Monday, December 29, 2008

Goodbye 2008



We're still doing some holiday family visiting & catching up from the year-end rush. By next week I should be ready to get back into descriptions of biological design.

Have a very blessed New Year and drive carefully!

Friday, December 26, 2008

ID Advocates

I really like the people who advocate for Intelligent Design Theory (of course I know of them mostly through the Internet). They are smart, brave, and dedicated. I think they are able to see the clash between certain limits of physical laws and the make-up of biological organisms. There is something that doesn't fit, such as the complexity of DNA compared to molecular movements in the kinetic theory of matter, and the ID people are hot on the trail.

Now, I am not saying the arguments of these advocates are perfect.

For one, some design advocates may concentrate on biological life and think about how it differs from non-living matter. Others focus on the universe and what we call the "Anthropic Principle," which describes the physical "coincidences" that have made our universe amazingly hospitable to life. However, if both the universe and biological life show aspects of design, the ID people are not proving design when they say one is more complex than the other. That just compares them. There may be discontinuities between designs, which is still significant, but not lack of design in one or the other.

Beside the first point, we must make the distinction between those advocates who believe in God and those who don't. This would be the first thing ID advocates would not want done, because they are saying their science of design detection is not related to any religious belief. I think they are wrong.

A Christian goes to church every Sunday (we hope) and says the creeds of that church or if not attending at least holds the creeds of that church. Christian creeds state we believe God created heaven and Earth, of all that is seen and unseen.

Therefore, the Christian does not have to scientifically detect design or prove it. S/he believes it is everywhere, and that science is the study of designed entities. That any of us recognize and admire design is an innate quality that God gave us in the first place. Christians do (or should) stand apart from the mainstream which has insisted for so long that science is supreme. Often secular scientists intimidate others who do not think the same way.

Even non-believers have the potential appreciation of design, though they may not yet have arrived at the belief that God is the Designer. Some of the ID advocates are not of an organized faith, yet recognize design in nature.

That leads us to the basis for our lives. It is Faith that is the foundation of our knowledge, not Science or even Reason (although we have to think to be functional, at least). Faith is what gets us on the right track and keeps us there. Then we can learn science to our heart's content, and praise God for His creation every step of the way.

Faith is a mystery. Perhaps I will write more about it as time goes on.

Update 1/21/2013: 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.

