Friday, April 4, 2014

God's Not Dead

My husband and I went to the movie, God’s Not Dead, last week. It was a surprising success and from the reviews I’ve read, many liked it but a wide variety of people, from atheists and Young Earth Creationist Christians (YECCies), didn’t.  If you know the premise (you can read a synopsis here), you know why atheists don’t like it. The main character, Josh Wheaton, is a college student who is in a philosophy class where the professor wants to skip the section of his class in which he spends time convincing students that God does not exist. The professor insists the students write “God is Dead” on a piece of paper, sign it and hand it in.  Josh Wheaton refuses, and so is assigned the task of standing before the class and defending his faith. Atheists either deny the movie is realistic or take the side of the professor who is clearly not the hero of the movie.

The reason some YECCies don’t like it is because Josh Wheaton argues for the existence of God by using the science of the Big Bang and Darwinian evolution theories. Both support an Old Earth, while YECCies believe in direct supernatural Creation of the planet and living species about 12,000 years ago. In addition, though the Big Bang broke through older theories of an eternal universe, both Big Bang and evolution theories now are supported by the scientific community under purely naturalistic explanations.

I learned from a National Review interview that the screenwriters, Cary Solomon and Chuck Konzelman, are Catholics. I was surprised because the movie has an Evangelical feel to it.  I have to give these writers credit for “getting it” about the Catholic New Evangelization movement that is supposed to be in effect.  This actually means EVANGELIZING, folks!!!

This leads me to say there are things I liked about the movie and things I didn’t. I have to give a mild spoiler alert: skip down a few paragraphs to the pictures if you don’t want to know any more about the movie before seeing it. First for the likes: the student takes God seriously. He actually thinks about what his actions have to do with his faith. He stands up for what he believes. I agree with the movie premise that the pressures are against believers in academia, and if you don’t believe this, just follow the Intelligent Design blog, Evolution News and Views (link on right column).  They keep a running tab on the discrimination against anyone who thinks biology is designed, especially in academia. Let’s not forget that Intelligent Design theory, much less Creationism, is not allowed in public schools.

Another thing I liked about the movie is that the tone for the most part was not hostility toward unbelievers but hopefulness for them to realize the truth. I felt this attitude came across several times especially in side-plots, and became more apparent at the end. This is a difficult attitude to take but necessary for all Christians.

For the part I didn’t like, it has to do with one of the points made by Josh when “defending” God’s existence. Like many other Creationists, I believe direct supernatural formation to be the best explanation for biological complexity. I don’t go along with the main character’s explanation of God directing evolution through seemingly random events. Though this is the line taken by many Catholics, I feel that if we had a clearer picture of biology, this is the very place where we can make an effective argument against the extreme scientism of today. Scientism is the cultural belief that science will answer everything and God doesn’t exist. Today’s cultural climate is where the movie premise is hitting the truth. The effect of science on philosophy is great, and well-known evolutionists take the lead in the discrimination and downright prejudice against believers.  It starts in academia and has filtered throughout the whole culture. Unfortunately, lawmakers and judges who hear arguments for teaching exclusively evolution in public school often are swayed by this cultural attitude.

The deep problem is that the people held as experts inform the public that evolution is true.  What can the public believe? They, like Josh Wheaton, must learn for themselves.  This training is just what I’ve been saying we need for the youth of today to defend their faith.  There are problems with that right now in the Catholic culture too, some of which I have discussed in other posts. But putting that aside for now, let me (again) show you biological complexity.

Photosynthesis is present in Cyanobacteria (pronounced sigh-ann-oh-bacteria). These organisms are among the very first the evolutionists tell us were on earth. They take energy, in this case light from the sun, and convert it to the building blocks of life. These are necessary for proteins, DNA, and other components. Evolutionists might tell you there were simpler systems earlier, but because they exist now, it means somewhere along the line they had to form. Plus, the entire photosynthesis system would have been evolutionarily early because these very early fossils show the pigments and bi-products of photosynthesis. And that means the atoms which form them must have been lined up in the precise way of functional proteins and not just a jumble of any old atoms. 

