third Way website, you'll find these scientists loud and clearly tell the reasons why Darwinian Theory is not a fact.  At The Third Way website under People, click on the individual scientists' names. You will see statements such as that from Denis Noble, another prominent biologist:

.... all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved. Moreover, they have been disproved in ways that raise the tantalizing prospect of a totally new synthesis...

Unfortunately, these biologists still do not see the forest for the trees. They look at the reams of biological knowledge and still want to pack it all in physical laws. From what we know of physical laws at this time, there is no positive proof these laws can act as sources of biological complexity.

Since it is becoming apparent that single amino acid changes are not possibly able to form the mechanisms for life, the underlying assumption for those like Shapiro is that segments of DNA that form domains are able to "mix and match" in order to form new proteins. There are elements in DNA that were experimentally found to be able to "jump" from one place to another. However, human DNA has 3.2 billion base pairs. How are the bases that form the proteins supposed to "know" where to fit in with the other DNA to make a new protein? There could have been only 10^50 organisms to play out the various combinations even in an old Earth. If DNA skips around substituting various groups of bases, it may still miss the ones that are functional. In a small example, if AAAGGGTTTCCC becomes AAACCCTTTCCC, you may instead need AAAATTTTCCCC for a specific new function. Though many proteins may use similar domains, there are many that are very different from each other. Douglas Axe reports that various species of just one small organism (E. coli) have been found to each have almost 1000 different domain structures (page 11 of the link). In the meantime, as described above, the new proteins can only tolerate a few changes to amino acids before they become completely worthless. You have all these molecules doing jobs and having to be arranged the right way so the right DNA can be copied at the right time. And yet we are supposed to believe that all these segments of DNA can be easily substituted so new proteins can form?

I nickname this type of biological theory "Total-Natural," which describes a totally materialistic basis for biological science in contrast to begin able to consider the Supernatural as a possible, or partial, cause. The concept of "total-natural evolution" is the worldview that totally naturalistic forces led to the origin and entire diversity of life. Total-natural is really the bottom line of the argument between materialists and Creationists. It's more to the point than the often-used "macro-" and "micro-" evolution arguments. Evolutionists say that macro-evolution is just the cumulative effect of micro-evolution. If there are at least some influences of the supernatural in the origin and diversity of life, our presence here is not explained in total-natural terms. There could be both supernatural and natural influences on diversity, but even differences in species are showing that many of the unique features are coded by orphan genes which are not related to others: Khalturin, et al., "More than just orphans: are taxonomically restricted genes important in evolution?" Trends in Genetics, 9 (Sept. 25, 2009): 404-413. And genes themselves are not the whole answer to development, as you will also find. Life has supernatural undertones.

If you have believed Charles Darwin’s Theory and are desperate to have the worldview of a total-natural origin and diversity of life, the best you have, as Denis Noble says, is a “tantalizing prospect.” I would ask you to reassess why you are so against the supernatural (or for theistic evolutionists, against direct supernatural Creation). It is wonderful to be able to believe in God and to increasingly appreciate His creative powers. Please don’t let anything, anyone, or any theory stop you from reaching the truth.

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.

Science and Culture

I will get to the title theme of this post soon, but I'd like to make some personal notes first. I don't know if you are new to my blog, but there has been a bit of a change. I had a book and several booklets in PDF form in the right column, but have taken them off. I have to admit that it was by accident. I wanted to erase an old reference paper I had on Google Docs, but somehow I erased them all. (2019 Update: I added these files again along with a few new ones which are free to read.)

Despite all this, it’s been good to write semi-regularly on my blog once again. I’ve been told my writing is didactic, basically meaning preachy. I know I can be heavy-handed and when I work on my mystery books, I try to keep the story moving and interesting in order to keep it easier to read. I still think a message is important, but I know people can be turned off if it comes across too strongly.

