Monday, December 1, 2014

Discerning Women

My post for today is on the first Monday of the Month. I had been doing it on First Fridays, the day of devotion for the Sacred Heart of Jesus. I’ve been attending mass on that day for a long time, but am planning a shift toward Monday devotion and will try to attend mass at least one Monday a month. Monday is devoted to the Holy Ghost and souls in Purgatory (you can see a list of devotions here). 

In my last post, I mentioned the Extraordinary Synod of the Family, called by Pope Francis and held in October. Pope Francis has called Catholic Bishops to give input about the family and work on the problems related to it. They are going to have another meeting next year in which there may be some revisions of the current status of teaching. The Pope is looking for input from the general Catholic membership also. Since the Pope and others have used the Holy Family as a model for families, I’d like to comment about that for my December post.

For a long time the Church leadership has insisted that all married couples seek to “develop a mentality of openness to life,” which to them means having a marriage in which every sexual act would potentially lead to children. Concerning the Holy Family, the Catholic Church holds that Mary was a virgin throughout her whole life and Jesus was her only child. In order for that to be true, Mary and Joseph had no sexual relations and apparently felt no compulsion to have more children.

Last month I talked about Christ saying that his true family are those who do God’s will. Ironically the example of the Holy Family, instead of backing the Magisterium's apparent interpretation, more clearly shows that God called Mary directly and personally (through an angel) to do His will. God did not consult first with Mary’s religious leaders, her parents, or even her husband-to-be. And Mary answered directly to God (through an angel) without first consulting with her religious leaders, her parents, or even her husband-to-be. She had to discern (I believe with God’s help) that the angel was a good one, since not all angels are. Mary didn’t know if, in her acceptance, Joseph would still marry her or if her parents would reject her or if the Jewish leaders would try to have her stoned. 

I don't understand how our Church leadership can be sincere in using Mary as an example to promote child-bearing. Of course, Jesus Christ was quite a child, but no amount of child-bearing could make another woman into Mary or another child equal to Christ.

John Paul II, in his Apostolic letter Mulieris dignitatem, also extensively cites Mary’s life. He says virginity and motherhood are complimentary, but it is a little hard to understand that in a practical way. He talks about consecrated virgins caring for others, such as the poor, which certainly is often the case. This is a form of mothering though it is not to biological children. However, perhaps a young woman does not feel the call to religious vocation but does discern that God calls her to be, for example, a doctor. Then she spends her youth in becoming educated and starts to practice. If she later falls in love with a man, she will probably discern that she still has that original calling to be a doctor. She then also needs to discern if this man is compatible as a life partner, and by “compatible” I mean someone who respects the woman in all her facets. Women and men both need to realize they first must seek God, then, if so inclined, seek a human partner.

Marriage is present in other religions, so to be married is not necessarily to evangelize for Christianity. Though lasting marriage is very important, it seems to be one aspect of Christ’s larger message. The priority of the Church is evangelization. The central point of Christianity is to believe Jesus Christ is one of the persons of the Trinity of God who came to Earth, lived a sinless life and died in atonement of the sins of humanity. We are also to proclaim such to others in the best way we can. It is vital for each of us to believe in Him and to continue to proclaim His divinity and inform persons that they also need to have this faith for the salvation of their souls and an everlasting life with God in heaven.

Most of us have long lives, and if a married Christian woman truly discerns that God is calling her to motherhood, the Church should support her and her family in every way they can. But if a married Catholic woman discerns that God is calling her to promote His kingdom using gifts other than motherhood, then the Church should also support her and her husband in every way they can. These women with other callings would indeed be wonderful assets to the Church’s mission. Not every career woman is selfishly out for herself in the way she is often portrayed. She might be giving to others in very important physical and spiritual ways. (And this is possible for married women without abortifacients, but NFP is just not sufficient. Women can be irregular and can't always plan for the wedding night.) The Church leadership is a long way off from this ideal of supporting women. This contributes greatly to the fact that American, European, and now Latin American women, and men along with them, have left the Church.