The pictures here show the overall photosynthesis pathway and three of the protein systems close up. The components are mostly proteins, although there are a few other types of molecules. I will shortly talk about proteins in terms of their sub-units called amino acids, but I have made rough estimates of the total number of atoms in the system. This is a very rough estimate, so if anyone has the exact number, I’d be glad to hear it.

The set of proteins known as “Photosystem I” are seen in the second image. There are over 50,000 atoms in this large set of molecules. That means they have to be specifically lined up by the cell enough to be in working order. Describing the system, Protein Data Bank says:
This structural information extends the understanding of the most efficient nano-photochemical machine in nature.

Photosystem II, pictured in the third image, has over 83,000 atoms in specific order.

When we add the atoms of photosynthesis molecules (very approximately), the cytochrome molecule has about 1500 atoms, and another integral part, ATP Synthase, has about 90,000. There are several other proteins to help with electron transfer, so we are looking at a total of around 225,000 atoms in a specific order for the photosynthesis system. Also necessary is a functional membrane so that an electro-chemical gradient can build to work the ATP synthase machine, and of course the genes which act as the template to make the proteins, the other proteins needed to copy the genes and make the proteins, and the regulators. The products of the photosynthesis complex go on to an entirely different set of molecules so they can be used to make the basic component of the parts of the cell (sugars, DNA, proteins, fats, etc.). 

When figuring probabilities that all of these parts could come together by chance, we often use the sub-unit of the protein called “amino acid.” This is because we can then assume the cell is already in working order and we can eliminate the chemistry involved in bringing all the atoms together. All biological amino acids have at least 10 atoms. The Photosystem I complex alone contains about 3100 amino acids.  Because there are 20 types of amino acids in proteins, this would bring a possibility of 20 to the power of 3100 combinations. Converting to a more familiar base 10, that would be 10 to the power of 4030 (written 10^4030). Even if the Earth is 4 billion years old, it could not have had more than 10^50 organisms (based on volume of water). In bacteria, a mutation only happens once about every 300 generations. The DNA that mutates during replication for another generation represents each "search" or "try" for the combination of amino acids that will function in the necessary way. The discrepancy is overwhelming for even one of the sets of molecules, and the total Photosynthesis machinery consists of about 15,000 amino acids (counted from composite parts in the RSCB Protein Data Bank).

Yet, when confronted with these facts, the evolutionist will say something like, “Maybe there was exchange of genes so that part of a previously functional protein became part of this system.” There are several answers to this. First, if evolution were true, all proteins would have to arrive at their functional state by chance. Even a short protein, about 70 amino acids long, would need 10^90 tries to get the right combination of amino acids, and that assumes that the genetic machinery is in full working order and there is an intact membrane. The number 10^90 represents the estimated total number of atoms in the visible universe. Some proteins do need the exact lineup of amino acids, such as histones. And for those less exact, the proportion of functional proteins is still only one in 10^65 or so. Second, even if there are two or more changes at once, the organism will then miss out on the other “tries.” In other words, if the DNA base code changes from CCCCCC to CCCCGG from one generation to the next, it will have missed CCCCCG, which might have been the necessary combination for function (the actual number of bases would be larger but this gives the idea). When you are dealing with random, the genes don’t “know” which parts are functional and which aren’t.

These are the types of facts every Catholic should know.  It is not that difficult, and this is the argument that should be set forth. We should not weakly accept naturalistic, materialistic evolution theory. The student, Josh, said in so many words that though evolution seems random, God could be directing it. This is the argument I hear from Catholics and other Christians and it is not a valid argument. The problem is not with the paradox which is posed. The problem is that they say biology SEEMS RANDOM when it actually DOES NOT SEEM RANDOM. The photosynthesis machinery needs to have proteins which are folded in exact shapes and have the exact matches to fit with critical molecules in order for our cells to work. It sure does not seem random to me. The atoms are arranged in specific order so they can make products like no other in nature.

