Tuesday, April 28, 2009

Bishop Lugo 1

If you've been following my blog, you know I try to describe biology and show how complex it is. I explain Intelligent Design Theory and how Charles Darwin's descriptions of evolution are showing to be incompatible with the new findings in science. I intend to continue ID once a week, probably Fridays, continuing with the cell membrane. But I've also said that I will eventually talk about other topics, and that time has come.

I am in favor of ordination of women in the Roman Catholic Church, especially as Deacons. I'll describe some history of Deacons in the Church as time goes by, but first I want to get to the reason I'm ready to pursue this subject.

This week outrageous revelations concerning former Bishop Fernando Lugo of Paraguay has made its way to the headlines. If I had written a novel describing his story, no one would call it believable. Now, I could write a novel-length discourse on how terrible can be true life.

Lugo first made his appearance in international papers when he became a candidate for the presidency of Paraguay. He came into conflict with the Vatican then, as reported by Catholic News Service. He was a Bishop who supposedly cared for and supported the poor, and was associated with the Liberation Theology movement. He won the presidency, taking it away from the ruling power of many years. He celebrated his victory with Hugo Chavez on the stage with him, singing "Cambio, Todo Cambio," a theme song of the leftist movement of Latin America. It means Change, Everything Changes.

And now, as reported by the International Herald Tribune, he has admitted to being the father of at least one child, with two other women saying he fathered theirs also. If true, at least one would have been born while he was an active bishop. To make things worse, a fellow bishop has admitted that Lugo's actions have been known, but not made public, by Paraguayan Church authority for some time (same article).

I ask you, is truth not stranger than fiction?

I am very distressed by the recent revelations. It is a sham to say you stand for the poor when you oppress them yourself. One woman stated that he took advantage of her through knowledge of her great material need. And then there are those who knew about it and covered-up. Did they not warn other young women of this predator? Did they not inform their fellow citizens who were asked to vote for a man who said he stood for the poor and yet, unknown to them, repeatedly broke his vows?

I try to be careful to avoid false logic. Though many would argue this tragic situation has nothing to do with women’s ordination, I believe in this case it does. The lack of equality in this area of the Catholic Church leads to a less respectful attitude on the part of individuals. I believe it contributes to an attitude that pervades all cultures, some more subtle than others. The Church authority calls on others to treat women fairly, but the Church has no equal in its own obligations and potentials in that regard. And yet it continues to insist on interpretations of the Bible which, whether or not sincerely believed by those in Church power, are too comfortable to those same persons to prompt re-examination. Many people have spent their time and energy into changing this 2000-year-old problem. I must join them, and we will not stop until it is solved.

Friday, April 24, 2009

Cell Membrane 1

Cells are the basic biological unit. Humans have an estimated 75-100 trillion cells. Our skin, our lungs, our liver, our eyes are made of cells. The cell membrane is the outer lining of the cell which keeps the inner workings compact and separated from each other and the outside world.

I'm going to spend several posts talking about the cell membrane, because it leads to some very important conclusions as to whether the cell, and subsequently life itself, could have come about by chance. Several subjects need to be considered concerning the cell membrane, including the environment inside the cell that is needed for its biochemical processes to take place. For example, the level of acidity, usually called pH, is critical for these chemical reactions. If the cell is too acid inside, the balance of particles, such as the hydrogen atom, proton and electron, will not be maintained at the proper levels.

In the picture at top, the layer in light blue is called a phospholipid bilayer. Lipids are fats, and two fat molecules (long strings) are attached to a molecule called a phosphate (chemical name for specific arrangement of phosphorus atom with oxygen atoms). The bilayer means that 2 rows of phospholipids line up with the fats inside and the phosphate part outside. The Wikipedia entry for phospholipids shows a close-up of the atoms, which I have at left. The part on the left has the fats, which continue to the left with carbon and hydrogen atoms (represented by R), and the right part is the phosphate. The fat is called apolar because it repels water (which is polar, described in Wikpedia at polarity) and the phosphate is polar because it attracts water (and other molecules which are charged).

These molecules have to be made by the cell so there will be enough of them when the time comes for the cell to divide (reproduce) and grow. I will not get into details of this mechanism at least for now because we'll have enough details to consider with the membrane itself.

More next time!