There was another conference on the family in November—this one ecumenical. Pope Francis said this about complementarities between spouses in a family, with a link to an article about the conference here at Vatican News:
The Holy Father began his address by dwelling on the word “complementarity”: “a precious word, with multiple meanings.” Although complementarity can refer “situations where one of two things adds to, completes, or fulfills a lack in the other” it also means much more than that. Christians, he said, “find its deepest meaning in the first Letter to the Corinthians where Saint Paul tells us that the Spirit has endowed each of us with different gifts so that-just as the human body's members work together for the good of the whole-everyone's gifts can work together for the benefit of each.”
Complementarity, the Pope said, “is at the root of marriage and family.” Although there are tensions in families, the family also provides the framework in which those tensions can be resolved.” He said that complementarity should not be confused with a simplistic notion that “all the roles and relations of the sexes are fixed in a single, static pattern.” Rather, “complementarity will take many forms as each man and woman brings his or her distinctive contributions to their marriage and to the formation of their children.”
Pope Francis has been encouraging discernment. Of course we all need the right foundation. Then the Church leaders and members should learn when to discern together and when individuals should be trusted to discern God's will for themselves. We need to pray that we can listen to God as well as Mary, the mother of Jesus, did so many years ago.
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May you have a blessed Christmas. I hope you have time (3:44) to play the video at the top of the page. The song is "Joy." Music by Cindy Morgan, Lights by eShepherds of Light. I saw it  here at the Vimeo website.

Friday, November 7, 2014

Family Discernment

Pope Francis had called for an “Extraordinary Synod of Bishops,” which was held in October in Rome. The group discussed the family and its relationship with evangelization. At completion of their 2 week meeting, they issued a statement called, ‘Synod14-"Relatio Synodi" of the 3rd extraordinary General Assembly of the Synod of bishops: "pastoral challenges to the family in the context of evangelization" (5-19 October 2014), 18.10.2014.’ If you would like to read it, link here

The Synod has focused on the family as the male-female-child unit (nuclear family), but the whole Church is also sometimes referred to as a family (Church family). Though I’ve seen quite a few references to what Jesus Christ said about divorce, here I want to point to another quote concerning what He said about family.

In Matthew 12, verse 47 (NIV), Jesus Christ had been speaking to a crowd and someone told him that his mother and brothers were outside seeking him. The Lord asked,
“Who is my mother, and who are my brothers?” Pointing to his disciples, he said, “Here are my mother and my brothers. For whoever does the will of my Father in heaven is my brother and sister and mother.”
God’s will is something Christians strive to do in our imperfect way, and our efforts have many aspects. If we are Christians, our nuclear families are to be considered in the greater context of what it means to follow Christ. In doing this, we try to understand the meaning of Christ’s words with the help given to us by the writers of the Bible and Christian leaders. But if and when possible, we also try to connect with God in an interior way. We pray to Him, we think about Him, and this already is beginning to make that interior relationship. Then, some of us feel movements deep within that lead us to believe God may be present. They evoke emotions of awe or love or other spiritual dimensions. They seem to us beyond those felt every day, perhaps as a part of special events of life or even deeper and wider than these.

Catholic leaders encourage young people to seek their vocation, meaning to try to follow God’s will. They also mean it in another way, since “vocation” stands for a life in specific religious service. I’ve often read of priests, religious or deacons who felt they had followed God’s will in pursuing their vocation. This effort to hear God’s call is an interior communication with God.

Romance books always have scenes of persons starting to notice each other and becoming aware that they react in a different way to each other than to anyone else. As most people know, these feelings can be very vivid and energizing. And of course if thwarted, they can lead to heartbreak and great pain.

The Psalms in the Bible are a reminder of the communion King David had with the Lord, with emotions not exactly the same but comparable to the romance books. Often he expresses anguish, but also joy and awe at God’s creation. Many people have experienced a great joy when they have first become Christians. But after time, the going can get tough. Saints have talked about their “dark nights of the soul,” and so it can be a little like the human relationships we experience.