There may have been a time when biologists were overcome by the number of species of beetles and in that way biology may have seemed random to them.  Then we discovered that DNA does mutate in a seemingly random manner. Perhaps the changes within DNA that come about when an organism reproduces may eventually be proven to have some explanation, so that small part of cell biology may actually SEEM random to us now and not be. But that small part of biological metabolism has not been proven in ANY WAY to provide the specific order that is necessary for fully functional biological systems. Therefore we can’t say meaningful evolution seems random because this kind of evolution is not yet proven. By "meaningful" evolution I mean the formation of all working systems that are present in the full diversity of living organisms, including those systems that make living beings diverse.

The arrangement of these atoms is more complex than simple random connections. Although chemistry depends on probabilities of atom movements, it also depends on attractions of types of atoms and the concentrations of each. Since scientists don’t know the exact original conditions on Earth, they cannot tell us that materialistic origin of life is a fact. Likewise, they cannot exactly account for the photosynthesis mechanisms in life. Evolution is not a fact because no one is able to lay out the scientific details of how such systems formed.

These are the types of arguments we need against the evolutionists who feed the public with “proofs” of evolution. There may be small changes after many generations of bacteria, such as in Lenski’s experiments with thousands of generations of E. coli.  However, there are explanations for these that do not point toward totally materialistic, naturalistic evolution. As Michael Behe points out in the link I've just given, most changes are losses of function that somehow help the organism survive but decrease its overall efficiency. Rarely, a very small change in protein can lead to better function, but it is a tiny part of a much larger biological system which already works.

The need in our culture, as demonstrated in this movie, is for Christians to learn the truth and then to evangelize. Let us do so!

Friday, March 7, 2014

Free Reads!

I have added pages to my blog that hold FREE reading material.  One is a booklet, Heaven’s Passport, and the other a book, Unto Others. The page headings can be seen above, just under the blog’s top picture. I like having the Home heading there too since otherwise in Google Blogger you have to go to the bottom of the column for the Home link.

I had written Heaven’s Passport back in 2005. It addresses some common questions about Christianity in a straightforward way. It is meant to be a tool for evangelization, and can be read online or downloaded. It can also be printed into a 20-page booklet by anyone with 5 regular-sized pieces of printing paper and therefore passed along to others in this form.  I had it on my blog for a while but had taken it off.  I had done the cover of Heaven’s Passport myself and it was not very professional-looking.  So I decided to make the effort to purchase a cover designed by a local printing business, and it looks much better. Heaven’s Passport can be read in one sitting or in sections, and I hope you will take the time to read it or download it now for future perusal and sharing. It is in PDF form, so it should come up with its own reader. If not, I have the connection for the free Adobe Reader. Many computers come with PDF readers, so if you prefer to download, you may not have to do anything else. But if it doesn’t come up after downloading, you may need to also download the Reader.

Catholics are called to a “New Evangelization,” and there are a variety of ways we are trying.  In some ways the Internet provides unlimited horizons, but on the other hand there is a lot of resistance to the message. It is important for each individual to realize that he or she is someone whom God cares about and wants as His own. And so I am happy to ask anyone who comes here to feel very special. We Christians want to tell YOU about the salvation that is possible through Jesus Christ.

The other page holds Unto Others, a fictional mystery with Catholic themes. It is also FREE. I put it in two file forms (ePUB and PDF) so you can choose what is best for you.  I also have links to the programs that display these forms in case you don’t have them. If you use ePUB, the free Adobe Digital Editions is the program that puts it close to book form on your computer.  This can also be used to read books from public digital libraries, so it is worthwhile to have. If you choose PDF, instructions are already mentioned above for Heaven’s Passport.

I hope you will take the time to check out these pages.  Heaven's Passport and Unto Others are meant to be thought-provoking and enjoyable too. Catholics need to widen their horizons in the world of literature, and I’m trying to do my part. Read my books and see what you think!

Tuesday, February 18, 2014

Some Research

In 2004, a research paper by Guo, Choe and Loeb was published by Proceedings of the National Academy of Sciences of the USA (PNAS) called “Protein Tolerance to Random Amino Acid Change.”  They wanted to know the probability that a protein would lose its function with one random amino acid replacement at any (also random) position on the protein. Amino acids are the sub-units that make up proteins. The researchers reported on their own experiments and also compared their results to others of a similar nature.