Tuesday, December 23, 2008

Happy Christmas and New Year


May you have a very blessed Christmas this year.

~~~~~~~~

I'm already carrying out New Year's resolutions and it is still over a week away. I decided I really need titles on my posts. I've never been very good at thinking of titles for some reason. But I'd like sometimes to do more than one subject in a single day and I need titles for that. I found once I added them I like having them. It looks better and the archives are more organized and helpful for locating past subjects. I see that they replace the partial sentences that were used to identify the post. This is much better.

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Congratulations to the Penn State Women's Volleyball 2008 Champions--one of the best teams ever!

Friday, December 19, 2008

Evolution Not a Fact Now

In the last post I talked about "Abiogenesis," which refers to materialistic, naturalistic origin of life. I had looked up the topic in Wikipedia and found short summaries of various theories for this origin. They also listed some of the problems to the theories. Though "Origins" research is not quite the same as "Evolution," some say that molecules evolved to form simple life which evolved to form more complex life. In any case, materialist, naturalistic origins would imply chemicals coming together under the laws of physics and chemistry to form organisms.

With continuing discovery of microbiological mechanisms, almost all Darwinian tenets of small change and survival have been found lacking, both in origins and in biological life in general. These discoveries have only made for more questions which have not yet found answers. It is OK for scientists to continue to question, hypothesize, experiment and learn. I'm sure there are plenty of grants out there to learn more about science. But scientists also should be willing to analyze and apply the past 50 years of discovery to the present and state where evolution stands now. As of now, evolution is not a fact. The chemicals do not go together in a way that forms life under physical and chemical laws as we know them now. Then why are people, often scientists, saying it is?

Those of us who do not insist on evolution being fact can only speculate. Can it be that the other hypothesis, that God created the world and life in one fashion or another, is not acceptable to them? When one holds two possibilities at a time, some call that open-mindedness. It seems that scientific discovery should take us to conclusions, not the other way around.

Classroom study of science should be called something like "Scientific Theory, Method and Discovery" (STMD). That would take away the insistence of theories as Truth and simply present what various scientists think, how they proved it, what problems remain, and leave the students to think about it themselves. And for goodness sake, include creationist scientists. Is the mention in a classroom of a scientist who believes in God a criminal act in this country?

As Christmas speedily approaches, my posts will probably be short. After the New Year, I'd like to dwell more on Origins of life and the relationships between the 3 major types of cells: bacteria, archaea and eukaryotes (true cells). Now that I'm done with my book I hope to have time to do more descriptions of biological science in my blog. Because biology is in such a state of exponential discovery, the facts are coming fast and furious. Therefore it's hard to summarize and/or make simple to understand. But I can make a start and hope that when people see the facts, they will be able to conclude for themselves what the commotion between creationists and materialistic, naturalistic evolutionists is really about.

Update 1/21/2013: 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.

Tuesday, December 16, 2008

Comment on Abiogenesis

Blogging on the fringes of cyberspace as I do, I am happy to receive comments whether they be yea or nay. There was a comment in the last post, which I'd like to thank the commenter for taking the time to make. I'll try to give an answer. He referred to whether biological life started by chance and that research in abiogenesis, the study of beginnings of life, presumably refutes chance origins. The commenter is correct that we should be aware of origins research. I have a list of evolution-related references (link in right column) that address some of these issues. But it is always easier to read literature that supports one's own theory, and I've meant to do more reading in this field. A challenge from someone else often moves a person to stop procrastinating. I went to Wikipedia for a start and printed out the "Abiogenesis" entry and read it. Wikipedia may be looked down upon by some, but it is a good place to get started on a technical subject and to get references.

I had written posts early-on in my blog about chance. One of them was from March 30, 2008, so I will not re-write the whole thing. But I do want to repeat that one of the references was from the book, God's Undertaker: Has Science Buried God? by John Lennox. He is a mathematics professor at Oxford University, so has a pretty good idea of what chance is about. He gives the probability that one protein of 100 amino acids formed by chance as 1 in 10^60. This includes only the chirality of the amino acids (whether they are left-handed as in organisms or right-handed) and the particular chemical bond they take, and not whether the protein is even functional (no information theory included). Therefore the chance that 3 such proteins formed with just the correct chirality and chemical bond exceeds the universal probability bound that is given by William Dembski (in other words, less than 1 chance in all the events of the universe so far). The smallest bacteria that I've seen has 1100 proteins, and free-living Cyanobacteria, thought to be one of the earliest organisms, has ~3500 proteins.

The example from Lennox directly addresses one of the theories of abiogenesis: that amino acids are made from natural processes which turn the "pre-biotic soup" into long chains of proteins that can then carry on metabolism. Yes, some amino acids on meteorites show a preference for "handedness," and maybe the numbers would change if you factor in those proportions, but only to a certain degree. One cannot say the problem is solved. Though this example covers only one of the models, the others meet similar types of so-far insurmountable blockages, some of which the Wikipedia author states.

