Cell Biology

When you start learning biology, there are new terms. With computers, your job, and/or your school, you learn new things all the time, so you are already acquainted with the activity. So I hope you will be open to learning about cell biology. It is a fascinating subject, and well worth the time. Perhaps you already know biology, but I hope you will still look at what I have here.

There are an estimated 75 trillion cells in the human body (and trillions of atoms in each cell). From bacteria to humans the cell is the basic unit of biology, and its activities are called “metabolism.” The cell absorbs and stores food, then breaks it down and converts it into energy. It uses energy to reproduce DNA (genes) and assemble proteins among other things. The DNA is used as a code for the proteins  which in turn do the work of the cell and the body. For example, your muscles have muscle cells which contain muscle proteins that contract and relax. They are called by specific terms, but we don’t have to name everything to get the overall perspective.

One of the basic parts of the ongoing process of metabolism is where several groups of proteins are embedded in a membrane of of the cell. The membranes are in folds, and in humans the folds are parts of what are called mitochondria (mite-oh-CON-dree-ah). First I have a short video (less than 4 minutes) for you to see how one of the groups works to form the energy molecule called ATP. ATP has chemical qualities that give it the ability to use a chemical bond for activity needed in the cell as I described above. It changes to ADP when used up, then is re-cycled back to ATP by this complex. You may hear some terms you don’t understand, but just try to get the concept of this series of steps going on in most of your body’s cells.

The video is done by North Dakota State University which has done other animations you can see HERE if you want to learn more. As interesting as the above video is, the protein complexes are drawn rather simply. Below is a more detailed picture of a series of complexes needed to make the last one, ATP Synthase (SIN-thase), work. They are needed to produce the electrical gradient which is described in the video. The mitochondrial membrane is pictured between the complexes, with ATP Synthase at the far right.

The image (link HERE) comes from a database called Kyoto Encyclopedia of Genes and Genomes (KEGG). The boxes in the picture give information for various parts of the complex when you click on them at the KEGG website.

Now, please stick with me a little longer to get more of the perspective of how complicated this series is. In the picture, the last group of proteins on the right is ATP Synthase. On the bottom part, there are blue-colored sections. The darker blue have a β on them for beta subunit (beta is Greek for “B”). Proteins are made of yet smaller units called amino acids (ah-ME-no acids, Wikipedia entry HERE). These are repeating groups of atoms, including carbon, oxygen, nitrogen and hydrogen (C, O, N and H). Here is a picture of one of the 20 types of amino acids found in biology, called alanine (AL-ah-neen):

Carbon is also understood to be in the angles of the molecule image. The types of amino acids need to be in correct order, according to their size, electrical charge and other factors, so the proteins can fold into the shapes in which they function. It is similar to machine parts which need to have the right shapes to fit and move together. Now I have just one more picture. It is the list of amino acids in this one part of the whole complex, the beta (B) subunit of ATP Synthase as pictured above. This particular one (human) has 529 amino acids, as listed in another database called Uniprot, entry P06576. Each letter stands for an amino acid, such as A for alanine (letters can stand for different things depending on their context):

All the proteins parts of this entire complex are made of various arrangements of the amino acids. Many are at least 100 amino acids and some are many more, as you have seen. These need to be constructed and put together within most of the cells that we have. There are many such complexes within each cell.

Thank you for bearing with me to learn about this part of cell metabolism. Remember, this is only a very small fraction of the complexity in the cells. Even small organisms need energy systems such as these to put together their own genes and proteins. Please think about whether this could have come about by chance, no matter what the time frame. After all, a computer would not form on its own, no matter how many billions years pass, and that is not nearly as complicated as we are.

Science and Culture

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

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

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

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

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

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

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

For it is written:

“I will destroy the wisdom of the wise,

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

(1 Corinthians 1:19 NABRE)

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

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

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

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

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

Special Creationism

It seems professionals and teachers in many religion-based institutions resist Special Creationism because they have a deep fear that they will not be perceived as savvy scientists in all respects. By "Special Creationism" I mean that God made biological species directly and separately, not relying on what we commonly mean as Darwinian evolution. I do not tie Creationism in with a literal time period of six 24 hour days, but am aware that many Christians do so.

