Friday, October 3, 2014

A Matter of Faith

This month a movie that comes out on October 17 and will be showing in Grand Rapids is “A Matter of Faith” which I’ll abbreviate MOF. In it, a young woman attends college and is influenced away from faith by her evolutionist biology professor. Her father becomes upset and ends up debating the professor.

I heard a producer of the film being interviewed on a Christian radio show I listen to on Saturday mornings, and I looked the movie up on the Internet. I found the website and played the trailer (at the link on the movie's name above). To my surprise, I saw the campus of one of my alma maters—Aquinas College in Grand Rapids! I did a search and found the producers, the Christiano brothers of Christiano Film Group, are from Grand Rapids and the production was headquartered at Cornerstone College which is located on the East Belt Line there. Scenes were indeed taken from Grand Rapids locations.

I attended Aquinas College for a certificate in theology, which I received after 18 credit hours. I had already earned a veterinary degree, but have been interested in theology and spirituality for a long time. Then, around the time I was going at Aquinas, I started reading the works of Intelligent Design (ID) advocates such as Michael Behe (Darwin’s Black Box), William Dembski  (Intelligent Design) and Phillip Johnson (Darwin on Trial). I already was convinced that biological life was not a product of totally natural evolution, but I enjoyed reading their works and learning more about the controversy.

I didn’t agree, though, with the Intelligent Design advocates in their approach to science. They wanted to prove design in a strictly scientific way, but I think that faith comes first. Of course, not everyone believes. But, IF a person believes in God, THEN s/he believes all things are Created and therefore all things are designed. You don’t prove design, you believe it. However, if you want to look at the scientific part of why totally natural evolution should not be considered feasible with the knowledge of natural laws as they are now, it’s as simple as this: the complexity of biology defies probabilities.

I wish I had bookmarked a conversation I saw recently, I’m pretty sure from Evolution News and Views, between an ID advocate and an evolutionist. I can’t find the article now, but the background is that, as scientists compare the proteins of different species, they try to match the sequences of their sub-units. If they match, the scientists say it proves that one species came from another. As I remember, the ID advocate, who wrote the article, asked how evolutionists feel that the low probability of matching protein sub-units in various species proves evolution whereas the overall probability of the proteins existing in the first place is much smaller by far. The evolutionist said something like: the comparison of proteins gives scientists frames of reference, but the origin has no frame of reference. Apparently chemistry, physics and mathematics don’t count as frames of reference when it comes to origin of life and new proteins along the way of species differentiation. Actually, the experimentally proven extreme rarity of functional proteins among all the combinations of their sub-units (amino acids) provides a very fundamental frame of reference. (The evolutionist also did not explain why the differences in proteins do not count in the determination of proof.)

The comparison of proteins can be accessed on the Internet in various databases. The UniRef database is from the UniProt consortium, which is a combination of particular European and American protein database providers. UniRef shows relationships between proteins in over 200,000 species, which NCBI describes here. This is about 10% of all formally described species. They identify each protein and give it a cluster identification, then compare proteins to different species. If the proteins are similar, they are put together in a category of "related clusters" or "cluster members." The charts on the database give the number of clusters that compare closely to others, along with the species names. And yet as of October 3, 2014, there are more than 7,750,000 single clusters of proteins that match less than 50% to other clusters out of a total of around 82,000,000 clusters.

I took one of the clusters and looked a little more closely at it. There were several species in this cluster, but the group for the "cluster" were still close cousins. The protein is called “histidine kinase” and it is in the organism "Halorubrum saccharovorum," part of a family of archaea (pronounced are-KEY-ah). Archaea are single-celled organisms that were first thought to be ancestors of bacteria, but were found to not be related once the genes could be sequenced (starting in the mid-nineties). So this particular protein structure is so far only found in one family of one type of organism. The protein is involved in sending molecular-level signals.

It can be hard to get an image of a specific protein since there are so many proteins--not all have been depicted. I apologize that I have not been able to find an image of this particular one, but think I am still able to demonstrate how different proteins can look and how different their structures are. The first image is from an Archaea species, Methanocaldococcus jannaschii, of a kinase that has histidine as an active site. The explanation of the protein is here.

The second image has a histidine kinase (ATPase) from a different species known as Thermotoga maritima. This is a bacteria instead of an archaea. When the sub-units (20 different amino acids) of the Halorubrum and Thermotoga proteins are compared, the identity is figured by the “Align” program in UniProt to be 14.2%. When I run the two proteins pictured here, from Methanocaldococcus and Thermotoga, against each other, the identity is less than 10%. And even the two Archaea proteins, from Halorubrum and Methanocaldococcus, matched only at 9.9% . You can run the Align yourself if you want by using the UniProt ID numbers of the proteins: Q9WZV7 for Thermotoga, Q60352 for Methanococcus, and M0E4M2 for Halorubrum. Though they have different lengths, all with hundreds of amino acids, the matches are very minimal for any of the sections.

(Some say that instead of individual amino acids, larger sections of various proteins might have randomly combined, and often you hear there is “horizontal transfer” from one species to another. But horizontal transfer depends on about 30 specific proteins, and besides the improbability of them forming in the first place, not all organisms can do this transfer. And once you get above single-celled organisms, the chances are even smaller because the transfer would have to involve the specific reproductive cells.)