As to whether the chance occurrence was needed only once in the theorized march of evolution, ScienceDaily reported here on Nov. 18, 2008 that many orphan genes are being discovered (the original scientific paper is here). These are unique genes which seem to make species-specific differences in organisms. The paper reports that these genes have no known homologs. In other words, they are not found in any other species and have no known shared ancestor. Granted, we are discovering new species all the time, and our knowledge is growing exponentially. Someday we may figure out where these genes came from , but do not know now.

The Wikipedia article about Abiogenesis has the statement (under Current Models):

There is no truly "Standard model" on the origin of life.
The article gives many theories of models from many possible starts, but they are theories. Therefore, evolution is not a fact now. This is the distinction that seems to get lost when we talk about evolution and/or teaching evolution. Intelligent Design Theory does not necessarily exclude "descent from common ancestor" as a possibility. But it excludes entirely materialistic, naturalistic evolution--that which occurs only by the laws of physics and chemistry as we know them now.

Another quote from the Wikipedia "Abiogenesis" article says:
The question "How do simple molecules form a protocell?" is largely unanswered but there are many hypotheses.
This is under the heading, "From organic molecules to protocells."

The problem is that I don't think we can convince those who are totally materialistic, naturalistic evolutionists of scientific proof that life did not come in that way. The unequivocal, totally convincing scientific proof against materialistic, naturalistic evolution may never come for some because they will always think a proof of "total-natural evolution" is just around the corner. And so, I think the real difference is our opinion of what we think is true, whether it will be proven or not. I'll try to expand on these points in my next post or two.

Tuesday, December 9, 2008

Cardinal Dulles

I gave a short introduction in the last post to my interest in the New Evangelization in the Catholic Church. There are perhaps many ideas of how to develop this new approach to teaching and re-teaching the faith. I am excited by the prospects. I read about it a few years ago, when I was a student in theology at Aquinas College. The book was The New World of Faith by Avery Dulles, S.J. (Huntingdon, IN: Our Sunday Visitor Publishing Division, 2000). On page 111, he explains that evangelization has always been a part of the Christian faith, but there are several reasons that the late Pope John Paul coined the term "New Evangelization."

For one, the Second Vatican Council in the 1960's renewed the call to the laity to be part of the preaching church. In particular, we are called to
join the profession of faith to the life of faith. This evangelization--that is, the proclamation of Christ by word and the witness of [our] lives--acquires a special character and a particular effectiveness because it is accomplished in the ordinary circumstances of the world. (Lumen Gentium, no. 35)

I think this applies to our modern world and the current scientific situation in an interesting manner, and I hope to elaborate in various ways in the future.

Another reason Dulles gives for the "New" part of evangelization is that many Catholics have fallen away from the faith, and should be "re-evangelized." There are young people who were not brought up in the teachings of the Church, and older ones who became disillusioned or convinced that religion is a myth. I think science, or better said the modern mind-set associated with science, it is a big part of this falling away. I think there are good reasons to evaluate what is happening and correct certain misconceptions. Also, we tend to act in ways we don't even realize, and our un-thought-out words and actions give away deeper values.

Some say that it is important that America continue to be first on the scientific forefront. They worry that with the introduction of Intelligent Design theory, we will lose our edge and be relegated to scientific backwaters. We may not be able to continue to produce Nobel Prize winners. Surely it is important to continue the scientific quest for medical cures and other legitiamte needs. But whether Americans win the Nobel Prize or not is certainly not the best reason to motivate our actions.

The new evangelization may mean for some a "re-catechization." I found a great section in the latest Catechism of the Catholic Church (St. Paul Books and Media, 1994). It says:

To adore God is to acknowlegde, in respect and absolute submission, the "nothingness of the creature" who would not exist but for God. To adore God is to praise and exalt him and to humble oneself, as Mary did in the Magnificat, confessing with gratitude that he has done great things and holy is his name. The worship of the one God sets man free from turning in on himself, from the slavery of sin and the idolatry of the world (sec. 2097).
It is hard to put into words the problem with science and scientists today. Research and inquiry are of course important, and our scientists are smart and sincere. Many scientists are not religious and some of the more vocal ones are outright obnoxious. But many science promoters who say they are religious still come across as caring more about science than religion. It is not the details of science that are the problem here. It is the mindset that says Nobel prizes and even money grants are so important that other considerations must take a back seat.

This does not even take into account whether evolution is right or wrong. It sets the stage for the discourse. Priorities we set show through in our speech and actions, whether we be religious or not.

Friday, December 5, 2008

New Evangelization

I have written about things in which I am interested besides Intelligent Design, but I think I forgot to list one of the most important--evangelization. I am interested in the Catholic Church's New Evangelization, and want to learn more about it. John Paul II had talked about it in his document "At the Beginning of the Third Millennium" (section 40). Benedict XVI mentions it once in a while. My book, Unto Others, uses characters to show the importance of belief in Jesus Christ.