Their own experiment was carried out on a human protein nicknamed AAG.  Its chemical name and biological activity are described in the paper. They found that the probability it would lose its function with only one amino acid replacement was around 34%, and the reviews of other experiments at the time showed similar outcomes. One of several interesting aspects of the paper concerned “indel” mutations.  Indels are where several DNA bases are inserted or deleted instead of a single base change in a gene which is copied to make the protein.  They translate into extra or deleted amino acids. These indels were not even considered in the numbers for calculation because, although they were present in low percentages, “they invariably produce protein inactivation” (p. 9206 on the .pdf version). Later the authors modify the description to non-3bp (base pair) indels, but still give a value of “≈1” (almost equal to one) to represent almost 100% indel destruction of proteins.

Guo's experiment was on a single protein, and other research may show that not all indels lead to total destruction of proteins.  However, it is very likely that a lot of destruction from indels would be taking place in an organism before any indel would  bring about innovations to form a new functional protein. Guo et. al. also quoted other experiments in which researchers replaced amino acids until 100% of the particular protein was inactivated.  The figures ranged from 5-16% of replacements to do the job.   

One of the citations used in the research paper above was for work done by Douglas Axe.  Axe earned his PhD at Caltech and went on to post-graduate work at Cambridge. He is now director of the Biologic Institute in Washington State where he does experiments on proteins and protein systems. The Institute publishes the BIO-Complexity Journal (link for Archives here). He has had articles published in the Journal of Molecular Biology and other peer-reviewed scientific journals, contrary to the widespread claim that Intelligent Design advocates have never accomplished this feat.

In BIO-Complexity, Axe wrote a paper called “The Case Against a Darwinian Origin of Protein Folds,” (2010). You can read the abstract at the link above and the site has a link to the .pdf article.  The article is 12 pages and well worth reading. There are pictures of proteins and their sub-units (such as the image to the left) and Axe explains why the makeup of proteins is specialized.  These are not conglomerations of simple repeating units that fall together in a warm pool. The sub-units, called amino acids, are structured intricately and when put together in various ways have biologically important and specific functions. Although Axe uses large words and numbers, he also tries to explain what he says in simpler terms.

The challenge for evolutionary theory concerning the origin and development of proteins is what Douglas Axe describes as “The Sampling Problem.” Many people do not recognize the vast combinations even small collections of molecules can make.  As Axe says, “Amino Acid chains a mere 12 residues long [composed of 20 possible kinds of amino acids] …can be built in 4 quadrillion ways (20^12=4x10^15).” A relatively short protein of 69 amino acids has about 10^90 combinations. 10^90 is the estimated number of particles in the known universe.  These numbers are not to be brushed off.  It takes reproduction of generations of organisms to try out ("sample") new amino acid combinations, and that takes time. Billions of years are not even close to being enough.

Friday, February 7, 2014

Histones Stand Alone

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

The long DNA molecule in many bacteria is “circular.” The DNA is one loop instead of separate chromosomes as humans have.  The cells don’t have a separate chamber for the DNA as ours do.  But a lot still has to happen for the molecules to get their jobs done.  One of the ways the DNA is organized is by what is called “supercoiling.” The above picture is from “Chromatin architecture and gene expression in E. coli,” Willenbrock H, Ussery DW - Genome Biol. (2004). The link gives more of an explanation, including the abstract:
Two recent genome-scale analyses underscore the importance of DNA topology [geometric properties] and chromatin structure in regulating transcription [DNA copying] in Escherichia coli.
Chromatin is made with the organizing protein, shown near the middle.

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

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

Bacteria are known as “prokaryotes” (pro-carry-oats).  As well as not having an inner wall around the DNA (nucleus) like the cells in animals, they have other differences as well.  There is another prokaryotic domain of life known as “Archaea” (are-KEY-ah). The grouping of biological life is shifting since it became possible for scientists to learn the entire codes in the genomes of species.  The fact is that the sequences are not falling in place.  But the “Tree of Life” project Root Page (link here) explains:
The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly [common ancestry] of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon.