I was contemplating this when I wrote some of my recent posts. I was getting rather wound up about the problems of the world, and I stopped to consider the tone I should take. I'm still going through some thought processes about this. As my husband said, many blogs are didactic. Sometimes preaching is necessary, and I hope you will take my sincerity into account. On the other hand, I'd like to be clear and inviting. Such, I guess, is the challenge of writing. (And I sometimes go in and edit a post, as I have done with this one.)

I write about various things, and sometimes I take breaks from the blog. If you look at past posts, you will see I have written a great deal about Intelligent Design Theory (ID). To clarify, I have moved on from ID to what I call "Special Creationism," which still has to do with complexity and design in biology as ID does.  However, ID still emphasizes evolution, and Special Creation accepts that God may have made various species directly from scratch. In my posts, I come back again and again to the question of Darwinism and the conclusion that totally materialistic evolution is impossible. It may not seem to you the most fascinating of topics to consider in today’s world. But you might find upon reflection it very much relates to our country’s culture and mindset.

Today’s scientists as a group have great influence on people. They have persuaded government lawmakers concerning various issues. It might seem logical to think that’s the way it should be, since science scholars are intelligent and have a lot of education. Yet a very vocal group has unfortunately not only boasted of their own lack of religion but loudly disdain other persons’ beliefs. They have changed the culture in various ways, including the enforced teaching of evolution in public schools and use of human embryos for research.

I can’t totally generalize, because some scientists are religious. A 2009 survey of scientists showed at least half have some sense of spirituality, reported by David Masci, "Scientists and Belief," Pew Research Center (Nov. 5, 2009). It is interesting that the religious leanings of scientists have remained very close to what they were about 100 years ago. Scientists on the whole, however, are less religious than the rest of the population.

Atheistic scientists may have knowledge of facts, but instead of praying for God's wisdom, they settle for human knowledge alone. One can read in the Bible about what God can do with man’s wisdom:

For it is written:

“I will destroy the wisdom of the wise,

and the learning of the learned I will set aside.”

(1 Corinthians 1:19 NABRE)

In this Bible chapter, Paul talks about teaching the “message of the cross” (verse 18). Though that may seem foolish to some, it saves us from perishing in the end.

It is very frustrating to see the prejudice against believers, and for a while I was angry about what some scientists say. But then I realized that there are some over-publicized spokespersons and not all scientists are like them. Unfortunately, the loud ones are saying that church and state must be separated in our country and are powerful enough to so far get their way. Adding to that problem is a conflict between what many of us believe and what is being taught to the public, both in schools and in the media.

Our culture is also tremendously impacted. The prevailing mindset of Darwin's theory is "survival of the fittest" instead of the religious theme of "Do unto others as you would have them do unto you." World views must affect the behavior of children, at least sub-consciously. Though adults may rationalize a motive for group unselfishness, I doubt that all adolescents desire to think that through.

Though I understand that some people are concerned that we teach the most up-to-date science, the irony is that the evolutionists are keeping our kids from learning just that. They keep the numbers of probability of functional proteins from the media, and the new facts of DNA and other complexities of the cell have not been proclaimed widely. So, of those who do believe Darwinian spokespersons, many of them have not been taught all the facts. That is where we need to come in and teach both children and adults what really is happening with new scientific research. When they learn about the fabulous world of biology, they can evaluate for themselves where it comes from. I have already written much about life processes in my blog. As time goes by, more and better animations and scientific data are available. As I explore the Internet, I am pleased to find people are learning about cell biology already, judging from the number of hits some of the animations are getting. They show ever more of the complexity of the cell, the basic unit of biology.

None of us know everything. It seems natural for us to see things with a certain mindset. We evaluate facts from the point of view either of entirely materialistic mechanisms, or from the faith that a Creator had the genius to put life together and get it to work. Believers appreciate the creativity of biology and can go from there to learn more. I pray that non-believers will come to see the Lord's wisdom.

Faith First

This past week a certain cartoon mentioned evolution and how it is supposedly the basis of all understanding of biology. The cartoonist is wrong. One of the foundations of biology is the biological cell and we find more of how its amazing structure works every day. It is truly irreducibly complex, as the people who promote Intelligent Design Theory say. Another, more important, foundation for biology is that God created it.