“Remember Galileo!” seems to be the motto of Catholic educators, which is only an echo of the non-religious scientists’ same outcry. The phrase refers to the 17th century struggle between Galileo Galilei (Wikipedia biography HERE), with his theory of planetary rotation around the sun, versus the Catholic Church who understood the Earth to be at the center. As the account is usually generalized, Galileo stood on reason’s side while the Church stuck with medieval superstition. The implication is that the Church always represents pre- and anti-science and knowledge will prevail. Of course we must ignore the fact that Galileo was and remained a Catholic despite the tensions.

But you don’t hear as much about Monsignor Georges Lemaître (HERE) vs. Albert Einstein (HERE). Maybe the name “Lemaître” seems too hard to pronounce (actually, I think it’s leh-meh-treh). Lemaître was a Belgian Catholic priest who taught physics back in the 1920’s and 30’s and came up with what is now called the Big Bang theory. At that time Einstein thought the universe was eternal and he was already recognized for his brilliance in relativity and other matters. Lemaître had the temerity to oppose the well-known genius. Who do you think people believed? Who did they laugh at? But after scientific experiments by Edwin Hubble (HERE), the scientific community, including Einstein, came to accept Lemaître’s theory of a definite beginning to the universe and subsequent expansion. What about reason and superstition here?

Our country is going through collective trauma due to acts of violence against innocent citizens, now including young children. There is government movement to control guns in some form. There is talk of making changes in the quality and availability of mental health resources. There is a discussion about the violence of video games and movies. Hollywood has made the shocking admission that maybe they contribute to the aggressive mindset of young people. Allegedly the man who killed children in the Sandy Hook Elementary School immersed himself in violent video competition.

I remember when people laughed at the suggestion that harm could come from violent TV, movies or video games or nearly unlimited gun sales. Concerning these issues, many people are no longer laughing.

You may ask what this particular problem has to do with evolution or creationism. I admit any connections may not seem apparent at first. But there comes a time when things that lie vaguely in the back of the mind must be looked upon and analyzed. Otherwise, something very important is missed when other themes are addressed.

Like the situations above, people often mock certain religious groups, often fundamentalists, who blame the prevailing materialistic evolution theory on some of our country's problems. For example, see this story by Ken Ham, "The Rest of the Story--Exposing Misquotes by an Atheist Professor," Answers in Genesis (April 23, 2010).

Most adults are not experts on evolution. Some accept what the scientists tell them and don’t think more about it. On the other hand, some believe God made animals and humans directly and don’t think evolution happened at all.

Others, including many Catholics, have vague ideas about how God may have guided evolution. They partially realize the vast differences in species which are supposed to come from each other, and the commonalities of those which are barely related. They hear news snippets about the wondrous discoveries of the complexity of cells, organs and whole biological systems. But they were told in elementary school that some bones found in Africa were pre-humans and we all came from that. Experts still say evolution is true. It all gets mixed together, with no cohesive outcome or plan on what to teach children. Except for home-schoolers, parents leave evolution to the current educators.

Totally materialistic evolution is the theory that all biological life came to be by chance. That is, random mutations of genes and natural selection which depends on the random mutations, have brought about all biological function and variety as we know it. For the most part, this is what is taught to American children from the age they can hold toy dinosaurs in their hands. It persists through college and is now vehemently defended by science groups and professors. More importantly, they insist evolution is without any intervention from the supernatural.

Theistic evolution is an attempt by some persons who belong to various religions, including Catholicism, to integrate the theory of evolution with theology. There are a few different forms of it, but most start with one common ancestor to all biological life and follow pretty much the line of totally materialistic evolution theories. When you look at so-called theistic evolution closely, you don’t really see God at all. In this way the professionals try to save face. It seems they don’t want to insert the supernatural into their theories because that would not look good to the secular world.

It is very hard to change certain ideas when we have been taught them from early childhood. It is harder when many professionals insist something is true. But paradigm shifts in understanding have happened, just as in the Big Bang theory. Some scientists, too entangled in the old ideas, die without accepting new proposals. But some theories persist that at first seem very strange. They are then accepted almost unanimously by the next generation.

Evolution theory, or the proof against it, is not just about bones and beaks anymore. It is about observing the complexity of the biological world and asking how it could have come to be. The academic discipline of cell biology combines with physiology and interacting molecular systems. That is what we need to know to make logical conclusions.