Tuesday, April 21, 2009

Uncommon Fun

This past week I made a few comments at Uncommon Descent, the blog of William Dembski. I have followed it for several years and never tried contributing. The threads can go on for hundreds of entries. All kinds of people are there, some very credentialed and some not-so. I'm a little inhibited about making comments elsewhere on the web, although I invite them here. One of the great features of the Uncommon Descent blog is that they seem to moderate around the clock. That is not true here! I know they don't take all comments, so I was delighted when mine appeared. Here are the posts (you can click the number if you want to link to the comment within the thread):


8:37 am
Going back to the original title of this post, “that uncomfortable subject, religion,” I agree it is uncomfortable but needs to be addressed in terms of the Intelligent Design movement. I think an important aspect that has been missed (as far as I know) is that there is a difference between the believer and non-believer, even among Intelligent Design advocates. Using Christianity as an example, the believer is bound to the Creeds of the Christian Church. We believe in God the Father Almighty, maker of Heaven and Earth. We hold our faith as foundational, whereas others may consider science foundational. We can’t go to Church in the morning declaring we believe God made us (included in our doctrine) and to an Intelligent Design conference in the afternoon saying the Designer could be anyone. (It seems that between the comments in the Bible about God creating and all things being created through Christ, [creation] can cover design.)

6:36 am
I think a problem in using the term “design” in the Intelligent Design movement is that for believers, all things are designed (I am taking for granted that design is part of creation). Del Ratzsch describes a hundred-meter, perfect titanium cube on Mars (Nature, Design and Science, p12). He says we would not think it was “natural,” using that as an example of an obvious artifact, implying design. However, what he misses is that the planet Mars is also designed: it is designed as a planet. The discovery of fine-tuned physical constants which make the universe the way it is has given us the idea of the Anthropic Principle. The laws of the universe are designed. Even random movements of molecules are a necessary part of the design of the world, very useful in things like the atmosphere and diffusion.

The opposite of design, like the opposite of Creation, is not randomness but nothingness. I believe God gives us the innate ability to sense design, and also the revelation in the Bible that He made all things.

The ID movement is important in showing the discrepancy between chemical and physical laws acting on molecules and the facts of biological laws. Though some may be confused by the differences, they do exist. Molecules are subject to chemical and physical laws, not biological laws like neo-Darwinian selection. You will not (or should not) find “survival of the fittest” in any index of a chemistry book. The probabilities of [biologically] usable combinations of atoms are sources of information for ID Theory.

I added some editing here [included in brackets].

I hope to do a little more commenting on other blogs as time goes along. It is a way to be a part of the world, to communicate and contribute what one can.

Note: Our Sunday Visitor had a very good cover section this week (April 19, 2009) on evolution, describing Creationism, Evolution and Intelligent Design Theories by author and teacher Benjamin Wiker. To my heart's delight, this sentence was enlarged as a highlight: "These intelligent design types of arguments have considerable merit, more than Catholics have been inclined to grant."

Friday, April 17, 2009

Dred-ful Decisions

As described on Wikipedia, Dred Scott was a slave who sued for his freedom before the Civil War. He had lived several years in a free state, where slavery was illegal. His legal wranglings came later. He had won one trial, where a jury declared, "Once free, always free." But he lost on subsequent appeals. The case made it to the Supreme Court, where he lost. The majority opinion included this point, among others:
Any person descended from black Africans, whether slave or free, is not a citizen of the United States, according to the U.S. constitution.
As Wikipedia says,
In effect, the Court ruled that slaves had no claim to freedom; they were
property and not citizens...
Now, not all of us are legal experts, but we know a bad law or Supreme Court decision when we see it. And there are some on the books today which are just as bad as this one was.

I will not name them specifically, but comment generally on one set of decisions and laws--those which have to do with science and religion in the American classroom. The first mistake was to effectively ostracize a group of people who believe that God created the Earth directly in 6 days. Whether one believes that or not, the question of religion in the classroom is not handled properly.

We have got to realize that a religious person brings religion into the classroom when s/he walks into the classroom. Science and religion cannot be separated within the believing person. The Young Earth Creationist believes God made science directly and supernaturally.

Now, of course, there are people who do not agree. Unfortunately, with the help of the courts, they now behave, in relation to this subject, like they are the only ones living in this country and need to unequivocally have their own way. They don't make the effort, with their supposedly superior minds, to see how we can work together. I am sorry I am venting this way. Perhaps I should not in a public forum. One becomes very frustrated, but it is our work to keep trying to work out a solution.

The problem is not easy, I admit. But it does not pertain only to Young Earth Creationists. Many people are becoming increasingly insulting to anyone with any religious belief which clashes with the prevailing, culture-scientific dogma. (And I say "culture-scientific dogma" because the real science is often abused for the sake of the cultural and atheistic beliefs.) How do we handle Hindus, Muslims, and others who believe God supernaturally created? Will all religious mothers be forced to home-school their children? We need wise guidelines from the courts.

Science can be learned by all. I think very few parents would protest having their children (safely) put chemicals into a test tube to see what happens. Experiment and discovery cannot be denied. What must be sorted out and dealt with, all around, are interpretations that do not show up in the scientific test tube.

There are other Dred-ful laws and decisions in other areas, including those for abortion. We all hope someday that they will be reversed and revised in a sensible way.