The cartoon is part of the cultural world at work. A prevailing cultural idea is that science rules. Or in a variation of the preceding, science gurus say if you must have faith at all, it should be separate from scientific inquiry. I'm becoming more and more confirmed in my belief that faith comes before science.

Persons who espouse Intelligent Design Theory (ID) say that religion has nothing to do with their work. They look only at the science, and design can be determined in a scientific way. This may be true, but there is a philosophical problem at the core. If certain (many) scientists refuse to allow the possibility that some things such as the biological cell may have been created supernaturally, the scientists will never give up looking for a totally material cause. Then the ID people have no chance of sharing their ideas in the scientific community. This, in fact, is what is happening and ID people seem to be unaware that their position of leaving religion out leads to just as much frustration as it would be to state their faith.

Another problem is that "intelligence" is itself not understood. Scientists want to reduce consciousness to the material brain, but it doesn't work. There is a thing known as "qualia," the state of consciousness that scientists can't deny if they are honest with themselves. The Stanford Encyclopedia of Philosophy defines qualia HERE. But how can ID proponents base their scientific theory on something that is itself not understood in scientific terms?

The ID people say that "anyone" or "anything" could have designed life. They do this to emphasize that science alone can prove that random movements of chemicals will not form into the complex systems that form the biological cell. They also are accused of saying this to try to sneak Creation into the classroom. This is another subject and I've already talked about it, so I won't belabor it much more in my blog. But if we believe God created, then we have the right to believe inside the classroom as well as outside it. I grieve for the wrongs done to the ideals of freedom of religion in this country and for the citizens who suffer because of it.

If you have the faith that God did it, that "anyone" who designed is not just "anyone." It's better to just come out and state your faith. Not all ID people are Christian, and some even think the cell may have been made by aliens. But for Christians, we believe in God the Father almighty, maker of heaven and Earth, of all things seen and unseen. At least those who call themselves Creationists are willing to state their creeds.

That's why faith is first. Many if not most people who don't believe in God will not even give the benefit of the possibility that life was formed by anything but totally material, random means. I give credit to ID people in that their biological analysis of the cell is very good, and some people actually eventually see the logic and realize that neo-Darwinistic (totally materialistic and random) evolution is a very poor substitute. But for the rest that refuse to see, there is a gap that won't be bridged by science alone. They will always be looking for the material explanation, and they will always be either disappointed or kidding themselves. For Christians, why not say where they believe life comes from? Then the others may finally come to the real Truth.

Random Cont.

The fact that atoms and molecules make random movements in gas and liquid affects how they interact. There is a theory called "Collision Theory" (Wikipedia entry HERE) which describes the interaction of molecules to form various substances. It is not hard to visualize, as shown in the picture. The random movements are accounted for in the calculations, related to the Maxwell-Boltzmann statistics as discussed in the previous post. It's not necessary to know all the mathematics to understand that atom and molecule interaction is random in nature. And, as the caption of the picture notes, the concentrations of the atoms can affect how much they interact. A higher temperature can affect the movements so that more particles collide when they are hotter, but higher temperature does not give more order to the movements. The properties of the atoms and molecules can affect how they interact, but as we proceed we can see how we can narrow down our focus so that we can eliminate some of the factors which would make it impossible to figure.

For example, the pre-life ocean and atmosphere may have changed from their compositions at the very start of things to what they are now. We may never know what the beginning concentrations of various atoms and molecules were. This limits our knowledge in certain ways. We don't know how many carbon atoms were available to interact with hydrogen atoms. But there are ways to theorize about these things, and many scientists for years have been trying to figure out how molecules could form into life.

Just recently a new paper came out saying that it doesn't look good for pre-life replication and biological-type behavior of atoms and molecules. This is what I've been saying--that chemistry rules at this level, while biologists were trying to impose biological laws on chemistry. They are not the same. The new research is Vasas et al., "Lack of evolvability in self-sustaining autocatalytic networks contraints metabolism-first scenarios for the origin of life," PNAS 107, 4 (Jan. 26, 2010): 1470-1475.