Christians in general experience difficult relationships among each other, easily demonstrated by the number of denominations we have and even the infighting inside each of these. And certainly we have problems relating to non-Christians.

All relationships can be joyous on one hand and terribly difficult on the other. How do we get to the right place in these relationships? I’d like to say I’ve figured it out, but my rapport with others can be as rocky as anyone else’s. Yet I do have an ideal that I try to follow in my life, and it has to do with discernment and prayer.

I know for Catholics, especially devote ones, that saying the Rosary is next to being in heaven. However, I’m a convert, and I don’t have the same connection to it that they do. I’m not saying they shouldn’t continue with it, but I personally prefer a prayer which expresses thanks, awe and supplications more specifically. I do this as my life rolls along, often praying for specific situations.

I’d like to see that happen in our Church families, with groups praying, discussing, and discerning together. Right now, we pray in the mass, which is good, but it sometimes feels like the prayers are done for us instead of including us. I’m not saying group prayer should be done in mass, but it should be part of the community beyond the prayers of mass and the small number of devout people who daily or weekly repeat the Rosary.

Now, I say this having experience with group prayer in other settings, and it takes a lot of commitment and patience. What can happen is that it can devolve into politics, with people praying for their party to win. Members would have to remember the Church is not the same as the state. Another problem is there can be almost as much repetition as with the Rosary, because people pray the same things over and over. This is not necessarily bad, but it is where other crucial elements come in: frank but civil discussion to express individual differences of opinion and evaluate progress toward agreement. The idea is not that everyone has to do everything one exact way, but that if we are disagreeing about serious subjects, we are not hearing God’s perfect will. (We thereby discern what subjects require further discernment.)

Group prayer should focus on listening to God and not to the individual desires of the members. That is where the discipline of discussion, prayer and discernment is distinguished from personal power-grabbing. When discussion reveals that members do not agree, they should go back to prayer and ask God for His guidance. Then, after a waiting period, there would be another discussion and if necessary the cycle repeated until agreement is reached.

And that is where it gets very tough, because many people, including priests and Church leaders, do not seem to understand the difference between what they want and what God wants. Any time anyone disagrees with them, they automatically assume they are right and the other is wrong. This is the very reason for the desperate need for discerning prayer in the Church family, as well as the male-female-child nuclear family.

Being the optimist, I think that prayer such as this is possible though it takes faith and great patience. In fact, it is a life-time commitment. We’ve heard the phrase, “Families that pray together, stay together.” If the people of the Church could pray together sincerely, specifically and with a heart to listen for God, we could communicate with the Lord and each other. Prayer would include praise and thanks but also supplication for spiritual, emotional, and physical needs, such as those which each family experiences. And on all levels we could seek solutions for problems and help against the temptations of separation experienced by Christians.

I hope to talk about the Holy Family next month. December seems like a good time to talk about family, since we focus on our Lord’s birth. May you have a blessed Thanksgiving and I’ll see you then.

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.

Friday, September 5, 2014

Probably--Not

Naturalistic evolutionists say that specific changes to the gene DNA would not be that difficult by evolution because once the gene has one beneficial change, the organism will out-reproduce others and then subsequent organisms in the gene pool will be more likely to come up with the right combination when other mutations occur. One change is supposed to build upon another. 

Perhaps one mutation in a particular protein will improve the fitness of the gene or the organism, even though research is showing that the more mutations, the more fitness declines.

Unfortunately, when the Darwinists describe evolution to the public, they are often mixing metaphors. One example they use is a string of nonsense letters which slowly changes to a readable sentence. The changes are supposed to play out in the DNA, where the mutations take place. This model leads to a lot of confusion. A very short word is pictured here to show an illustration of their model.

To give some background, inside our cells some areas of DNA are copied for the production of proteins (known as coding DNA), and some areas of DNA are not (known as non-coding). The coding areas must have very close to exact sequences of the sub-units, called "bases," in order to produce functional proteins. Previously, before the latest results of the Human Genome Project (ENCODE), it was thought that non-coding DNA was “junk” from millions of years of evolution, and could mutate freely in order to experimentally produce entirely new proteins. However, the ENCODE Project showed that these areas also have important functions, such as regulation and organization.

