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) 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 not made with Catholic leadership. 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 does? 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.