You might say cell biology is too difficult to teach to children. I think that if kids can learn computer terms and directions, they can study cell biology. In fact, adults should no longer let themselves have vague pictures of evolution floating in their heads. They can become students right along with their children.

There are many digital enactments of cell activities. New discoveries are being made every day of which adults should become aware and share with the family. Which is better—for all of us to learn together or to let the kids watch violent movies and play violent games?

Many Americans wring their hands that this country is not keeping up academically with others. When I gave talks on cell biology and genetics to various groups, they were amazed. One college-age person kept asking why she was never taught these things. An engineer in his 70’s exclaimed he had never studied biology and had no idea of the facts I presented. The education of Americans has been heavily influenced by materialistic evolutionists, with their cries that we can’t mix church and state.

Please be aware that the damage done by evolution theory has already taken a measurable toll. Some scientists already admit, as in this article abstract by Laura Poliseno, "Pseudogenes: Newly Discovered Players in Human Cancer,"  Science Signaling 5, 242 (Sept. 18, 2012), for some time they actually avoided studying parts of DNA that are now proving to be crucial to the cell and to our health. Evolutionists claimed that these parts were only “junk” left by the evolutionary changes over millions of years. A big scientific study, named ENCODE, has shown at least 80% of DNA is functional, reported by the ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome,"  Nature 489 (Sept. 5, 2012): 57-74, and some project an even larger percentage. There are major implications for understanding cancer and other diseases.

Yes, others may laugh at the belief that God created us directly. They may mock our suggestions that the logic of Darwinism tells humans our lives are nothing special or worthy of respect. They may chuckle that we even suggest that the American education system is adversely affected by their theory. But you decide whose side you would rather be on.

Discernment 101

In the last post I talked for the most part about two groups of persons, Catholic Bishops and women. I named three topics which are of interest in today’s Church: the child sexual abuse scandal, women’s ordination, and abortion. Of course, it is not a given that Catholic females who participate in legal abortion also favor women’s ordination, and I admit I lumped the two together. (2019 Update: I had statistics for Catholic women with abortions at the time but link no longer available.  2014 Catholic women abortion statistics from Guttmacher Institute website are HERE.) Often we think of those who abort as independent personalities but some are, as I understand, under the pressure of a boyfriend or husband to do so. However, we also hear of females who want their freedom to work or study and feel they don’t have the resources, whether they are time, energy, or money, to have a child.  One expects these types to also desire gender equality. To add to the mix, there are many other issues of contention in the Church today. Among them are contraception, celibacy and marriage of priests. Many issues have caused tensions between nuns and bishops, priests and laypersons.

These themes seem to collide often in discussions of problems of the Church, and are tough to sort out. Of course we are all unique, and anyone could say they think one thing but not another. What we surmise about how people are thinking comes from our own thoughts, the evaluations we read and comments from various sources. In the example above, it seems most women who want equality in all areas of life, including the religion to which they belong, tend to also want the freedom of reproductive rights even if it means abortion. But I myself would like true gender equality in the Church but feel abortion is wrong.

If different people think they are right in totally opposite ways, who is correct? Discernment of the Holy Spirit is difficult, and I think one can be too easily convinced that God agrees with one’s own wishes. Difficulty in discernment is not just a problem for individuals, but for the whole Church. The Church should be the expert in how to discern, and lead and teach its people how to do so.

Most people see that there can be confusion when trying to understand exactly what God wants. Though some say the Bible is inerrant, most notice some contradictions. The existence of many Christian denominations attests to the fact that we interpret Scripture differently. Most of us need the guidance of those who are experts. They gather together to determine the best way forward. The Catholic Magisterium is made up of men who have dedicated their lives to the Church. Though not privy to their meetings, I imagine they pray for guidance from God. The parishes also pray for them. But is it safe to assume that God will give them all they ask for right away? What if the lowly Catholic parishioners, who also ask for guidance for themselves, see things differently?