Tuesday, April 14, 2009

Intelligent Design Theology

I'd like to make some further comments concerning the approach of many ID proponents. They insist that their theory is totally scientific. It is about detecting design in nature. I find a few problems that are related but not exactly like the ones often used against them.

One is that the very people who criticize them do not believe or understand the separation between design and designer. I think this is more inevitable than the ID people realize. The concept of design necessarily connects with the concept of designer. It seems psychologically too much for many people to separate the two. Hence, the repeated frustration of not being understood is something IDists should not be surprised about.

An even more critical problem is that ID proponents are needlessly complying to the science community culture, which places science as foundational, with faith a far-trailing second facet of our lives, if present at all. In this situation, it is as if the science community has their way that really, science is more important than religion. This is something we need not swallow, defend against or feel intimidated by. I am Christian, and God is fundamental, foundational, and first in my life. I don't care what others say, shout, feel or make laws about--it changes nothing for me. This is what any Christian in ID needs to get straight, and I'm afraid they will have some re-thinking to do. We do not insist that ID is only science, because we believe all things are made by God.

Yes, I understand that not everyone who is an ID proponent is Christian, or even a believer. But for those who are believers, the mindset has got to change. This is not only about science, though science goes hand in hand (for most of us) with faith. But it is about our faith, and being able to profess and live it in whatever country we find ourselves.

So, unfortunately, the argument about ID being only science, as repeated constantly in blogs and at state school board meetings, is not completely correct. Though Christians can understand science (an atom is an atom), the worldview is different for believers than it is for non-believers. For believers, the Designer is not just "anybody." The Designer, the Creator, is God the Father, through the Son.

There are real differences in the lives of those who believe and this is one of them. We are in the world, but not of the world. It is something many need to get straight in their own minds.

Update 1/22/2013: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species separately and directly. Much of the biological science in ID is similar to Special Creationism.

Thursday, April 9, 2009

God's Creation

It seems these days that for some Christians, especially those in the academic community and/or committed to education in science, the thought of God creating a biological cell after the Big Bang is unacceptable. But I don't see it as all that far removed from Thomas Aquinas when he discussed the 5 proofs of God's existence, which he elaborated in his Summa Theologica, Part 1, Question 2.

Thomas talked about effects and causes. If we know the effect but not the cause, we can logically deduce the cause. Thomas speaks of the material nature we see and know. And he proceeds in thought from this material nature to speak of the supernatural God.

At some point these Christians must consider that God made Creation the way He saw fit. For some, the blockage of acceptance is the fact that evil exists, even though God is perfect. But there is no difference in the need to explain evil whether God made all creation through the Big Bang or whether he intervened afterwards. Many people understand the nature of evil as a consequence of the free will God gave us. Yet others analyze, agonize, and apologize, without letting this simple concept sink into their own minds. They decry the pain suffered by animals in nature, to which I am sympathetic. But animals don't suffer forever: they either escape or die. I don't want to trivialize the sufferings that humans may undergo after death, but let's just say it is within a person's power, combined with the grace of God, to avoid them.

There are a few other reasons that some Christians don't allow God to touch His own creation. It is beneath His dignity, they say to do less than plan out the whole thing before the start. So all He is allowed to do is watch. He can't tinker, He can't wait for perhaps a more timely moment to do His work. One wonders whose dignity is really at stake here, when it seems the pronouncers keep at least one eye focused more on the opinions of secular scientists than the actual facts.

Or, they say, some scientist may come up with a physical reason for the cell. I ask they just start reading about the cell. Click on my Topics link for "ID" and / or "Creation" and take your time. If there is any law of physics which is ever discovered that makes the cell, it will be as finely tuned for the possibility of life as they are finding the Universe to be (see Anthropic Principle).

That God interacts with biology is believed by Christians. Christ changed water to wine, He healed, He raised persons from the dead. It is time for all Christians to stand up when we are called Creationists and answer, "Yes, we are!"

May you enjoy a Blessed Easter.

Tuesday, April 7, 2009

Evolution's "Open" Debate

The National Catholic Register has run a story about the conference on Biological Evolution the first week in March in Rome. The conference was co-hosted by the Pontifical Gregorian University, University of Notre Dame, the Pontifical Council for Culture and STORP (Science, Technology, and Ontological Research Project).

The conference was supposedly an appraisal of Darwin's theory 150 years after his Origin of Species was published. I say supposedly, because an appraisal usually implies that criticism is heard and evaluated. But any critics of evolution were kept outside the doors. (And by evolution, I mean by total materialistic, naturalistic means, as is the present working theory.)

Edward Pentin interviewed one of the main organizers, Gennaro Auletta, Pontifical Gregorian University professor of philosophy, after the conference. Pentin asked why persons who back Intelligent Design (among others) were excluded. You can read the article at the link above, but one of Aultetta's answers was that "We should never have recourse to a supernatural cause when we are dealing with rational matters."