The randomness we are talking about is what we usually mean with the term "chance." We are talking about nature and not the supernatural. Now there are laws that govern the planets, such as gravity, but gravity is not going to make atoms form into proteins. Atoms of different elements have different chemical properties, such as charges and types of bonds between them. I will get into that more next time.

And, we can still apply probabilities in some cases. We know what the cell has now, so we can look at what needed to take place to get us to the present composition. No one has a realistic scenario of how that could have taken place.

Learn from Mistakes

Recently I wrote about Fr. Robert Spitzer, a priest and physicist who is trying to bring science and religion together. He was in a conference at the John Paul II Center for the New Evangelization in Denver, CO, reported by the Catholic News Agency HERE. The point in my previous post was that not everyone believes in God even though they know the science.

But, Fr. Spitzer makes a different point which is just as important. Not everyone knows the science. One should at least have the chance to make up one's own mind about whether DNA, proteins, the cell, and life itself could have come about by chance, and that is not happening. Amazingly in this day and age, science is being censored.

I had a very nice presentation last week about Intelligent Design Theory to about 50 persons. These people heard privileged information. They heard the numbers for the improbabilities of the origins of life. They heard what high school and even college students don't. And even Christian college students don't hear the facts though they point to God!

These students will have to seek out their own facts. And they can find them. The internet will have them. There are books (also censored!) that have them. The latest, bound to be great book about them is by Stephen Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (HarperCollins Publishers, 2009). The book is very readable for anyone who has the desire and patience to try to learn.

Many Christians in the scientific community do not seem to want to admit that God may have created life directly. They are embarrassed by the history of the Galileo affair, where the Church denied for centuries the centrality of the Sun in our Solar System. They forget that the ancient scientific community put the Earth in the center just as well as the Church. The Church reacted against this scientific novelty as well as their own ideas of doctrine.

The Church, which includes all Christians, must learn from mistakes, to not inhibit learning. To stifle facts is to deny that reason and faith go hand in hand.

Proof of God

I've been writing about the progress of science and how it has replaced some of the ideas of the ancient philosophers. Yet the Church believes God is accessible to humans through reason. That is still true, but I think science is changing the details of how He is found through reason. Aristotle thought the universe was eternal. Now there is evidence of a Big Bang, which means there was a beginning to the universe. Aristotle promoted the idea of "spontaneous generation," in which living things continually arise from non-living. Biologist Louis Pasteur in the 1800's proved that life now comes only from other life (Wikipedia biography HERE).

Our new findings of cell complexity and specificity point to a Creator. Anyone who knows the details of the cell and the vast numbers involved in the improbability that it would form by chance should surely recognize that only an intelligence could make such a thing.

A recent article about Fr. Robert Spitzer, "New astrophysical discoveries leave little to no room for Atheism," Catholic News Agency, Sept. 30, 2009, reports on a conference at the John Paul II Center for the New Evangelization in Denver, CO.  Fr. Spitzer brings the latest in cosmology to religious people to show how science and theology can fit together. He speaks about the amazing fine-tuning of the universe, and how in many ways it may not have formed the way it has.

Yet, at the bottom of the CNA article about Fr. Spitzer are comments which various persons have left, and they show that these commenters do not accept what Fr. Spitzer is saying. They give alternate theories which include infinite universes, so that ours is nothing special. They mock the priest's reasoning. (2019 Update: the article is still accessible but the comments are no longer there.)

This mindset is common in our day and is very telling. The point I have been trying to make in the last few posts is that proof of God in scientific terms does not get to the very bottom of belief. The Apostle Paul wrote of the problems even in his day,

20 Ever since the creation of the world, his invisible attributes of eternal power and divinity have been able to be understood and perceived in what he has made. As a result, they have no excuse;
21 for although they knew God they did not accord him glory as God or give him thanks. Instead, they became vain in their reasoning, and their senseless minds were darkened.

Romans 1 (NABRE).