Even though there is a big variety of molecules throughout living systems that do similar things, this doesn't mean every protein can do every job. Just like in factories, the thousands of specialized jobs need specialized tools to do them. Or think of cars, trains and planes. Each of them are used for transportation, but you don't use car parts for a train, and train parts do not have intermediates for plane parts. Each part is made specifically for its purpose. To take the analogy a little further, there are different kinds of cars, trains and planes, and though some parts may interchange among the various types of each, many can't.

In naming clusters, UniRef compares proteins and the manual says it looks for 80% match. However, in the UniProt "Align" section, the comparison of proteins described above shows you how well short fragments match. When you get very low matches, this minimizes the idea of functional sections from different proteins somehow finding each other, at least so far. It is becoming known that about 10% to 20% of proteins of every living organism are ORFans, or those which have statistically little to do with each other (see my booklet, Creation Biology). And millions of fragments would have to unite at the exact junctures to become functional within the limit of 10^50 organisms that could have existed in 4 billion years on Earth.

All Christians should consider themselves Creationists because, as it says in our creeds, we believe God made all things, visible and invisible. Unfortunately in today’s academic atmosphere, even Christian colleges are blocking the attempts by certain Creationists called Special Creationists to make their cases. Special Creationism is a belief that God made humans and “kinds” (similar to species) directly without long-term evolution. Many Fundamentalists are Young Earth Creationists, but one can be open-minded about the age of the Earth and still believe people were created directly, in a way that they did not stem from other species.

Even Theistic Creationists, who are supposed to believe that God intervened along the way of long-term evolution, don’t seem to want to talk about the supernatural part. Many from their main think tank at Biologos seem to insist that evolution is totally materialistic and at bottom a random process.

The situation is worse in secular colleges, where the mere mention of supernatural biological Creation by God brings condemnation. But it is a shame that the Christian universities are almost as bad. From the overall situation comes the movie MOF which, as said above, involves a college student who is being taught evolution by her biology professor. Her father is fearful she will lose her faith altogether which is why he debates the professor.

The MOF movie does not have the wide distribution of “God’s Not Dead,” but the movie conveys very real problems felt in the Catholic world. The Catholic philosophy of “Thomism” in which St. Thomas Aquinas, the great scholar of the 13th century set out to blend faith and reason, is very complex. But to address one point, I have heard it said in the name of Aquinas that God created the universe in a way that all things were laid out in order and that He would never contradict that natural order by intervening in a supernatural way once it was laid out.

A problem in Aquinas’ time was that the Greek philosophy had recently become available to European minds through its translation into Latin. And for one thing, there was an apparent conflict between this “Reason” and “Faith” over the source of the universe and its contents because the Greeks (such as Parmenides) had said “Nothing comes from nothing.” Christians believe that God made the Universe from nothing. So Aquinas held that though things are usually made from other things, there must be a “First Mover” and a “First Cause.” But he also specifically commented about the creation of humans.

In Summa Theologica, Part 1, Question 92, Article 4, he says this in his answer (after laying out the contrary argument [objection] first, which is at the link here if you want to read it):
As was said above…the natural generation of every species is from some determinate matter. 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.
 Darwin’s Theory of Evolution was causing problems for the Church, but there was philosophical upheaval before then. In 1879, Pope Leo XIII put out an encyclical called Aeterni Patris. He said that science is good, but it needs to be combined with faith, and used St. Thomas Aquinas as the ultimate model in the combination of the two.

I'll never know all the in's and out's of philosophy and theology. I do perceive we've gotten to the point where anyone who argues against neo-Darwinian theory is considered either an anti-science Fundamentalist or an anti-reason, anti-"form"ist. We are treated in a hostile manner by many Catholics as well as atheists. Well, the complexity of biology is showing that the Fundamentalists may just be right after all.

It is a little risky to speculate on what God would or wouldn’t do. Some think He’d never “trick” them by making genes “look like” they have mutated over time when they really hadn’t, such as they say is the case with Vitamin C gene. However, the Fundamentalists have long associated imperfect (fallen) nature to original sin. In fact, it would be contrary to our doctrine if nature were still perfect. But I’ve never heard this aspect discussed by the detractors.

We are left with the question of whether God created species or kinds in increments, with parents of different characteristics. Though Darwin claimed it was a slow process, in the intervening years we have found the difference in body make-ups between parent and child would have to be pretty big in some cases. Can the parent bug give birth to a fish-type child?  (I'm exaggerating, but only a little.) The body type comes from the egg as well as the DNA, so the egg would have to have major changes from within the parent. I’ve never heard any proposal of scientific-supernatural solutions for these problems from Theistic Evolutionists. Maybe I’ve just missed them, but I doubt it.

I used to accept that people come from apes, but I don’t anymore. People were made by God, and I think He did it directly and supernaturally and not by evolution. I am not saying God wouldn’t make people by evolution, because He does as He sees fit. But it’s just as logical to think He didn’t have a person born to an ape as that He did.