For example, during the time of Pope Paul VI, a Pontifical Commission on Birth Control (Wikipedia description HERE) worked to determine whether it was allowable for married couples to use contraceptives. They concluded there was no intrinsic evil in using them, but Paul VI ignored them. Some speculate the Pope made a political decision, based on the number of Catholics that could be produced without the barriers. The Pope even made predictions for the problems which contraception would bring, such as loose morals in his Encyclical, Humanae Vitae, (July 25, 1968): Sec. 17. Some contend that the existence today of contraceptives produced by drug companies and other factors, such as television and other modern media, would have caused the loose morals to be about the same today as if Pope Paul had accepted the panel’s recommendations. What the Pope didn’t predict was that his own apparent lack of understanding of a certain group of women would drive many of them (along with men) away from the Catholic Church. And now we are all focused on a “New Evangelization,” which, among other things, is supposed to bring lapsed Catholics back.  While the popes decry the influence of the culture and other external factors for this exodus, they do so without evaluating their own part of the reasons for it.

Perhaps bishops think they have more direct access to God than anyone else by virtue of their standing. But how do they evaluate that God bypassed the religious leaders of the day in order to tell Mary directly, through an angel, that He had chosen her to become the mother of Jesus? Through angels He called the shepherds of the fields to come and see the baby. Christ Himself walked with the lowly and criticized the powerful.

Though I’m sure not all bishops agree among themselves on all the Church issues, the fact that these leaders isolate themselves by not allowing women or married men into their tight circle would tend to limit their range of ideas. Sure they think that the next set of priests and bishops should be just like them. Is that really the Holy Spirit talking?

But I’d like to make another point about discernment. The latest confrontation of the Church leaders with the Leadership Conference of Women Religious (LCWR) is seen by many as old-fashioned bishops against the crusading efforts of social justice by religious sisters. But that is not all that it encompasses. Though contraception, abortion and women’s ordination is part of the contention, it is only a part.  A more important factor is that many of the nuns are teaching contrary to Catholic doctrine in the area of Christ’s Lordship. He is our Savior from sin and belief in Him is the only way to the Truth. Many religious orders are embracing Universalism in which it doesn’t matter what you believe and everyone will get to heaven. What’s worse, these orders are in the forefront of teaching spirituality to the Catholic laypersons, and many of the religious individuals claim to be Spiritual Directors. If a person does not hold Christ as the Lord and the only way to Truth, he or she is headed in a false direction and is in no position to be guiding anyone else. According to Scripture, the Holy Spirit is present in those who believe in Christ:

On the last and greatest day of the feast, Jesus stood up and exclaimed, “Let anyone who thirsts come to me and drink. Whoever believes in me, as scripture says: ‘Rivers of living water will flow from within him.” He said this in reference to the Spirit that those who came to believe in him were to receive (John 7:37-39 NABRE)

These problems did not necessarily start with religious women. There is a good book out by Malachi Martin, Jesuits (Simon & Schuster, 1988). This order, founded by Ignatius of Loyola, had started as a group with the sole purpose of being obedient to the Pope. Perhaps it would have been a little better to have the goal of being obedient to God. Be that as it may, they got off the track, starting with members who began doubting the sovereignty of Jesus Christ. The book talks about the ensuing fights between the order and the Magisterium. In similar circumstances, the Church leadership has contended with liberal theologians.  History reveals that intellectuals can be just as right or wrong as anyone else when it comes to spiritual matters.

Only through Christ and belief in Him can individuals, orders, the Catholic Church and other Christian denominations find their way. There is one Truth and He is The Truth.

In the 1960’s, The Second Vatican Council called for changes in the Church (documents available at the Vatican website HERE). People interpret those changes differently. Some took them to mean we could explore other religions and accept that different cultures believe different things. They think it is more loving to let non-Christian people alone in terms of their religion than to tell them about Christianity. This has been quite apparent with some orders of religious, both women and men.  The very people who think they care for others by keeping them in the dark need to evaluate their own faith and, frankly, be re-evangelized.

The most important issue for Catholics is to believe in Jesus Christ as the Son of God who came down as a sacrifice of atonement for our sins. That is the first step in discerning, together, the guidance of the Holy Spirit.

Conversion for All

On Nov. 12, 2012, Timothy Cardinal Dolan gave a presidential address to the General Assembly of the United States Conference of Catholic Bishops (link HERE). This was shortly after the US presidential election, and was uncharacteristically humble for the Cardinal. The link above is worth reading, although it takes him a little while to get to the point. When he does, you find that he talks about conversion and penance. One would not be surprised if he meant for the people who voted for Obama, an action he and his fellow bishops heartily tried to prevent. But he actually meant first and foremost for bishops themselves.