~~~~~~~~~~~~~~~

My husband, Thomas Carlson, and I have listed some of our books on eBay! Several years ago, Tom wrote a historical novel, Sawdust Fires, about the logging industry in Muskegon, Michigan. It's set in the late 1800's, when logging was coming to an end because of depletion of the pine forests near the Muskegon River. The lumbermen came up with audacious schemes to move their investments west. We have had very positive feedback from people who have read this book. Tom also put together many scenes of the lumbering days in a pictorial to provide a background for the novel. This is called Muskegon at the Peak of the Lumber Era. The book and pictorial are in the Muskegon County Museum which has provided a wonderful outlet for them.

I wrote a book, Mission: Faithful, about 10 years ago. Before the digital revolution, Tom and I had to print out quite a few of our first 2 novels to bring down the individual cost per book. We still have some! As I've said, we are writers, not marketers. But now is our opportunity to sell some through the Internet. And included with our eBay lot, of course, is my latest book, Unto Others. This set can be found on eBay here. It was listed Wednesday and goes for 7 days, until Wed., Dec. 10. After that, we hope to list again soon. We'll give you the link again when we do. These books would make great Christmas presents!

Tuesday, December 2, 2008

Young Earth, Big Bang

Evolution has become a contentious issue among Christians. The obvious division is between those who think God created people and animals and the Earth about 10,000 to 14,000 years ago and those who think He created the universe through a Big-Bang 14 billion years ago (bya) or so, with life coming about on the Earth sometime around 3.8 to 3.5 bya. This is a pretty big difference, all right. Some of the Young Earth Creationists (whom I affectionately call Yeccies) are concerned with matching their ideas with scienctific discoveries, such as carbon-dating, and others start strictly with Bible readings and let the chips fall where they may.

The other area of contention is between Christians who believe God started the complete design of life at the Big Bang and never needed to intercede since then. Life as we know it therefore came about by the physical and chemical laws placed within the fabric of the Universe. These people are called Theistic Evolutionists. On the other hand, we have those who believe God made the Universe in the same way (Big Bang), but interceded to make life. They believe that life shows a more direct Design that is counter to the laws of physics and chemistry. These are the ones who hold to Intelligent Design Theory (IDT). To confuse things more, not all advocates of IDT are Christian. Some believe in other gods, others think there is another designer. But many are Christian.

It seems we get quite emotional about which motif the Lord chose to create us. There are some key theological issues that are involved. For the Yeccies, the point is that the Bible tells us that death came about by human sin. They take it literally that no one died, including animals, before the sins of Adam and Eve.

Others see possibilities of reconciling this doctrine with evolution, such as human awareness of sin and death coming at some critical time in evolution. Or, some say, animals and plants evolved but God made humans directly and when Adam and Eve sinned they became destined to die.

It is not trivial to seek an answer to these questions, but there are several layers of priorities here, I think. The first is to worship God and praise Him for His creation, no matter how He did it. Another near the top is to respect the opinions of fellow believers in discussing these matters and behave accordingly. Each has his or her own reasons for believing a certain scenario.

Another priority for us is to not presume we know all that God knows or why He does what He does. Isaiah 55 tells us His thoughts are above our thoughts and His ways are above our ways. We humans can only speculate. For example, though some say He has revealed everything about Creation in Genesis 1, a different description appears in Genesis 2. And so it seems not quite as black and white as Yeccies profess.

Whatever else I believe, I believe God can do whatever He wants to do. It is not for us to impose, but to understand what God imposes upon us. He tells us to "Be Holy for I am Holy" (see 1 Peter, Chapter 1). That's the priority.

Friday, November 28, 2008

Common Ground

I am not so naive as to think that the love and unity I urged in the last post comes easily, among Catholics and other Christians as with anyone else. We are humans and all have our faults.

I was at a seminar recently where the age of the Earth was discussed. This is a contentious issue for scientists and laypersons, mostly old- against young-Earthers. One person from the audience asked whether we can find common ground (paraphrased, my pun). The presenters indicated they respect those who learn the facts before arguing instead of relying on hearsay or unscientific sources.

I think there is an even more basic area from which Christians can start. We who believe want to do God's will. At some level, we want to be pleasing to God. That's our common goal and desire and it gives us a very important bond.

Unfortunately, things go downhill from there. When individuals think we know what God wants, each of us takes for granted that s/he is right and anyone disagreeing is wrong. This is where things get bogged in arguments.

It is still necessary to keep trying though the going may get very tough. We must remember our common ground and work toward several goals. One consists of sharing our knowledge so that all may benefit. Another goal, which includes the first but goes well beyond, is to discern what really is pleasing to God and to ask for the grace and strength to do it.

Monday, November 24, 2008

Conflicts Within

We're having some major snow today (Monday) and I'm very glad my book, Unto Others, is printed and safely on the shelves of three local stores. Thursday is Thanksgiving and I hope all of you have a safe and blessed holiday. We are not going anywhere--I need some catch-up time from all the work I've been doing to finish, print and place my book. Then maybe we'll run down to Ohio in a few weeks to make a Thanksgiving-Christmas visit with my mother.

