Friday, February 27, 2009

Global Poverty

A renewed effort of Catholics to confront Global Poverty was launched Feb. 23 by the US Conference of Catholic Bishops (USCCB) and Catholic Relief Services (CRS). The website which seeks one million Catholics and suggests ways to deal with global poverty can be found here (update 3/15/13: the site no longer exists). The announcement was tied to a meeting this past weekend of Catholic leaders in the area of social justice held in Washington DC.
Of course, global poverty is a pretty daunting subject and we know each one of us can only do so much. But, when we work and pray together, great things can be done.

Some might think it a bad time to focus on the "Global" part of poverty right now, given our present economic woes. But we get in trouble, I think, when we ignore our neighbors. It leads to too much focus on ourselves, and too much waste of natural resources for too small a percentage of people.

Naturally, there are times when we our survival depends on hard, concentrated work. The American pioneers could hardly worry about the plight of, for example, Bolivians of the time. But when we become prosperous, the tendency is to gather more and more for ourselves--larger houses, cars, luxuries. You know the story--you've seen the CEO's on the news. But even many regular Americans have become square-footage and electronics conscious to the point of seeming as though we think we are some kind of celebrities who deserve more than others. Bad times can even be helpful in that we find we don't need all that we thought. We just have to remember that when times get better.

A concern for others is exactly what we need to curb these appetites--ones that have gotten us in heaps of trouble at the present. We all have consciences and know where we've spent too much or wasted too much. The economy should not be based on how much credit we get, but how we all can live wisely, sustaining the environment and sharing resources fairly. I think there is enough work for all--it's a matter of what we are doing when we work and the earnings we gain from it. We must remember Who truly sustains us. That is the key. I believe we could all, here and abroad, live much better in the end.

Painting from Web Gallery of Art, .

Friday, February 20, 2009

Horizontal Gene Transfer

I gave you a link in the last post to the New Scientist article from January 21, 2009. The cover page pictured a tree on which was written "Darwin was wrong." The related article describes why new scientific discoveries have proven him wrong. The ability of scientists to "read" all the letters of the DNA of many different species has allowed them to compare each of them with the other. The comparisons are not what they expected. They do not show a small increase over the time and species changes which were predicted by Darwin and his followers. The gene patterns do not match, they do not blend from one to another. Even though all species are not tested, the differences are so large that fitting in the spaces even over a few billion years and the species yet to be discovered would not be possible. (This is not a case of ignoring the fossils of so-called missing links. It is the fact that the predicted progression of cell structure from bacteria to human does not "match" with recent discoveries of scientists.)

The researchers now shift their attention to what is called "Horizontal Gene Transfer" or sometimes "Lateral Gene Transfer" (HGT or LGT for short). They are looking at the genes themselves and saying they have a history of their own, going from one species to another by a variety of mechanisms. The link given to HGT at Wikipedia gives more description. In other words, they are implying that genes evolve by complete chance, and organisms just turn out the way they do because the genes end up where they do. The small steps of gene mutation and natural selection of the neo-Darwinists is of much smaller consequence.

One scientific article about LGT is "Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution," from PNAS, Jan. 16, 2007 by Dagan and Martin. This, like many of the technical papers that I link to, is for those who know something about genetics. But anyone can understand that things are changing in biology. And the simple picture of one cell happening by chance and slowly changing to all the present species does not fit the new facts.

I talk here about LGT because it already has become the new mantra to replace or at least co-exist with neo-Darwinism (the modern version of Darwin's theory). But many people(mathematicians and engineers, for example) had told biologists that neo-Darwinism was wrong, starting over 40 years ago at the Wistar Institute, once the structures of proteins and DNA were discovered in the 1950's. The biologists were told that these structures could not have developed by chance mutation and selection. The book from the Wistar conference is Mathematical challenges to the neo-Darwinian interpretation of evolution by Paul Moorhead et al.

Mathematics can also tell us, as William Dembski among others has been saying, that materialistic, naturalistic HGT, alone or in combination with neo-Darwinism, is insufficient for life. Will people listen?

The world is a beautiful place, and there is still much to learn. The next generation has multiple challenges: cure disease, clean the environment (whether or not there is global warming), provide enough food and water for all people. We cannot find complete answers if we start with false information. And each of us can learn how to pursue what is true.


Clip art from , Jupiterimages s.v. tree.