The evolutionists have been fighting the ENCODE results and still claim that accumulation of mutations in the DNA leads to selection of the fittest, so that the reproduction of organism with the better changes gives a bigger pool of the better genes. This is supposed to then mathematically reduce the number of “tries” for the gene to get it right and therefore the gene does not have to go through a completely random series of changes until it produces a functional protein.

The naturalistic evolutionists use the nonsense sentences to represent both coding and non-coding DNA at different levels. This mixing of metaphors is important since evolutionists use the computer simulations to make people believe that evolution is easy. They start with the nonsense sentence, and when a letter randomly becomes “right,” it sticks (in my short word illustration above, the “A” sticks once it appears). The computer programmer knows what letters should accumulate in order to get the end meaning and manipulates the letters to stay where s/he wants them. For many of these changes, the sentence is still nonsense. Only at the last few changes will you figure out what a sentence says. And in the word illustration, there is no reason that A should stick until the whole word "CAT" is present, with this functional word representing a functional gene.

At first they are saying the nonsense line of letters stands for individual sub-unit bases in the “junk,” non-coding DNA which can mutate freely. But as soon as one of the letters is right, the single letter stands for an entire set of coding DNA that is a workable, superior gene. This gene is supposed to be selected because it makes the organism more fit and that is how they justify the “sticking” of the letter. But a string of nonsense letters can NOT represent a gene that has to code for specific proteins because these gene sequences have to be fully functional in the very beginning of when protein’s biological function in the organism exists. And to make one letter stand for a whole gene that is selected because it improves the organism is to change the metaphor.

Evolutionists want you to think the working genes came about this way, but the nonsense letters can only simulate “junk” DNA that is not used by the organism and can therefore make “tries” for functional proteins with each mutation of the next generation. Nonsense DNA does not produce the functional proteins needed in life from the very beginning. The systems are things like photosynthesis, citrate cycle, carbon fixation, and glycolysis, to mention a few.  And if you start with a meaningful sentence and change letters by chance, you will see how quickly the sentence becomes unreadable and therefore represents a non-functional gene.

In journal articles and places like Wikipedia, those who insist on evolution often say something like: this or that system “is very ancient in evolution” or “was evolutionarily early.” Yes, they would have had to be early all right—like from the start. There are no partial enzymes here trying to work up step by step into working enzymes. And they did not come from previous systems and reform for these jobs, as so many evolutionists claim about functional proteins, because there were no previous systems.

The mixing of metaphors can confuse people when scientists write articles about the origin of life and how chemical reactions can take place in “natural” settings like oceans. It is true that different biological molecules don’t need a cell in order to combine with other molecules and either break or combine into something else. But for them to produce the right products, have the side-products removed, do it in the right time-span and concentration, there needs to be pretty much coordination. Otherwise, why would the cell bother to use so much energy to make the protein enzymes that are now found in all living things? And that they are fully present now means they must be accounted for.

The second image shows the process of one of the systems, glycolysis. This is the breakdown of glucose, which is made from the products of photosynthesis and is critical for the cell's energy. (I describe some specific proteins of photosynthesis in my booklet, Creation Biology.) Each step in the chain of events needs its own protein enzyme. The first enzyme in some bacteria is glucokinase (others use hexokinase as marked in the second image). Glucokinase is pictured in the third image. This protein has 355 amino acids in a Cyanobacteria species, supposedly one of the first organisms on Earth. That would require at least 1065 DNA sub-units (bases) in close to exact order (I say "close" because there are usually some substitutions tolerated). Since there are 4 subunits, the number of possible combinations for the 1065 DNA sub-units needed for the protein is 4^1065, which in more familiar base ten is about 10^640.