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

It is true that not all species have been sequenced.  But these DNA-bending proteins are so greatly different that it is obvious that they could not all have come from the same source.  Even if another animal species showed up that had histone sequences half-way similar to those of a human, they could not account for the spread of differences already found. And so far, none have shown up with Archaeal-like histones (species Methanothermus fervidus), as you can see in the boxes in the image below. (This result is from a BLINK database which compares proteins from different species, run in February 2014. The query page is here and you put in the Uniprot number, then click on Blink: in this case P48781).
The "similar" Archaeal histone protein that is mentioned above is 69 amino acids long (M. fervidus). Since there are 20 biological amino acids, the possibilities for this length of chain are 20^69 (20 to the power of 69, using ^ for an exponent), or about 10^90 (a 1 with 90 zeroes after it). Contrary to simulated computer programs of mutation, there is nothing to stop the DNA from mutating the bases which cause the protein to work correctly.  Natural selection would eliminate those organisms which mutated from useful to less functional (they die or reproduce less). So even if the proteins have a small proportion of the same amino acids when compared now, say 10%, there would still have to be an average of about 10^90 tries to get from one of the structures to the other. (I want to add that as of Feb. 2014, when you run the human histone H3 [Uniprot number P68431] in BLINK for matches, it brings up 0 Bacteria, 0 Archaea and 0 Viruses).

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

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

These comparisons are just for histones.  Many of the proteins in animals and plants are much longer and would have to undergo much greater transformations. Many scientists and the media do not bring these types of things to attention.  They seem to want you to think evolution is easy.  I guess it is wishful thinking on their part, but why do they wish these things are by chance?  Life is so much better when you can appreciate the Creator of all.
Nelson, Fred.  "Needed: A New Vocabulary for Understanding Evolution." Perspectives on Science and Christian Faith, 58.1, 2006, page 31. The link here is for another link to the .pdf file of the article.

Pictures 2 and 5 are from NCBI:
Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. "MMDB: 3D structures and macromolecular interactions." Nucleic Acids Res. 2012 Jan; 40(Database issue):D461-4

Wednesday, January 15, 2014

Thomas Aquinas Continued

In my last post I was talking about St. Thomas Aquinas and Catholic thinking related to him. Aquinas has had influence in many ways, but is ignored in others. I compared two specific areas: the treatment of Catholic women by the Church because of Thomas’ opinion of them, and the misuse of his name for worldviews other than his belief in direct supernatural Creationism. But I made my point about women in the last post and now I want to say something about Creationism.

In Summa Theologica, Part I, Question 91, Article 2, Thomas stated:
The first formation of the human body could not be by the instrumentality of any created power, but was immediately from God.
  The definition of “immediately” is here . It means instantly and directly. Thomas again talked about direct creation by God when he discussed the creation of woman from the rib of a man in the next Question, 92, Article 4 which can be seen here .

But, a 2009 Vatican-sponsored conference on evolution excluded Creationists and Intelligent Design advocates.  They said we weren't scientific enough, although they are the ones ignoring science as well as the words of Thomas Aquinas.  The science is revealing biological systems way too complex to be answered by chance genetic mutations even when natural selection is factored in.

The human condition is to have all kinds of ideas bombard us from inside our heads and out. Some of these take hold and we are convinced they are true. Sometimes the ideas are right and sometimes not. As our science research discovers more and more, we are overwhelmed with facts and opinions about them. As our communications improve, we discover new religions and cultures. How do we sort it all out? It takes time and effort and discernment.

Of course, people have argued about things for a long time and for philosophers, argument is a living. But all the worldviews can be hard to learn and follow, and facts can be lost or mangled in our minds after time. Concerning the relationships between philosophy, theology, Creationism, and Intelligent Design Theory (ID), a good series of posts in 2011 by Jay Richards of the Discovery Institute describes some of the problems. Even if you don’t agree with him, he is very good at explaining the situation. The fourth post has links to all previous so I will give that one link here. He of course emphasizes ID compared to Creationism, but much of the biology of Creationism is linked to this scientific theory.