Tuesday, February 17, 2009

Grand Dialogue 2009

I'm pleased and excited to announce I will be speaking on March 14, along with Dr. Dennis Marshall, at the Grand Dialogue in Science and Religion Annual Conference 2009. Dr. Marshall teaches Theology at Aquinas College. As the website tells you, the "Grand Dialogue is an association of colleges, universities, and related organizations exploring the relationship between science and religion."

The Dialogue was started a few years ago and is held it at the beautiful Grand Valley State College campus near downtown Grand Rapids. There are links to maps for DeVos Hall. The "breakout sessions" which are the afternoon presentations, are listed from my link and in the top left list of the main page.

One more link to add today--from the Jan. 21 2009 New Scientist article "Why Darwin was wrong about the tree of life" by Graham Lawton. It talks about the new understanding gained by whole genome sequencing of organisms. This will be one theme of my part of the Dialogue presentation, combining these findings with the predictions of Intelligent Design Theory.

Hope you can make it!

Friday, February 13, 2009

The Church and Evolution

This year the Pope and the Vatican have become more accessible by way of Vatican You Tube (I've added a link to the right column). It started in January, and there are about 3 videos per day of the Pope and / or Vatican events. It gives a view of Vatican happenings, and to see the Pope and the people and even the buildings makes me, for one, feel closer. The Internet brings those who have seemed distant, such as Bishops and the Pope, more into our everyday lives. It is a connection that I believe will help the Church in the long run. (Another website along these lines is the United States Conference of Catholic Bishops).

There is a video dated Feb. 9, 2009 called "Benedict XVI: Reduce Material and Spiritual Poverty." In the film, the Pope receives the ambassador to the Vatican from Brazil. He praises Brazil's efforts to decrease poverty. He says the Church appreciates governments which encourage dialogue among people to reduce poverty, both material and spiritual. The Pope has been careful, I think, in his ongoing teachings, including encyclicals, to try to keep the spiritual always before us.

The view of spirituality as imparting riches, or its lack as poverty, is an interesting one. Of course, those with material poverty do not necessarily have spiritual poverty, and likewise the rich are not necessarily spiritually rich. I'm sure the Pope refers to our belief in and relationship with God, and the thoughts invite reflection.

Also on Vatican You Tube there is a film of a press conference dated Feb. 10, 2009 called, "Biology and Theology for Understanding Man." This is the announcement of an International Congress on Evolution to be held March 3-7 in Rome. I will give more updates and links about this in the coming weeks. I want to note, however, that a point was made to not invite any ID advocates to the meetings, as reported, among others, by Catholic News Service (CNS), "Vatican evolution congress to exclude creationism, Intelligent design." (In a Fox News story dated Feb. 10, it was announced, "Vatican to Discuss, but Not Endorse, Intelligent Design." The decision to exclude ID was reversed, but organizer Saverio Forestiero said it would not be discussed on "scientific, philosophical or theological grounds.")

The CNS headline about "Creationism" being excluded is in reference to Young-Earth Creationism, but introduces my point. In fact, the word Creationism has been used to describe that particular type of Creationism, but the word really means a belief that nature and humans were created. It seems a bad start by the Church to exclude Creationism itself from discussions about how humans got here. Of course, what people really mean can get lost in translation through media and otherwise. But the CNS article quotes that the organizers "wanted to create a conference that was strictly scientific." (These organizers are persons from Notre Dame Univ. and Pontifical Gregorian University among other groups. I do not believe they include the Pope himself.)

The history of the Church in relation to science is caught up in the mistake with Galileo. Church authority took centuries to acknowledge the scientist was right about the position of the Earth around the Sun. Now many scientists (and others) who are Christian seem very sensitive to criticism from the prevailing academic leaders who insist on strict naturalism (where nature is allowed only to behave as a result of materialistic forces). Many Christians are themselves so convinced that God would do things in only one particular way that they have trouble seeing other perspectives concerning the changing the face of biology.

After Galileo, Newton was convinced God touched the planets every so often to keep them in place, but Laplace showed they could stay there by natural law. However, Laplace was a determinist, believing, for example, that we could theoretically make perfect predictions about atom movements and positions. Quantum physics proved him wrong. And, recent scientific discoveries about the universe show measurements with degrees of fine-tuning unimagined by any of these great scientists. Data on gravity, electromagnetism, the structure of atoms, indicate a very fine balance of forces which are necessary for existence. What is being called the "Anthropic Principle" is an understanding which brings us full circle from strict naturalism to the magnificence of God's creative powers upon the heavens.