Many proteins and the counterpart DNA sub-unit sequences would have had to be there in close to exact order from the beginning. As I show in Creation Biology, even if all the atoms of the Earth were lined up in strings of bases, it would be vastly improbable for even a short protein to form.  Though it might be hard to believe at first, if you follow the numbers you can see that the beginning of life AND evolution by chance are virtually impossible by the natural laws we know now.

Evolutionists don’t seem to like Creationists using probabilities to disprove evolution. But they are the ones who insist the functionality comes by chance mutations of DNA, so they are the ones who introduce the concept of probability in the first place. The facts used here are from data given to us by the scientific discoveries already accomplished. Though our knowledge of science changes through the years, what the public needs is a clear picture of what the facts are telling us right now. The question is, why isn’t the public receiving it?

Friday, August 1, 2014

Creation Biology

It is another First Friday and I am posting this time about Creation Biology, the title of my new booklet and video PowerPoint presentation. They are now available at the link of the same name right under the top blog picture here at womanatwell. I have put them 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 these are works in progress. I’ve re-done them already a few times and will probably continue to edit them if I think of ways to explain the facts better.

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 all types directly and supernaturally? 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 Lemaitre, 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 and/or watch the video. The video is about 45 minutes long and may be the best way to start if you don’t have a science background. The booklet can be downloaded and has direct links to references.

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.

Friday, July 4, 2014

True Freedom

As I add this post, it is July 4 and I wish all of you a blessed Independence Day. It is First Friday as well, our monthly renewal of devotion to the Sacred Heart of Jesus.

This past Monday we had an important decision made by the US Supreme Court. It has ruled on the case brought up by Hobby Lobby and other companies against the Affordable Healthcare Act known as Obamacare. The company owners objected to supplying employee insurance which includes coverage of abortion and certain types of contraception. Many see it as a ruling about whether companies can claim religious rights in this country in the same way as individuals.

As you may know, the court decided that closely-held companies, such as those with family ownership, are not bound to supply their employees with benefits to items which the leaders of the company find morally objectionable. However, the Hobby Lobby ownership is not opposed to contraception as long as it has no possibility of aborting a newly formed embryo.

This seems reasonable but things are not always as simple as they seem. I don’t know much about business law, and I just read an interesting perspective from Fox News Latino by Raul Reyes which I link here. He claims Hobby Lobby sells many items made by China, a country with enforced limits in the number of children a family may have. He brings up other interesting facts and links to Latina organizations who seek to maintain the coverage for contraceptives in order to help against poverty (and this includes millions of Catholic women).

A “yea” for the decision was also found at Fox News by Robert Jeffress, a prominent pastor. The link is here. He cites other cases and mentions the pertinent fact that Americans should not be forced into supporting abortions if it is against their religious beliefs.

Many objections to this ruling tend toward the question of women’s rights more than religious rights. Much as I support women’s equality, there seems to be a disregard for whether the embryo is killed or not. A better answer is needed and at the least women need contraceptive products that will not cause abortion. But until then there are barrier contraceptives which are fairly cheap and though not as convenient as pills, a lot better in that sense than Natural Family Planning endorsed by Catholic leadership. Barrier contraception keeps the sperm from fertilizing the egg and therefore no abortion is involved.

When we evaluate political priorities, religious freedom in our country is one of them. It is how that works out for the best that is not always clear. Yet there is another even more important religious freedom, available to all individuals. Jesus Christ frees our bonds from the slavery to sin. Some may think that sounds strange, but those who have had this experience know exactly what I am talking about. Our humanity is imperfect, and though we can desire good things such as harmonious relationships, we also want many of the wrong things. We often seek to fulfill our desires to the detriment of others, want more than our share of money, and spend it on the things that purposely attract the envy of others. But when we surrender to Christ, we are released from these desires, and therefore feel the weight of needing these things fall away. Now, I am talking in general terms, and not all alcoholics are instantly released from their desire for alcohol (although I have heard that some are). People can become Christians and still have many faults. But some things do change right away, and I can tell you from experience it is plenty sufficient to notice the internal difference.