The arguments in Aquinas’ day (13th century) didn’t concern materialistic evolution but whether man was made by angels, as St. Augustine had said, or according to Aristotle’s philosophy with which Aquinas was wrangling. The Greek elements of Fire and Air seemed a more noble make-up for man than Earth and Water, the ingredients of the “Slime” which was closer to the Biblical account of God’s action. Aquinas takes his stand with the answer (also Question 91):
On the contrary, It is written (Gen 2:7): God made man of the slime of the earth.
Some of the totality of Thomas Aquinas’ thought, and it is a lot, still resonates to this day. He had a lot of detractors in his lifetime, and we can wonder if Thomas sometimes got discouraged and felt he was wasting his time.  As a matter of fact, he had a mystical experience at the end of his life, put down the pen and never wrote again.  He said then, “All that I have written seems like straw to me.” (As quoted in The Thought of Thomas Aquinas (1993), by Brian Davies, p. 9). And yet before that he used his gifts at a time when many were probably confused by the different interpretations and theories floating around in that day. He probably helped many get back to the faith or remain more solidly in it.

I’ve lately been reading Paul’s letters in the Bible and in Timothy 2:23-25 NABRE he says:
Avoid foolish and ignorant debates, for you know that they breed quarrels. A slave of the Lord should not quarrel, but should be gentle with everyone, able to teach, tolerant, correcting opponents with kindness….

I wonder sometimes if it is worth arguing about materialistic evolution. Since science changes so much, how long will these details be relevant? But in this day when scientism (belief that science is everything) is taking over like wildfire, I think science is a good approach for conversation. It is in this way people can think about whether biological life and diversity is beyond what can possibly be formed from the other currently known forces of nature. Though biology is complex, it can be appreciated on a certain level by everyone. Like it does with so many things, the Internet grants access to biologic wonder. With video searches, people can view muscle molecules contracting, DNA being copied, and a multitude of other biological functions. Then they can ask the harder questions: could these have formed in even billions of years? Was that time enough to randomly build a house or even make a brick? Did a computer chip form out of the primordial soup? Why then does the concept of billions of years answer the question of how and why we are here?
Ironically because science changes so much is one reason individuals need a more solid foundation in their lives. The researcher gets old like everyone else. My suspicion is that the Theory of Evolution has led many scientists to the sad conclusion that they consist of only atoms. But their inner feelings of fear and love must be inescapable. The unchanging and absolutely necessary foundation, hard as it is to believe for the hard-driving atheistic evolutionist, is Jesus Christ.

The overriding priority of Catholics is to evangelize the Good News of the Gospels, and we must find a way to work together to carry out our commission. Sometimes I get very discouraged and heartsick about our problems in the Church, particularly the child abuse scandal. Yet I believe our new Pope is trying to reform the Church as others accomplished in previous dark times. His recent homily about hope was uplifting to me and I link to it here.  We know our Lord Jesus has conquered evil. Thomas Aquinas would have agreed:
Our help is in the name of the Lord, Maker of Heaven and Earth (Psalms 124:8 NIV).

Thursday, January 9, 2014

St. Thomas Aquinas

If a Catholic has the unusual combination of interests in women’s dignity and the sister subjects of Creationism and Intelligent Design Theory, s/he (she or he, pronounced shee-hee) would probably view the uproar caused by a US New and World Report op-ed column about Catholics with a corner of one eye on St. Thomas Aquinas. A columnist at US News, Jamie Stiehm, was outright hostile toward the decision of Supreme Court Justice Sonia Sotomayor in favor of the Little Sisters of the Poor.  These nuns did not want to sign over the right for an insurance company to pay for contraceptives and abortion for their employees. The problem has been festering ever since Obamacare made its move to include this cost in insurance coverage. The law is for the insurance to pay for contraception, not about whether the employer can force its employees to use or not use contraception. Many Catholics are responding in great anger and indignation to this column, both in comments at the site and at various blogs like the one linked above. The Little Sisters apparently felt that in agreeing to the payment of contraception and abortion even by another party they would still be violating their religious conscience about it.