The world of science has without doubt given us fabulous accomplishments. So has the world of economics. But in economics, money can rule and even for Christians, subtle rationalizations can take place. The Pope pleads for us to consider distributions of income and to help the poor. In science, a scientist or educator rightfully learns from past successes, but can be slow to adjust when totally new ways of thinking are in order. One can even honestly believe he or she knows the facts, and hence miss other factors that need to be considered.

There are facts yet to be discovered, and perhaps we've put the facts we do have together in wrong ways. That is the case for naturalistic evolutionists, theistic evolutionists, and people who believe God actively created organisms at one point or another after the universe began. We need to be open to new ideas when new discoveries come along.
And all Christians are Creationists and should have no hesitation in saying as much. When we start with the proper priorities, the rest will fall into place.

Tuesday, February 10, 2009

Information Theory

The past few days I've been reading and re-reading articles and books about Information Theory. William Dembski has been working with Robert J. Marks II on various aspects of Information Theory and their pertinent website is The Evolutionary Informatics Lab. They have several papers listed under their Publications link. I read one of them which is to be published soon called, "Conservation of Information in Search." It addresses, for one thing, the use of computers to "prove" evolution by programs which pick out some final answer when a random search is used. They describe how the information in these programs is "partitioned" so that each part of the the programmed answer, such as a letter in a sentence, will stay in its place when it turns up in the random search. The outcome in these cases is dependent on information fed to the computer program.

The "father" of Information Theory is considered to be Claude Shannon. He used statistical information about language to improve methods of communications. I can follow a lot of the explanations, and some of it is easy to understand, but other parts are complicated. The link to Information Theory in Wikipedia has some mathematical explanations and other references for those of you who are interested and mathematically-minded.

Another man, physicist Hubert Yockey, applied Information Theory to biological systems. I've re-read some of his papers from the 1970's and 1980's. One of them is "A Calculation of the Probability of Spontaneous Biogenesis by Information Theory," from the Journal of Theoretical Biology (1977) 67, 377-398. (I was unable to find it on the Internet and got this and other articles by him through inter-library loan). He used data previously worked out by Grantham in 1974 on a particular molecule in most species called cytochrome c. He compared 101 amino acids which make up cytochrome c in the categories of composition, volume and polarity (electric charges). Yockey worked on the number of molecules which could function as cytochrome c compared to the number of molecules that couldn't, using the 20 amino acids that make up protein. Though he found a tremendous number that could function as cytochrome c (about 4 x 10^61), the probability that the 20 amino acids would form any of them by chance is only about 1 in 10^65 (10^65 being a 1 with 65 zero's after it).

Yockey refutes the prevailing theories of evolutionary pre-life formation by showing how improbable are the events that would lead from random molecules to formation of functional proteins and/or genomes. His calculations eliminate even the possibility of life forming at any time in the universe on any available planet. It is interesting how these pre-life theories persist even today.

One personal note: it's my husband's birthday. Happy birthday, Tom, and may you have many more!!

Also, Thursday is Lincoln's birthday and Washington's is to come soon. Tom and I watched several shows on slavery and the Civil Rights movement Sunday on PBS. It was interesting how the former slaves adjusted to freedom very soon after the end of the civil war. They became a part of government very quickly, but then were attacked by the persons who remained prejudice and unwilling to follow the new laws. The African-Americans were again oppressed. If Lincoln had lived longer, perhaps permanent changes for the good would not have taken so long.

Friday, February 6, 2009

Origins 10, Molecules

Since, as we have seen, the smallest free-living organism is too large to have begun by chance (needing about 1 million DNA nucleotide molecules in sufficient order to function), some say that smaller entities could have built up to the whole organism. They use terms such as "selfish cooperator" and "gene pool" and "pre- or proto-biont."

These pre-bionts (meaning molecules waiting to be living things) would have to be composed of thousands of atoms in enough order to carry on specific chemical reactions under the laws of physics and chemistry. Let's look at just one very simple molecule made of 3 atoms, Water. As we see in the 1st picture, to the left, it is composed of 2 hydrogen atoms (white) and 1 oxygen atom (red) in a certain configuration.

Don't be turned away if you don't understand all the terminology of the "Information and Properties" below the picture. I would just like you to see for yourself the complexity of a simple molecule of water. Most people know that water freezes and thaws and boils at certain temperatures. These temperatures are listed below the first picture and called melting point and boiling point. There are many other physical and chemical properties of water which affect how it stays together, comes apart, or reacts with other molecules. The link takes you to Wikipedia, Water (data page) where there are 12 charts-full of information about this one little molecule. I have added two charts to the right which are both just a part of one larger chart. (You can see the chart details better by clicking on the picture for a larger version).