If, instead of turning to Christ, we persist in holding on to our personal shortcomings, we move on to the level of group failure when trying to work with other people of the same sort. This leads to never-ending strife. We start to wonder how we can find not only a common answer to each question but the right answer. Since Jesus Christ frees individuals from the bonds of sin when they repent, accept Him as their Savior, and give themselves to Him, does He also free human groups from collective sinfulness? I believe it is perhaps possible at some level, because the right answer is God’s answer. His is the true wisdom. This answer would be a spiritual one, though the political scene would certainly benefit. It would be enlightenment for loving our neighbors and enmeshing our various unique gifts for the benefit of all.

I have had experiences where I’ve sought His answer and things happen that are not only clear but ingenious and joyful. It is hard to describe but the way forward is opened up, at least until the next challenge arrives, where I again seek His wisdom. 

Remember the verse:
“…if then my people, upon whom my name has been pronounced, humble themselves and pray, and seek my face and turn from their evil ways, I will hear them from heaven and pardon their sins and heal their land.
2 Chronicles, 7:14, NABRE.
Like political freedom, spiritual freedom isn’t always easy, for individuals and groups as well. It is a long journey to get to the right place and we can be on the right road for a while but sometimes take dead-end detours. If we seek Jesus, He gets us on track. Though Church leaders and members are sinners, with Christ our whole outlook and our very being can change. Individual inner freedom is a glorious thing. It would be great for all Christians to get together and seek it for the collective body.

Friday, June 6, 2014

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: 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. The link for the paper is here and the reference is: Tokuriki N, Tawfik DS. Stability effects of mutations and protein evolvability, Curr Opin Struct Biol (2009), doi:10.1016/j.sbi.2009.08.003 .

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 are results found in the long-term evolution studies of the Richard Lenski Lab at Michigan State.

Proteome discoveries:

A news release from Johns Hopkins University titled, “Extensive Cataloging of Human Proteins Uncovers 193 Never Known to Exist,” 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 abstract, reported in the journal Nature on May 29, is here. 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 saying things like this 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. 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. 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. 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.

Sunday, June 1, 2014

Mission: Faithful

Back in the day, as they say, I wrote my first book, Mission: Faithful. I self-published it, since it is not the kind of book many publishers, even religious ones, were interested in. Though the book is an action-adventure fiction, the underlying themes are about unity of Christian denominations and discernment among Christian individuals. Unity has not seemed to be a priority of denominational publishing houses. Perhaps that will change now that Pope Francis is actively encouraging it.

At the time, Barnes and Noble was open to promoting local authors, and I am thankful to have had a book signing at our nearby store. It was attended by friends and relatives, most of whom had already received the book free from me. To say I am not a dynamic marketer is a vast understatement, and I sold very few. So, I gave several to local libraries and a few to others and more or less called it quits.

At the time I published the book, printing businesses had not yet gone to digital publishing. They were using the old way of making a typeset proof or whatever they called it, and printing from there. The initial setup costs were high but the printing lower, so the more books you got, the less they cost each. However, I knew I would probably not sell many, and did it more for the promotion of the ideas than to make money. I did not want to order a large number. Unfortunately, my husband was of the “less cost per book” mindset, so we ordered one thousand of them.

I don’t know exactly how many I had left after my efforts at distribution, but it was a lot. I made room in the basement for all the boxes and they have been there for a long time. Somehow, this experience did not dampen my desire to write, and I self-published a fictional mystery, Unto Others, in 2008. Fortunately, by that time our printing businesses had acquired digital, print-on-demand capabilities and I ordered 100 paperback copies of Unto Others. I loosely followed the same pattern as the first book in my marketing, but this time did not have so many left over. This book also can be found at local libraries. I was not making money on it, but when I occasionally checked the status in the various library catalogs, I was pleased to find it was often checked out. At least people were reading it.