I am unfortunately reading about tensions between Catholics which have been flaring since the election of Barack Obama. Many Bishops are becoming more vocal about Obama's record on abortion, yet many Catholics voted for him. There are also tensions involved in the debates about Evolution vs. Intelligent Design Theories. Several of the major players are Catholic. Michael Behe and Kenneth Miller testified against each other in the trial in Dover, Pennsylvania. Behe believes that life is too complex to have come about in the small, naturalistic steps which neo-Darwinism claims. Miller believes nature's forces after the Big Bang are sufficient to have brought about life, even though it's "OK" if God made prior design for a universe which supports this life.

Arguments have deeper associations which cause us to make our stands. The bishops, of course, believe the embryo is a living human and therefore in need of legal protection as any human is. Some apparently do not see it that way, and are affected instead by the inhumanity of poverty and oppression. In the evolutionary debate, Miller fears we will stop trying to understand biology if we say, "God made it," whereas ID advocates say the evolutionists are not willing to correctly evaluate all the facts.

My book, Unto Others, does not address either abortion or evolution. But it does start with conflict within the Catholic Church. There are more areas of conflict with which we must grapple. Yet Paul in various places calls us to get along together. Perhaps at this time of year, it is good to recall the things for which we can be Thankful, which are many. Then, in prayer and joy of the Christmas season and the promise of a new year, we can work toward unity and love.

Friday, November 21, 2008

Unto Others


It's finally here! My fictional mystery novel is called Unto Others. Suspects abound in this exciting mystery! It would make a great Christmas gift, or fun winter reading for yourself. Or both!

The protagonist is Yesenia Rios Rivas. She came to the United States illegally when her home country, El Salvador, was fighting a Civil War. She endured many hard years before finding happiness as a custodian at Santa Rosa Catholic Church. But now, a person disappears and an investigation commences. She is worried that her status will be questioned.

Unto Others incorporates many issues that the United States and the Catholic Church are dealing with today. Some of the major themes are the need for immigration reform, political tensions between socialism and capitalism, and even women's ordination. And yet, these sweeping problems affect ordinary individuals who cope with their lives the best they can.

The book retails for $12.50. Three bookstores have graciously agreed to put it on their shelves. They are:

Michigan Church Supply, 360 Division St., Ste. 1B, Grand Rapids, MI (1-800-521-3440), which is in the newly renovated Cathedral Square Center.

Hage's Christian Supplies, 4949 Harvey, Muskegon MI (231-798-9824)

Oceana Pharmacy, 39 State Street, Hart, MI 49420

It can also be found at FaithWriters website and purchased for $5.00 as an e-book! Just click here to see a description and excerpt. They accept PayPal.

Friday, November 14, 2008

Symposium on Evolution

I watched some videos from the Evolution Symposium that was held this spring at Rockefeller University. I found it pretty interesting in the sense that the researchers are at a loss to interpret the findings of the last dozen years of genome sequencing and other scientific discoveries. What could be a victorious meeting for Darwinists from all our new knowledge is anything but, because the molecular make-up is not confirming materialistic, naturalistic evolution. The facts do not match their ideas of slowly evolving micro-organisms. They now say the microbes switched genes "rampantly," yet we know that organisms stay as true species throughout time. If the biologists would analyze the present situation objectively, they would say that total-natural evolution is falsified at this time. Falsification is a philosophical outlook advocated by Karl Popper which says that theories are scientific if you can devise experiments that show whether the theory is true or false. Instead, biologists these days do not allow Intelligent Design theory into the science classroom because "it can't be falsified." What does falsification matter if they won't recognize when it happens anyway?

Then I got to the lecture by Katherine Pollard about her group's research of human accelerated regions, or HARs. The information came out in 2006, but I was not aware of the details. If you know something about RNA and DNA, are interested in the question about evolution of humans from chimps and have a half-hour or so, please watch it at the above link. Or if you prefer, a full article of one of her papers and an abstract of another, (Katherine Pollard, et al., An RNA gene expressed during cortical development evolved rapidly in humans, Nature, August 16, 2006.) are at these links.