One may cynically wonder if he had a victory speech prepared with entirely different substance if Romney had won. Though we may wish he spoke more plainly about his motivations for the need for conversion and penance, I think we all know what he meant. The half-year since their last meeting had brought court convictions for Msgr. Lynn in Philadelphia and Bishop Finn in St. Louis for the concealment of various forms of child sexual abuse. Along with the trials came media reminders of the failures of many, many other cardinals and bishops, including Popes.

If Dolan doesn’t know of the animosity many people feel against the Church leadership, he doesn’t deserve to be president of the USCCB. It seems this speech shows he gets it, at least in one form. Now if the words actually translate into action, we might all be a little happier. Penance is one thing, but conversion means the courage to change. Our strength is in the Lord  (cf. Psalms 118:14 NABRE), and we all need to pray fervently for it.

Many people have written about the need for accountability for Catholic bishops, such as defrocking and even excommunication. But a deeper question exists: why are there so few consequences? We can’t say there are none, since in the case of the Legionaries of Christ, the leader, Marcial Maciel, was so horrendously guilty he was finally taken from his post by Pope Benedict XVI. An obituary appears here by Adam Bernstein, "Marcial Maciel, 86; Founded Controversial Legionaries of Christ," Washington Post, Feb. 1, 2008. However, even this took a long, long time after years of his accusers being ignored. But most bishops who passed pedophile priests onto unsuspecting parishes and still hide some of their identities go on with their lives and their jobs while other Catholics are excommunicated for things like promoting women priests.

Though Cardinal Dolan may have had certain things in mind when he talked about penance for bishops, he may himself not understand the deeper reasons for this inability to deal with the problem. Well, of course, we would not be wrong to say it is because of their sin. But perhaps a little more analysis would be helpful toward conversion.

Though I usually like to separate different issues to analyze them, there are some things in common with several themes here: the dismal behavior of bishops in the child abuse case; the desire of bishops to stop abortion (I generalize but believe most bishops want to stop abortion); and their rejection of women in true equality (and by true equality I mean not just nominal or “equal but different”).  The commonality is the way we think about these things, whether we listen to other persons problems and ideas, and what we do about them.

In the abortion issue, the bishops want the potentially aborting woman to consider the life within her and not reject it. This woman has her reasons for aborting, which she thinks are valid: she does not think the fetus is yet a human; she can’t afford it; she is afraid of what relatives will do if they find she is pregnant. However, none of these reasons are valid according to the bishops. They would object in some way: the fetus is a real human; help is available; the family may accept her anyway. Furthermore, they expect these potentially aborting women to listen to their answers.

However, in the case of treating women equally, they have all kinds of reasons why ordination and leadership should not be inclusive: the 12 disciples were men; Christ was a man; Christ is the bridegroom. But there are also objections to these arguments: 12 men represented the old ways of the law of the 12 tribes of Israel, and when Christ arose from the dead he showed Himself to women first and told them to proclaim his resurrection to others; Christ was human and so are women; if only men can represent Christ as the bridegroom as priests, then only women (the brides) should be in the pews.

When Cardinal Dolan asks for conversion of bishops, one hopes he refers, at the least, to the child sexual abuse crisis of the Church. It is good to see some sign of acknowledgement, but the bishops should know better than most that there must be changes in action if conversion is true. This is not just about going to the confessional and a fellow bishop telling them their sins are forgiven. If they expect to be satisfied with that, they are not converted.  They need to think about why they are doing these things and what needs to change for good.

These three issues relate to each group having their mindsets for doing things and whether they can listen to others.  There are differences in how we think about issues and how some things may be right and wrong in each group.  If bishops expect Catholic women who plan to undergo abortion to listen to them (and perhaps even influence non-Catholic women), they should think about whether they themselves accept women as equal or reject them and their ideas. They could start by reviewing their reasons why they keep women in the out-group, and evaluate if these ideas are true theology, or man-made rationalizations which sit among the genuine doctrine.