In the time since then, the digital age has truly come upon us, and people are reading books right from the electronic files. I’ve decided to self-publish my most recent book, Biotech Swirl, in the ePUB format, and plan for now to keep it at that. Boy, does that reduce costs! However, since it isn’t in a library, my quandary was whether anyone would ever hear about this book. It’s on my blog, but this is not a high-volume traffic kind of place.

So, I decided to take the extras of my first paperback, Mission: Faithful, and wrap one at a time in a plastic bag with a half-sheet filler that gives my blog address and pictures of the other book covers. I decided to place them in the community one at a time so that people can discover the free book inside the bag, read it and also be aware of my blog.
However, just after I started to place a few per week in various locations, I learned about the rich person who is anonymously placing envelopes of money in San Francisco and tweeting clues of their locations. It seems to have created a fad across the country where various groups and individuals are copying the idea (article about it here). This threw me off because I wondered if the people who found my book would have heard about the money envelopes and be disappointed at the lack of cash.

So I added a text box to the filler in which I quote a part of Proverbs (from BibleGateway). It talks about wisdom being more valuable than silver, gold and rubies. I remember reading that when I was young and it somehow stuck. As I get older, I increasingly appreciate and believe the words. In case you can't read it in the entire filler above, I have a separate image of it here.

Though we might have varying opinions on specific aspects of wisdom, I hope my books are wise, especially in the sense that I try to bring out, through the characters, ways our relationship with God affects our lives. The books are meant, like many fictional stories, to provoke thought about deeper things.

I wrote Mission: Faithful on a computer program so old that I would have to re-type it to make it available digitally. I am not planning to spend the time on that, but I have put Unto Others into accessible digital form. I also have a few non-fiction booklets available on the blog. The names are lined up as links under the top picture of the blog. You can read and download any or all of them, which I heartily encourage.

To clarify, I am not sending electronic clues like the millionaire to find my book. I don't tweet at all--I figure one Internet interface is enough for me. I just put each book in its individual bag at a variety of places where people eventually go by and hope it catches their attention. And when you talk about marketing, that is about as high-pressure as I get.

Friday, May 2, 2014

Biotech Swirl

I am happy to present my new fiction book.

Biotech Swirl is a medical mystery thriller set in the current explosion of biotechnology.  The Catholic Chaplain Jan Pace is pulled into the dark side of scientific research when Dr. Hunter Balik suspects dangerous genetically engineered bacteria in several of his patients and asks her to help him investigate. Though she is not a medical expert, he feels she is trustworthy and he frankly needs a friend. As they proceed, they fear bioterrorism but the crimes seem personal and murder can’t be discounted.

Dr. Balik, who practices at Fenwood Hospital in West Michigan, has a harsh bedside manner and has made no time for relationships. Though he resents the workaholic habits of his physician parents, he is repeating their mistakes. As Hunt and Jan work together, she attends to his spirituality as much as investigating the mystery.

Though the story starts with a medical crisis, the plot leads to persons with the tools and know-how to manipulate genes and with disturbing disregard for life. The suspects include a biotechnology business director who desires her company to embrace human embryonic stem cell research, a professor who wants to develop made-to-order genetically enhanced babies and an in-vitro fertilization clinic manager with questionable motives for disposal of the unborn.  The reader encounters today’s culturally misguided sense of “bioethics” through these and other characters.

Dr. Hunt Balik starts on this dangerous investigation without friends or faith. Jan Pace confronts potential terror. Somehow the two of them must summon the courage to overcome the deadly threat.

Please enjoy this new medical thriller for free! Just click the link below the main blog picture or on the right column and go from there. It is in ePUB form, and if you do not have a program for that, I have a link to the free Adobe Digital Editions.  This program is worthwhile to have since it can be used for borrowing digital library books and reading classics available at various online sites.

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 large, 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, since all reactions in a 14 billion year old universe are less than 10^150. 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 though they say evolution, they imply that biology SEEMS RANDOM when biology 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 to provide the specific order that is necessary for fully functional biological systems. Therefore we can’t say meaningful evolution seems random because only very small changes have been shown to produce new function when it is possible. 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 R. 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 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. If you download and need a reader program, 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.