Unfortunately, the arguments about contraception and abortion are caught up in each other and distinction of types of contraception beyond “natural” and “unnatural” are ignored. Chemical contraceptives taken internally can cause death of a fertilized egg. However, man-made barriers can keep the sperm from reaching the egg and avoid embryonic death, but they are still deemed wrong by the Church. The reasoning stems from the Natural Law, derived in great part from Thomas Aquinas, the greatly venerated 13th century Doctor of the Church. The thoughts of Aquinas are carried down to this day within Catholic theology and philosophy.

We probably all know by now that the Catholic teaching is that every sexual act, which is allowed only for married persons, should be done with procreation in mind. A recent survey put out to the bishops by the Vatican concerning the deterioration of the traditional family refers to this Natural Law. The questions of the survey are listed in the bottom half of this post in Vatican News and Natural Law is mentioned in Question 2 where the bishops are asked if Natural Law is still accepted (The first half of the link is current reasoning by the Magisterium about family ). Paul VI, in Humanae Vitae, (Sec. 16) expressed a very limited exception of consideration for the burdens of giving birth continually, but they were only to be interrupted by natural means. These developed into what is known now as Natural Family Planning (NFP). NFP makes use of biological factors to prevent pregnancy and probably works if there is absolutely no human weakness between partners. In my experience of encountering couples who teach it, I’ve found they have had between 6 to 12 children.

Many women active in their field, say medical doctors, do not have time to properly care for 6 to 12 children unless they have superwoman levels of energy (some do but many do not). The Church does not seem to think that God would personally call a married woman to be a doctor instead of a mother. Perhaps this is because of St. Thomas Aquinas.  In Part I, Question 92, Article 1 of Summa Theologica seen here, Thomas gave his opinion of women’s roles.  (His Summa is set up by first posing questions made by others and then he answers them below). The question, bad enough, was whether women should have been made in the production of things. His answer:
It was necessary for woman to be made, as the Scripture says, as a ‘helper’ to man; not, indeed as a helpmate in other works, as some say, since man can be more efficiently helped by another man in other works; but as a helper in the work of generation.  
By generation he means reproduction.  He goes on to describe sex between man and woman, then says:
But man is yet further ordered to a still nobler vital action, and that is intellectual operation.

In other words, Aquinas said women can’t think. But unlike Thomas I assert that all women are intelligent and should be treated as such. Perhaps the existence of female Nobel Prize winners will assure that women have intellect. I am not saying that intelligent married women shouldn’t be mothers.  I am not saying all married career women are in their careers because they believe God called them there.  I am saying that when intelligent married women discern they are called by God to serve Him in specific ways other than motherhood, no one should tell them they must be mothers instead. 

Now what does the Church’s gender problem have to do with Creationism? Let’s go back to Thomas Aquinas. It is a curious thing that his teachings are ignored when so-called experts have other agendas. His name is used to press the idea that science will one day have no gaps, since God supposedly created an ordered world that man will thoroughly understand. This order in the world has taken, as a prominent example, the form of totally materialistic, naturalistic evolution. Evidence of this mindset is found from the exclusion of creationists and intelligent design advocates from a Vatican-endorsed conference concerning evolution.

Though the conference was back in 2009, the Thomists keep the worldview running. Consider a statement from Mark Shea at the National Catholic Register.  I link to a pertinent column here and will not quote the whole thing.  But very succinctly, he talks about why Thomists don’t agree with the Argument from Design.  He says there are several problems with this approach: 
The first is this: St. Thomas himself never says “We can’t explain X, so God did it”…

In fact, Aquinas addresses in Article 4 the creation of man and woman in the very same question at the very same link I gave before. Thomas Aquinas says:
Now the matter whence man is naturally begotten is the human semen of man or woman.  Wherefore from any other matter an individual of the human species cannot naturally be generated.  Now God alone, the Author of nature, can produce an effect into existence outside the ordinary course of nature.  Therefore God alone could produce either a man from the slime of the earth, or a woman from the rib of man.