Perhaps the American political election brought the situation home to Dolan. He finally started, however tenuously, what needs to be done. The question is, how far will he and other bishops go? Because their conversion journeys will be very long and painful for them if they are to be done right.  May we all realize that true conversion is worth the pain, and may we have the courage to do it.

Peace Amidst Horror

In the wakes of Super Storm Sandy (Fox News story HERE) and the Sandy Hook Slaughter (Fox News story HERE), most writers probably feel compelled to write something about them, no matter how inadequate we feel. My sincere prayers and hopes for recovery go to sufferers from these and other disasters, both natural and human-wrought.

Since the Newtown, Connecticut, Sandy Hook Elementary School killings on Dec. 14, there is already the usual talk about gun control. People are very upset and maybe something will change. But people were similarly shocked about the Columbine High School shootings in 1999. We’ve had the same type of occasions since then. We are still arguing about the availability of firearms.

It is human to want to manage events, and in some cases we succeed. We want to make schools and workplaces, not to mention homes, totally secure. Very few can stomach the way the young kids died in the school. We work to do our best in the physical sense so that no one has to endure that kind of end.

But there are those situations which will be beyond our control. We must also work on our attitudes, including coming to grips with the fact that there will be an end to all our lives as we know them sooner or later.

Many are concerned about the Mayan Calendar and the implied end of the world on Dec. 21, 2012, but some people didn’t even make it that long. There are those who are worried about an international economic collapse and are arming themselves, but that doesn’t guarantee survival. You can buy high-powered weapons for self-protection, as did the mother of the Sandy Hook gunman. Her son used her expensive equipment to kill her in her own home and himself in the school.

Christians believe there will be a Second Coming which will end the age as we know it. Though Christ told us not to put a date on this event, it is important to be ready for it in a spiritual sense. Many of us have heard sermons to that effect. But then we go off and seemingly forget how soon the end can come for any of us personally. Each of us should learn now how to follow our consciences and use proper spiritual discernment to determine which of our ongoing plans should be pursued and which forgotten.

The Sandy Hook Elementary School killings and other disasters have shown us that even little children need to know that there is life after death, and there is only one way to have a good one. That is through Jesus Christ, the Son of God who came to save us from our sins. He asks us to believe in Him. This is the spiritual work we each must do, so that the attitude we have will help our actions fall in line with what is important. Once we have the right mindset, we are to help others find it too.

Enjoy the music in the video, by Third Day. Listen to the lyrics. And please, no matter what your circumstances, have a blessed Christmas.

Gain Application Probability

Statistics are being used in the arguments about biological origin and evolution. Advocates of Intelligent Design Theory (ID) are prominent among those attempting to link probabilities of events with mathematical proofs of biological information but they are not the only ones. This post, though dated 12/5/12, is an update (8/27/13) and a new compendium, called Biological Information: New Perspectives, was just released and can be read online HERE.  The book is an overview of the work being done to align biology with information theory which uses probabilities in trying to understand biological systems. Its authors are both ID and non-ID advocates. 

I have a new theory that I present here, but like all new theories, it needs some more work.  In fact, I've come back to re-write this post several times and instead of re-writing it another time, I'm going to eventually post about it again. But, if you are so-inclined, read on.  Then catch up with a newer post called GAP Theory that should appear Nov. 2013.

Mathematics can be applied to reality. Probabilities in thermodynamics and chemistry predict quantities and actions of energy and mass. They exist and behave in a certain way that can be measured.  But human judgment and mathematics are two different things. People rely on their own judgments about many subjects without being experts in probability theory.

It's pretty hard to imagine converting all of nature into strict mathematical terms.  Evaluating a pattern is done by humans and therefore has subjective elements.  Perhaps Information Theory does and will reveal certain hidden secrets about biology.  But I doubt if even chaos theory could give all the answers.

Some examples might be helpful.  A straightforward one goes like this:  someone "blindly" picks all red balls from a bag which contains equal numbers of red and black.  After about 20 times a pattern emerges that is different from the expected 1:1 ratio.  One might suspect the red and black balls have unique surface features which allow discrimination.  Maybe the red surface is more sticky.  But in another example, consider a different type of situation. For a while my husband and I went to the store and they didn’t have any fresh grapefruit. The produce people could not answer our questions of why they were not there, so I looked on the Internet to understand. I found that some of the Southern US produce had been damaged by storms, and Mexico had droughts that affected their exports. What was the probability that a grapefruit would be available by the next time we went to the store? Wouldn't even the experts in distribution have trouble being precise due to the unpredictability of long-range weather? Even though they have their formulas, in certain circumstances they still incorporate judgments.  It is of a different nature than pulling balls from a bag at a particular place and time. 