Pollard, Salama et al. did a study on sequences of genes which were detected as the same throughout many vertebrates, including chicken and mice, but different between chimps and humans. These areas could be better compared now since entire sequences have been completed in many organisms and they have more powerful computers to sift through all the data. They found several gene sections with significant changes. The changes in the gene sections, called bases, were far above expected in the normal mutation rates of genes that happen with each new generation. For example, while only .27 were expected, 18 happened in the HAR1 segment. The HAR stands for Human Accelerated Regions and the HAR1 codes for an RNA molecule, which you can see on the bottom right in the illustration below. RNA molecules can have either coding (for protein) and non-coding jobs. The most strikign thing is that the changes were all the same, from the T-A pairing to the C-G pairing (there are only 2 types of pairing on the DNA strand and all previously known mutations have occurred equally in both directions). The HAR1 is found to be active in human brain development in the embryo in critical times of its development.


One can not imagine the importance of this discovery. In one of the papers, an explanation was attempted. They said perhaps it is because the genes are at the end of the chromosome where recombination takes place. The C-G bonds are stronger than the T-A and so maybe they survive better. If that were the case, all organisms would have these bonds at the end of their chromosomes by now after millions and millions of years. A check on the rest of the genome showed that mutations are totally balanced except in these HAR regions (shown in the video). These genes were discovered for the very reason that they stayed the same for hundreds of millions of years and then changed dramatically over only a supposed time of 5 million years or so. That is the time from the proposed last common ancestor of the human and chimp. With only about 10^12 (Michael Behe) or no more than 10^17 (Fredric Nelson) individuals to work with, the number of combinations on the HAR1 (118 bases), much less the other HARs, would be very unlikely to produce the language, mental abilities and other improvements of the brain through random mutation and selection.

At the end of her presentation, Pollard said their findings lead to the conclusion that evolution researchers will have to seek other "directional forces" besides the ones they have previously believed would give the answers. In so many words, she says Darwinism, or neo-Darwinism, is not the answer for explaining the human body. However, this same pronouncement was made by mathematicians in a conference at the Wistar Institute in 1966, not long after the structures of DNA and proteins were understood. The question will be just how long evolutionists can ignore that these are not random processes.

Update 5:20 -- I'm now calling totally naturalistic, materialistic evolution "total-natural evolution."

Tuesday, November 11, 2008

Blog Clog

Had some trouble logging into my blog today. I deleted cookies and cleared cache and I hope I cleared out the problems. And, I found the post I scheduled for today has the wrong date. So today's post will be a little short as I make sure my cookies and Java Script and all of that is cleared up for the future.

Might as well just make one remark about Penn State football. "Lamentable" is the word.

Friday, November 7, 2008

Congrats to Obama

It's early Wednesday morning and we congratulate Barack Obama on his historic presidential win. The scourges of slavery and prejudice have cause suffering beyond our capacity to imagine. Yet human beings overcome in amazing ways. Groups of people persevere with the help of God through generations and centuries.

That said, there are still many problems to overcome. The economic challenges and the wars will not automatically go away. And though African-Americans individuals feel a new freedom, they must remember that they are capable of their own mistakes. Some A-A's, along with many persons from other ethnic groups, support abortion. Catholic bishops have been quite vocal about the problem of abortion, and the results of this election will not stop them. There is a good article at Catholic Online to express the thoughts of many in this regard. Though the Democrats have taken what Catholics consider the wrong stand in this issue, more are realizing how the Republicans have let us down in many ways. Some are looking to make a movement toward a "new alliance" that supports all the right values.

Another important consideration is Obama's attitude about evolution. He has said he believes it happens, and does not seem interested in ID debates. But how informed is his opinion? Is he aware of all the data that points to areas where life has emerged without help from the physical laws? Does he know about the Cambrian Explosion where animal types appear without apparent ancestors? It looks like there will be challenging work ahead for the Intelligent Design movement to teach the facts, especially in the face of prejudice of a different sort.

Politics is a part of our lives, but I am very glad the election is over. It was getting to the point I couldn't watch the news any more. Now that we know who has won, we can think about the future and the stands that Obama has taken.

Tuesday, November 4, 2008

PSU, Voting, Shopping

Texas Tech did it. They beat Texas. Quite a game, I hear. I went to bed at half-time. My husband Tom is a night person, I'm a morning person (got up at 3:30 this morning because of the time change). I went to Penn State (BS in Animal Science) and have been a fan through thick and thin. It's been pretty thin for the last few years so it is very nice to have a good team again. We would love to play in that championship game. Actually, I'm not as deeply into college football as my husband and mother, but since they like it so much it is a good pasttime. Tom graduated from Michigan and is a big football fan, so he's having a bad year. My mother has loved Penn State football ever since I went there, which is quite a few years ago.

