Thursday, January 31, 2013

Beneath the Surface

I am adding another post to my blog about the subject of biology. This is not to confuse you but to hope you appreciate the vastly complicated interactions that must take place in order for life to occur and proceed. Evolutionists talk about fossils and bones, but beneath the surface of individual bacteria, plants and animals is a vast interacting world which must function in order to get life going and continuing.  I have a few pictures below to give you an idea of these activities.

Did the organized biochemistry of life happen by totally materialistic, naturalistic means through chance? On one hand, the current theory, called “neo-Darwinism” claims that natural selection, known as “survival of fittest,” is not by chance, but comes about by competition of those who reproduce. But on the other hand according to the same neo-Darwinism, any superiority of individuals depends on random mutation of their genes. They can't get away from the fact that materialistic evolution is ultimately based on chance.

Neo-Darwinism is not better and is actually less logical than the belief that God made species directly. I wonder sometimes what evolutionists are thinking. In fact, I’ve got to believe there are many scientists out there who are not saying much publicly but must seriously doubt whether totally materialistic, naturalistic evolution can be true.

That is why I am taking the time to show you some of the facts. Though I’m not an expert in cell biology, I have a background in biology (I graduated from two universities with a BS in animal science and a VMD in veterinary medicine). I have spent a lot of time reading scientific research on genetics, biochemistry and cell biology.

My last post was about the complexity of the cell’s energy-making system. But, it was actually only a part of that system. Another part is needed to process food we eat in order to get pieces of it to feed into this system. In humans, the process is known by a few names, one being the citrate cycle .

Chemical interactions between molecules are the underpinning of biological function. The molecules are made of atoms, with which most of us are familiar. The air we breathe is made of various atoms, including oxygen. These combinations of atoms are often described with terms we don’t recognize unless we study them, but we can still understand some concepts without knowing all the names of the molecules. There are more and more databases of information about biology and other disciplines available. Scientists add to this data from their discoveries and use it for further research. A lot of the information is accessible by Internet, which is a wonderful service to scientists and anyone else who wants to learn.

One of these databases is called Kegg, for Kyoto Encyclopedia of Genes and Genomes. I had a picture of part of the energy system from Kegg in my last post. Here I will show an overview map (picture 1) of the biochemical activities of cells which they have put in their database. (You don’t have to go to the website since I have a picture here of what you would find, but if you want to go, you can click on the "overview map" link.  You can also click on the picture here to get a larger view.) The paths contain biochemical reactions for various species.  For example, it describes how the body processes things like fats and proteins that we eat. These chemicals must have precise coordination of molecules for fitting together and producing the desired outcome in each species.

The map does not nearly cover all the biochemcial reactions that exist. In fact, the current estimate for the number of species on Earth is over 11 million. The National Institutes of Health did a 2008 study on the single-cell organisms of bacteria and what are called archaea (are-KEY-ah). They found that “remarkable biochemical diversity is a hallmark of bacterial and archaeal biology.” So you can be sure there is much out there that is not yet on this map. These are the chemical data that the people who do the map know about and have inserted.

The citrate cycle is a small portion of biological metabolism. In the overall map, the cycle is named inside the small round blue line in about the middle near the bottom. If you go to the Kegg site and click on the “citrate cycle” name, it will bring you to a chart of the chemical reactions that happen in the cycle. I have a picture of the human citrate cycle here (picture 2). The green boxes are links to further information about the human biochemical reactions. They show facts about the proteins called enzymes (EN-zimes) that work to change molecules within the cycle so they produce the necessary segments for energy production.

Don’t be concerned if these terms sound foreign to you. I’d just like you to get an idea of what goes on in our bodies. One of the green boxes shows the number 4.2.1.3. This is a protein enzyme called aconitate hydratase (ah-CON-ih-tate HI-drah-tase). If you click the box at the Kegg website, you get information, with more links, about aconitate hydratase.  The rectangular box here is what you would see (pic. 3).

The box contains a picture of the protein. I want to show you a similar, larger picture from another database of the aconitate hydratase protein as they use it in models. The last picture here (picture 4) is from Swiss Model Repository, which is a database that shows the 3 dimensional models of proteins. The swirls and arrows show the types of folds that the amino acids make in order to form the protein so it does a specific job. This protein is made up of 780 amino acids which must be in a particular order (if you are interested in more details of the protein, you can get them at yet another database, Uniprot ). At the bottom of the third picture, there is a list of amino acids that make up the enzyme that we are talking about. (For information on amino acids, go here.)  For purposes of saving space, I did not add the bottom section of the box, which lists the specific order of the DNA of the protein's gene.

If you have gotten this far, I appreciate that you have been interested enough to read about the complexity of cell biology. It is important because of what I’ve been talking about concerning the question of neo-Darwinian evolution and whether it actually happened. Though you may hear some scientists or their spokespersons say evolution is a fact, the possibility and reality of it is something you have to decide for yourself.

Thursday, January 24, 2013

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 and 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 picture comes from a database called Kegg, standing for Kyoto Encyclopedia of Genes and Genomes . 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 middle has a B on it for beta subunit (beta is Greek for “B”). Proteins are made of yet smaller units called amino acids (ah-ME-no acids). 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):

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 . Each letter stands for an amino acid, such as A for alanine:



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.

Saturday, January 19, 2013

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. I was upset at first, but I realized I probably had them here long enough. Sometimes we plan for change and sometimes it just happens. I know there are ways to protect your documents on the web, but I have them on my own backups and I can use them if I want to. Maybe this will prompt me to modify the whole style of the blog, although I'll be afraid I'll erase all my posts. I did delete some of the old posts that had to do with the booklets.

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 Pew Research Center survey of scientists showed at least half have some sense of spirituality. It was interesting that the religious leanings of scientists have remained very close to what they were about 100 years ago, as reported in the link. 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 man’s wisdom in 1 Corinthians:

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. Here is a link to one of them, called "Journey Into the Cell," by Dr. Stephen Meyer of Discovery Institute.

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.

Friday, January 11, 2013

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, 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 Georges Lemaître vs. Albert Einstein. 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 20’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, 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. The same happens when scholars such as Richard Weikart tie social Darwinism with eugenics and roots of the Nazi holocaust.

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. As some scientists already admit, for some time they actually avoided studying parts of DNA that are now proving to be crucial to the cell and to our health. They were told by evolutionists that these parts were only “junk” left by the evolutionary changes over millions of years. Now a big scientific study, named ENCODE, has shown at least 80% of DNA is functional 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.

Sunday, January 6, 2013

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. (And yes, Catholic women do have abortions.) 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 panel of persons 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 (Humanae Vitae, 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 about the Jesuits. 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. 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 apparant 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.