In the next statement, Reply to Objection 1, Aquinas says:
This argument is verified when an individual is begotten, by natural generation, from that which is like it in the same species.

The points here are many, but for now I will emphasize this one:  if the bishops are nervous about whether women can discern wisely, they would be better off teaching discernment than dictating to half a billion people exactly what they should do. How do they know each heart better than God? The answer is, they don't. When the Church leadership trusts women to discern God's personal calling instead of assuming Thomas Aquinas' opinion of women, a New Evangelization may truly start to take hold.


Friday, January 3, 2014

Bilingual DNA

The University of Washington's Dr. John Stamatoyannopoulos has been a leader in the ENCODE Research, which is an extension of the Human Genome Project.  They continue to study human genes and DNA, the molecule on which the genes reside. The DNA contains coding and is copied in order that the proteins that do the work of our cells are produced.  But it takes a lot of inner cell regulation to get things just right.  Now that they know the genes, the researchers are trying to understand the regulation.  They are making surprising discoveries. 

From the University of Washington website: 
Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

It goes on to say:
Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

DNA contains 4 different types of “bases” which are molecules that form a code (see first image, from Two bases form each "step" of the DNA "ladder." The groups of three bases, called “codons,” line up in precise order to give instruction to other mechanisms for the production of proteins.  We think of the codons as a language because their sequence affects the outcome beyond strictly chemical interactions.

The bases have an “end” for connecting to the side of the ladder and an “end” for producing the code. When DNA is copied, the middle splits open the long way and another molecule comes along to copy it.  This is done in the middle of the cell called the “nucleus.” Then the copy leaves the nucleus and is processed in the outer cell compartment to make the proteins. The protein production takes several intermediate steps, and the codon code is read to put together the protein.

DNA codes for proteins that carry on the functions of biological life.  Among these proteins are “transcription factors” (TF) that regulate gene production by binding to other parts of the DNA. The second picture is of gene regulation and the abstract for its article is here. You can see there are several elements involved in the regulation, both close and far from the gene (the black line is the DNA). There is often a feed-back system so that when the gene product is available, the chemical interactions lead to repression of further copying of the gene.  When the product decreases, the gene once again is activated. When the mechanism was first discovered, it seemed the transcription factors attached to DNA close to but a little bit apart from the actual gene.  It has been known for a few years that they can attach both to gene and non-gene areas and both near and far from the gene. But now the scientists have discovered an even more surprising situation.

The amazing part that was just announced is that the regulatory protein uses the same type of 3-base-per-codon language used in protein production. So, a protein can come back into the nucleus and combine with the DNA for a regulatory role using a set of 3 codon “letters” for a different function.

The paper is in Science, December 13, 2013.  It is limited access, so perhaps you can find it at a library, but it is written for those who understand the jargon.  Casey Luskin at ENV further explains aspects of it which you can read here.

Though much more research is needed, it will likely be necessary to understand the interplay of these molecules in order to cure certain diseases.  Over 85% of genes are already shown to have these regulatory codons, and the study has not covered all types of cells.

This discovery is BIG. The research shows that DNA has even more complexity than we imagined, and it greatly limits the possibility that all the functions of DNA simply came about from random molecular mutations. Because of the different language, current evaluations of natural selection are even less convincing than they were before. It shows the regulatory job of DNA is at least as precise as the production of proteins.  As researchers discover more activities for the genes, they find there are fewer changes the sequences can make without wrecking the whole system. That means even less chance for totally materialistic evolution.

To add a little related information from another paper, they have found that the genes themselves are involved in further activities.  Of special interest are the HOX genes which regulate organism development.  They have been found to interact with regulatory elements, and there may be “a largely unknown regulatory network relying on nucleotide sequence elements embedded within the ORFs [open reading frames] of most of these key developmental genes (Woltering and Duboule 2009)” from Lin et. al., “Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes”.  In other words, the genes read regulatory proteins  as well as producing the protein code when the individual is developing.