The people to whom Paul refers made false idols from wood and stone and worshiped them. In our day the falsehood is in a mindset that puts materialism as the base of being and scientific research as the only answer to life's questions. Yet Paul's words are as true today as they were then when it comes to the rejection of God by some people. It is interesting that Paul states in verse 21, "although they knew Him." We may think that disbelief comes from not knowing, but Paul does not think so. There is something else going on, and the word "vain" describes their reasoning. Eventually, their minds were darkened, and things went downhill from there.

As I said in a previous post, faith is a gift from God. It is a precious gift, and I believe He gives Christians important roles in the process of bringing more persons to Himself. Some people have come to faith by perceiving the wonders of nature, and that is fine. But I don't think the wonders of nature are going to convince everyone. In that case, Christians can pray for unbelievers and share what Christ has done for us in our lives and our hearts. God has many facets, and we should try to learn more about them ourselves as we help others understand.

Classical Greek

The Greeks are considered the fountain of Western thought. They believed, even before Socrates, that all things were composed of Four Elements: Air, Water, Fire and Earth. Aristotle added a fifth essence called Aether (pronounced ether), which he thought made up the heavenly realms. Actually, the Eastern philosophers came up with systems not so different from this and can be compared (Wikipedia HERE, right column).

As early as the Middle Ages people started experimenting with various substances. Around the year 800, a Middle Eastern alchemist known as Geber (Latinized version of Jabir, Wikipedia HERE) discovered the separate elements of sulfur and mercury. In 1869, Dmitri Mendeleev presented a table of known elements which showed they have certain repeating properties. This "Periodic Table" is still used to classify elements. It starts with Hydrogen, which has one proton and one electron, and as of June 2009 includes 117 elements. Other elements include carbon, nitrogen and oxygen.

Therefore, we have a replacement of Aristotle's elements with those we know today through scientific research. I've also read that Aristotle believed one could discover science through logic, not experiment. The example I read a long time ago was that he proclaimed how many teeth a horse has without looking into the horse's mouth. Later someone actually counted them and found Aristotle was wrong. I don't have a reference for this story and it may be a fable, but it does illustrate the general idea.

Though Aristotle knew about magnetism, Hans Christian Orsted in 1820 realized magnetism could be generated by an electrical charge flowing through wire. This eventually led, through others, to the understanding of electromagnetic radiation. This energy is one of the basic forces of the universe, along with gravity and the strong and weak nuclear forces. The understanding of natural physical forces has replaced, in the opinion of many, the understanding of causes as Aristotle described it in his theory of Universals. (A universal is a quality which exists in itself that is seen in physical things, for example, "red-ness" of red things and "human-ness" of humans.) Aristotle said there were "Potentials" of existence which a First Mover would have had to put in motion in order to get something to exist in matter and form.

There is an interesting entry on "Theodicy" HERE on the New Advent website in their 1917 Catholic Encyclopedia. This older version of the encyclopedia can be helpful in historical matters and general definitions. Theodicy is the attempt to prove God through natural means. You may like to read the information on it at the link above.

Can Man Understand?

Can the human being really understand God? The verses from the Bible that come to mind are from Isaiah 55 (NABRE):

8 For my thoughts are not your thoughts, nor are your ways my ways, says the LORD.
9 As high as the heavens are above the earth, so high are my ways above your ways and my thoughts above your thoughts.

This is not to say we shouldn't try to understand God in some way. It is not right to shrug our shoulders and say that if we can't know Him we might as well move on to some other interest (science, for example). We have to juggle a little, and not let a concept either dominate us or be immediately rejected. Pope John Paul II wrote a very interesting encyclical called Fides et Ratio. He describes the interaction between faith and reason, and it is worth reading.

I've been reading Church history about the reaction of the magisterium concerning evolutionary theory. Though I started in Darwin's time, the relation of science and philosophy to Christianity actually goes much further back and I'm becoming increasingly aware of its relevance to my interests. So I'll just give a very general overview here.