Included in human judgment is the sense that the extreme complexity of  biology is improbable and not random. (Some would argue here that neo-Darwinian evolution is not random due to “natural selection of the fittest,” but nature needs something worth-while to select first, which is claimed to come from random mutation.)   And yet there exist many things with very low probability, including every hand you get in a card game.  This is where critics come in and say low probability doesn't prove design. Design advocates then refer to "specificity," meaning that specific molecules are needed to perform biological tasks and that the exact combinations of these molecules are extremely improbable.

Specificity implies different values placed on equally probable outcomes. As in the grapefruit example above, I don't think we can always know exact probabilities.  And yet the concept of probabilities still might give us some insight to whether nature itself could have come up with biological function and complexity. In some cases, an evaluation of probability can affect how a person judges an event.  I'd like to talk about putting value on similar probability outcomes.  I'll call it “Gain Application Probability” (GAP).

If you have only one second to toss a coin and it takes 1 second to toss it, you will either get heads or tails (no edge landings or double half-second flips allowed). Each outcome has a probability of one half, and one of the possibilities will occur. In this example, nothing is special about either unless one outcome is assigned to a prize. If a football team calls heads and the coin lands heads, they get to choose whether they receive the ball now or later. If I say I’ll give you a hundred dollars if it lands heads, you will perceive the difference in the outcome.

Now we move on to a dice. You have only one second and it takes one second to throw. I’ll give you a prize (say, 100 dollars) if you get a 1, but not on any other number. Each outcome has one chance in six, but there is still a difference in what happens if the number 1 comes up as compared to the others. The award or denial of the prize is in a related way a measure of the outcome.

Then we take a full deck of cards. We shuffle them fairly and put them face-down on a table. You have only one second and it takes a second to draw the top card. I tell you I’ll give you a prize if the top card that you draw is an Ace of Diamonds. But now you only have one chance in 52 that the card will be the Ace of Diamonds. Is this different than tossing a coin and getting a prize if you get heads? Which would you pick to take your chances?

While we’re talking of cards, it is true that each combination in a game hand has the same probability.  But with a good grouping according to the rules of the game you are playing, you can win the hand. You might win money if there is a pot. You therefore gain with the good combination (if you play it well) more than with the bad.

Amino Acids are molecules that make up the various proteins. They have 20 different forms in our bodies and their various properties make their different combinations unique. The chances for one amino acid combination to occur might be the same as another, but if only one in 10^70 will help to break down a food molecule to produce biological energy while the others in that number don't do anything biologically active, then to me that one protein is different from the rest. If there is function for the few molecules among so many, I would apply a value of gain to those which can carry out biological tasks.

These examples demonstrate, in my term given above, Gain Application Probability. To say there is no difference between certain low probability events is to ignore the possible results. We can deliberately attach an extra benefit to an outcome or we may observe a benefit which comes naturally. We can evaluate events of low probabilities in relation to the gains they bring.

I think we can reasonably say that some improbable outcomes have more value than others. And the lower the probability and the more we gain, the greater the value. One might also be able to apply loss and neutrality to probabilities (LAP and NAP). After all, there is a losing side to a football coin toss, and many improbable events have no appreciable effect. And I suppose that zero times GAP is ZAP.

You might say Gain Application Probability is as subjective as other biological information theories (if you are a critic of these theories).  But I’m not claiming to entirely eliminate chance. I don’t even want to quantify the values of gain and loss. I think there is worth in acknowledging that values can be applied differently for different probabilistic events even when they have similar probabilities. And some outcomes are so valuable that our human judgment can take over to tell us they did not happen by chance.  So it is with functional biological materials made from combinations of molecules.

The value put upon the probability outcomes is a dimension above the science of nature.  When you have faith, you can still be scientific and yet not get bogged down by needing all-encompassing mathematical and scientific proofs.  Faith is given to us as a gift (Ephesians 2:8-9 NABRE).  This is a mystery which transcends our understanding.