Well, exactly how, then, is our world created by God at all? Does Auletta count the Big Bang as a rational matter? After all, scientists came up with the idea and are still studying it. Auletta apparently does not see that as a vehicle for God's creation. Yet many Catholics believe this is the initial point of Creation. The Big Bang was proven by science about 80 years ago even when an eternal universe was predicted by Aristotle and Einstein.

When asked what the conference achieved in terms of finding compatibility between Catholic theology and evolution, Aultetta replied, "I would like to think that we've shown the world that it's possible to discuss these very relevant and critical issues in a way that is fruitful and at the same time open."

How can something be open when certain groups are actively excluded? It is not. The question is, "Why?"

Most people know about the history of the Church in relation to the scientific discoveries of Capernicus and Galileo. These early scientists realized, against the general scientific mindset of the day (which was an Earth-centered system), that the Earth rotates around the Sun. The leaders of the Church denounced Galileo and it took until the late 20th century for a pope, John Paul II, to truly acknowledge the faults of the leadership in this question. Yes, the Church made a long, ongoing mistake here, and part of the problem is the complexity of scientific knowledge. Church leaders such as popes are not scientists nor should they be expected to be. Eventually scientific knowledge comes to light, and we should pray for knowledge as much as for wisdom. Knowledge is one of the gifts of the Holy Spirit.

As humans we are curious how God created and want to know as much as we can to improve our lives. But the decisions on how to make the world were God's business. It is our business to believe that He created, not to second-guess or claim inside information on His accomplishment.

We all make mistakes and we learn by them. It is no answer when we refuse new ideas because we might make a mistake. A mistake in the other extreme is to accept everything that is told us, even by scientists, without question or critical thinking. Scientists have been wrong, as in the example of Einstein and Aristotle above.

Many people, scientists and others who have studied biology and nature, believe that biological life is too complex to have come about by natural processes, chemistry and physics, alone. The more they know about the amazing cell, the more convinced they become that only a Designer could have made something like this. There is an excellent paper (2009) by David Abel, "The Capabilities of Chaos and Complexity," in the International Journal of Molecular Sciences that cuts to the true state of research into life's origins. There is much speculation and wishful thinking on the part of many materialistic, naturalistic scientists, but NO HARD PROOF that nature has formed life by chance.

This is the concept that seems so hard to get through to people. They don't even want to hear that God may have created the cell after the Big Bang. Even the suggestion of the possibility, the "MAY" in "He may have directly, supernaturally created the cell," elicits shuddering, incredulity or anger.

I ask that we learn from our mistakes but do not overreact to the other extreme. Though Christ came and lived on Earth in a pre-scientific age, his miracles had to do with life and nature. Wine is a product of biology, healing is to restore biology, raising persons from the dead most certainly has to do with biology. If we can't have recourse to supernatural explanations to science, then we will have trouble believing that God had anything to do with creation and miracles. Next time, I will elaborate on where His interactions with biology lead us.

Mutations 2

Recently I talked about mutations to genes which cause changes in proteins. The DNA has sets of molecules called nucleotides which pair (therefore also called base pairs). The nucleotides eventually get "read" by biochemical means to produce specific proteins, which do much of the work of the body. I spoke about changes to the genes, one nucleotide at a time, as when it is copied for the next generation. There can also be larger changes to the DNA, as pictured to the right. However, these changes do not account for the whole story of getting from one protein structure to another. As an analogy, if you duplicate a paragraph in a book, it doesn't increase the information you receive. Michael Behe vividly describes in his book, Edge of Evolution, multiple possible changes in Melville's Moby Dick, and their potential effects upon the whole story (pages 116-119). To summarize, there is not much improvement from the original with random changes, as you might imagine.

The base pairs in a gene still have to go through the individual changes in the code so that the new protein/s will be produced.

Friday, April 3, 2009

Notre Dame's Open Minds

Bruce Chapman of Discovery Institute wrote an interesting comment on the Institute's blog about Notre Dame and the recent flap concerning their invitation to President Obama for commencement.

Many Catholics are distressed, since President Obama is very pro-abortion and the Catholic Church teaches against it. But, the president of Notre Dame, Father John Jenkins, has taken the stand that open dialogue is useful for universities. Fr. Jenkins and his spokespersons claim they value academic freedom, where various views may be heard and considered.

Yet, at the beginning of March, Notre Dame co-sponsored an evolution conference in Rome, where it was made clear that Intelligent Design Theory would not be considered. I wrote of it here. Chapman complained that the organizers seemed willing to discuss Michael Behe's theory of Irreducible Complexity as a cultural phenomenon unworthy of the name "science," but refused to invite Behe, a Catholic, to defend himself. Behe was refused an ear, but not Obama.