When philosophy began in the West, some 600 years before Christ, it was an attempt to understand things in terms of reason, not mysticism or mythology. It therefore included the study of nature which we now consider science. The first Greek philosopher was Thales of Miletus (Wikipedia biography HERE) who lived around 600 BC. The famous Greek philosophers followed in this order: Socrates, Plato, and Aristotle, who died in 322 BC. Aristotle worked out a "Natural Philosophy" in which the natural world was defined in terms of movement (in rather complicated interactions of place and time) .

Greek philosophy became known to scholars throughout the ancient world. It did not take very long after Christianity spread for someone to try to combine the understanding of Christ with this Greek thought. Frederick Copleston, in A History of Philosophy, Vol. 2, lists Maricanus Aristides (Wikipedia HERE) as one of the first to do so in about 140 AD. Then came Justin Martyr who used philosophy even more openly, and Clement of Alexandria, a scholar who lived in Alexandria, Egypt between 150 and 215 AD. He headed a school for teaching Christian theologians known as the Catechetical School of Alexandria. Pope John Paul considered St. Augustine, who elaborated on Plato's philosophy about 400 AD, to be the first to truly produce the "first great synthesis of philosophy and theology" (Fides et Ratio, Sec. 40).

St. Thomas Aquinas (Stanford Encyclopedia of Philosophy HERE) combined Aristotle with Christian understanding in the 13th Century. Others disagreed with their speculations, and there has been wrangling throughout history on the importance of reason in contrast with faith. In particular, a monk named William of Ockham (Wikipedia HERE) placed more emphasis on faith than intellect in order to know God (as I understand it). Ockham, though, seems these days to have the reputation of cutting away faith altogether in favor of science, in which case he is misunderstood. He was concerned that Aquinas, in his effort to incorporate what Aristotle called Universals, limited the free will of God. (Universals were supposedly essences of things which existed outside physical things, such as "red-ness" for all things that look red.) If God could only create according to Universals, Ockham felt He would be limited in choice.

Well, philosophers and theologians have wrangled for centuries about God and our relationship to Him and how we understand Him. Of course, with the scientific revolution, people have wondered more and more if we could "cut away" God altogether and be left with nothing but the material world. Many indeed have done just that in their personal worldviews. But now biology is showing that some things cannot be explained by the laws of physics and chemistry, at least as we know them now.

Many think that physics and chemistry will never be able to explain the codes of DNA, and how the DNA is arranged in ways that resemble the computer systems created by human intelligence. Many, however, believe scientific research will eventually be able to explain everything.

This, in a very condensed version, is where we stand now.

Cultural Intelligentsia

On this past Weekend Edition at NPR, I was listening to Scott Simon interviewing a Jesuit author, James Martin, S.J. Martin is the culture editor at America magazine and has written about humor as it relates to religious persons. I won't go into a lot of detail of the conversation (the transcript of the interview is HERE). However, at one point Martin and Simon were discussing prejudice against Catholics, and Simon used the term, "popular intelligencia culture" to describe the mindset of the people who feel free to make derogatory statements against Catholics. (Wikipedia spells it Intelligentsia and defines it HERE. The term signifies the social group of intellectuals and those related, such as teachers.)

In another website, Evolution News and Views, Michael Egnor describes the people at the New York Times who fired Ben Stein because of his support of Intelligent Design and others like them. He uses the term "scientific materialism" to demonstrate the idea of the modern understanding of reason. Persons who hold this especially claim that science has replaced religion and to believe in God is to be ignorant. And they make no effort to respect any other point of view.

I am interested in these terms, because I think they describe a whole group with a certain mode of thinking. Perhaps their concepts can be further developed, but I think the idea is clear enough.

Now, what does that have to do with Francis Bacon, who is pictured here (Wikipedia biography HERE)? He lived in England from 1561-1626 and was the scientist and philosopher who introduced the modern scientific methodology. However, his own method of induction and experimentation for science should not be interpreted as making God obsolete. It is very interesting to note that Bacon himself believed in God. From Wikipedia "Works by Francis Bacon" HERE you can read:

Regarding faith, in De augmentis, he writes that "the more discordant, therefore, and incredible, the divine mystery is, the more honour is shown to God in believing it, and the nobler is the victory of faith." He writes in "The Essays: Of Atheism" that "a little philosophy inclineth man’s mind to atheism; but depth in philosophy bringeth men’s minds about to religion."