I do not understand all the terms myself, but I am amazed when I look at all the details of just one little molecule of three atoms. Often, the longer the molecule in a solution is, the slower the reactions to make it longer and the more likely it is to come apart (unless real physical effects like pressure might compress them into things like rocks). Many reactions need help from other atoms or molecules just to take place within a short enough time period to be useful biologically. The chemistry of water does not depend on what this molecule is supposed to become. Life's organisms are full of water molecules, but water outside of life is not called a "pre-biont." It is a water molecule.

Water is not "selfish." Nor are any other molecules.

Water may occupy the nooks and crannies of the bottom of the ocean, but the heat of the thermal vents is sure to keep it moving. In fact, it is estimated that the entire water of the ocean is filtered through the thermal vents every 10 million years, which limits the origin of life to that amount of time (in a 1996 article in Cell by Lazcano and Miller called, "The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World and Time," ). That is because the molecules of life are pulled through and torn apart in that extreme heat.

Water molecules have followed the laws of physics and chemistry, which is the point. It is not that Intelligent Design advocates deny the laws of physics and chemistry. We are saying they are discontinuous with the existence of biological life.

Tuesday, February 3, 2009

Origins 9, First Cells

The three domains of life are divided into Bacteria, Archaea and Eukaryotes. Every organism has a set of genes which is used as a pattern for building the organism itself and passing along the pattern to the organism's offspring. The collection of genes in an animal is called the genome. Scientists have been able to do what is called full-genome sequencing, determining the entire make-up of these genes within individual organisms, since 1995. The genes are made of DNA or RNA, molecules made up of atoms in specific orders. On Oct. 23, 2008, an article which compares Bacteria and Archaea, which are mostly one-celled organisms, was published in the journal, Nucleic Acids Research, 36:21, pp 6688-6719. It is called, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," written by Koonin and Wolf. (A link to the entire free PDF article is found at the right on this abstract link).

Though only a small percentage of species have been sequenced, the introduction to the article explains that the researchers feel the work done so far is representative enough to survey patterns. One of the purposes of whole-genome sequencing is to compare the make-up of the genes and see if the orders of the molecules matched what scientists expected according to evolution theory (including the order in which organisms may have appeared on Earth).

Perhaps you have heard already, in the news or elsewhere, that the pattern of organism genomes has not produced a "tree of life" as Darwin predicted. At first, the term "web of life" was used as a substitute to tree. But now, Eugene Koonin, one of the authors of this article, asserts that web is even too clear a term for the genetic patterns. If you look up the article, you can see a picture on page 6708 which represents the new dynamic view of the genetic pattern for life. It is a group of circles representing genomes with lines connecting them every which way.

One of the reasons for this lack of clear, Darwinian progress is believed to be "Horizontal Gene Transfer" or HGT . Bacteria and Archaea are able to switch genes from one adult to the another by a few different mechanisms. Therefore, the patterns of adult to offspring are not closed or caused by internal mutation. Genes (part of the genome which is productive in protein make-up) are present when they shouldn't be and not present when they should be, according to what is expected. Many genes are found only in one or two organisms, never to be seen again. Considering the complex protein products they make, the sudden appearance and disappearance does not sound like slow, random change predicted by Charles Darwin.

There are limits to HGT and how much it can explain. The closer the organisms are in type and location of growth, the closer the genes to each other. Also, we are talking here of one-celled organisms. Multi-celled would not be so easily affected by HGT. The article states that HGT is still controversial, unable to explain all the differences. And, most obvious, there have to be genes in the first place in order for them to be exchanged. I had talked about LUCA, the last common unknown organism, in a previous post. Because the Archaea and Bacteria cells are so different, there would have had to be a great variety of genes in a single organism that existed previously that can be figured to be the original organism. The computer program came up with a cell with at least 1000 different genes, probably much more. Koonin, in the article mentioned above, interesting points out on page 6701 that a free-living cell would need a minimum of about 1000 genes.

Genes are an average length of 1000 nucleotides. A free-living cell would need at the very least about one million nucleotides of DNA in specific, functioning order to survive well enough to reproduce. Though not all those would have to be in one exact order, a large percentage would have to be in specific sequence to make functional proteins. As you might guess, this is far beyond what we would expect from the random movements of atoms, which themselves follow certain laws of chemistry.

That leads us to next post, where we will take a look at smaller organisms than cells--the viruses--and see if their genome patterns lead us to any knowledge of how life began.