Bacon was right about needing a new approach to the development of science compared with that of the Middle Ages. He said:

"Men have sought to make a world from their own conception and to draw from their own minds all the material which they employed, but if, instead of doing so, they had consulted experience and observation, they would have the facts and not opinions to reason about, and might have ultimately arrived at the knowledge of the laws which govern the material world."

Bacon was fighting the notion at that time that magic and/or alchemy could produce gold out of any other material. What is ironic is that people today have replaced their pre-conceived notions in a way that is just as wrong as it was in the middle ages. To assume that biology has developed by blind material forces alone keeps a person from being open-minded enough to evaluate facts correctly. At this time, there are no physical or chemical laws which can explain the existence of biological life. Those are the facts. But the opinions, that God does not exist and therefore could not have any supernatural hand in biology, keep some away from the possibility of true knowledge.

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

2019 Update: Image was retrieved from Wikipedia in August, 2009 but is no longer accessible so link removed. Other images are available at Wikipedia entry for Francis Bacon, link above.

Young Earth, Big Bang

Evolution has become a contentious issue among Christians. The obvious division is between those who think God created people and animals and the Earth about 10,000 to 14,000 years ago and those who think He created the universe through a Big-Bang 14 billion years ago (bya) or so, with life coming about on the Earth sometime around 3.8 to 3.5 bya. This is a pretty big difference, all right. Some of the Young Earth Creationists (whom I affectionately call Yeccies) are concerned with matching their ideas with scienctific discoveries, such as carbon-dating, and others start strictly with Bible readings and let the chips fall where they may.

The other area of contention is between Christians who believe God started the complete design of life at the Big Bang and never needed to intercede since then. Life as we know it therefore came about by the physical and chemical laws placed within the fabric of the Universe. These people are called Theistic Evolutionists. On the other hand, we have those who believe God made the Universe in the same way (Big Bang), but interceded to make life. They believe that life shows a more direct Design that is counter to the laws of physics and chemistry. These are the ones who hold to Intelligent Design Theory (IDT). To confuse things more, not all advocates of IDT are Christian. Some believe in other gods, others think there is another designer. But many are Christian. However, as part of Intelligent Design Theory, they feel it is more scientific to keep to themselves "who" they think the designer is.

As a Christian, I feel the Designer can't be kept out of the overall outlook. I believe science is the study of designed physical things, and life was made and shaped by God's direct supernatural touch. This is called "Special Creationism." I am open-minded about the age of the Earth. I try to learn facts that come my way about this subject, but I am no expert.

It seems we get quite emotional about which motif the Lord chose to create us. There are some key theological issues that are involved. For the Yeccies, the point is that the Bible tells us that death came about by human sin. They take it literally that no one died, including animals, before the sins of Adam and Eve.

Others see possibilities of reconciling this doctrine with evolution, such as human awareness of sin and death coming at some critical time in evolution. Or, some say, animals and plants evolved but God made humans directly and when Adam and Eve sinned they became destined to die.

It is not trivial to seek an answer to these questions, but there are several layers of priorities here, I think. The first is to worship God and praise Him for His creation, no matter how He did it. Another near the top is to respect the opinions of fellow believers in discussing these matters and behave accordingly. Each has his or her own reasons for believing a certain scenario.

Another priority for us is to not presume we know all that God knows or why He does what He does. Isaiah 55 (NIV at link) tells us His thoughts are above our thoughts and His ways are above our ways. We humans can only speculate. For example, though some say He has revealed everything about Creation in Genesis 1, a different description appears in Genesis 2. And so it seems not quite as black and white as Yeccies profess.

Whatever else I believe, I believe God can do whatever He wants to do. It is not for us to impose, but to understand what God has provided us. He tells us to "Be Holy for I am Holy" (see 1 Peter 1 NIV). That's the priority.