It's voting day. I'm writing this Sunday and plan to be at the polls before they open since I think there will be long lines. Since I'm awake anyway I might as well go. It will be good practice for the Thanksgiving Day sales. I've been a competitive shopper for a few years now. I once went to stand in front of Best Buy at 4:00 am in a blizzard. That was for my projector. It was chaos in the store and I ended up in line behind a guy who had been there all night. So, it will be interesting to see what the voting lines are like. All indications are that a lot of people will turn out.

Friday, October 31, 2008

Galleys, Phillies

After looking through my book's galleys, I found some more mistakes (mine) and so I changed the file and re-submitted it to the printer. We also worked on the cover--I don't have the right color for the title yet and I'd like the picture adjusted a little. I'll pick up the new galleys tomorrow and I hope to get it back the beginning of next week. Then only about a week to print them!

I have learned a few more things about copyright. The US office recommends we read the circulars they have about it, so I opened the first one, Copyright Basics. They said the copyright starts when the book (or music or poem or whatever) is published. So, we don't have to wait for the office to tell us it is copyrighted:


Copyright protection subsists from the time the work is created
in fixed form. The copyright in the work of authorship
immediately becomes the property of the author who created
the work. Only the author or those deriving their rights
through the author can rightfully claim copyright.


I thought I had read somewhere (a long time ago) the copyright starts when it reaches their office. Still, I will be sending in the application as soon as I get the book. They want to know the date it was put into printed form, so I'll be filling that in when the printer tells me it's done.

The more we do, the more we learn. I'm excited to get on with the process. We have a lot to learn about marketing, too.

Congratulations to the 2008 World Champion Phillies. I am from Pennsylvania and my family was a big fan of the Phillies as I grew up. I went to the University of Pennsylvania and worked in Philadelphia for a while after graduating. I moved to other places and didn't follow them as closely, but I'm surprised how emotionally involved I got while watching the post-season. I saw the last pitch and was very happy for them.

Tuesday, October 28, 2008

Great Lakes Naval Museum

It's a beautiful, blustery fall day (Sunday) and my husband Tom and I went to the Great Lakes Naval Memorial and Museum at the Muskegon Lake Channel. A big addition was added this past year and is shaping up although still in progress. There are many models of ships there, including the ones that are docked in Muskegon. I'm sure it's a lot of work. We think they are planning to put some of Tom's pictures of downtown Muskegon in the 1940's there which he had drawn for a pictorial of Western Avenue. They aren't there yet, so we'll check it out next spring.

It was pretty chilly by the lake already. We walked a short distance along the channel, but it's so windy we turned around soon. We also saw the new bike trail along the road to Lake Michigan. They changed the lanes to give bikers more room. I'll have to also plan to take the bike next spring to try out the new setup.

The book galleys needed some work, so this week I'll try to get the final form in to the printer. I had taken a picture of a country church in the general area I used as my setting. However, the town and country are fictionalized and the names are changed. The geography is similar but not the same in my story as the real thing. I was pleased with the picture when I first saw it and so far it looks good on the cover. I am hoping for good resolution on the finished product.

Well, I hear thunder so I'll finish this post. No use taking chances with blowing the laptop.

Friday, October 24, 2008

Deadlines, Cafe Scientifique

My book is at the digital printers and I will meet with them to see the "galleys" today. One of my favorite TV programs was (on CBS from 1984-1996) "Murder She Wrote" with Angela Lansbury as Jessica Fletcher. She wrote mystery fiction and also solved a murder every week. I loved it when she was on a deadline. She'd be busy at her typewriter (the word processor came later), telling everyone she had to get finished with her manuscript by so-and-so time. Then a murder would happen and everyone knew she was the only one who could really solve it. In fact, when the police arrested someone you could always eliminate them as a suspect. Somehow she managed to finish the book and solve the mystery! What a relief until the next episode!

So, I thought of Jessica a lot as I was trying to get my book done before Christmas season. I've been very busy, but fortunately no townspeople have been around asking me to solve a local murder mystery! I've talked with a manager from a book store who might be willing to take it on consignment. She wants to see it first which is totally reasonable, so I want to get it to her as soon as I can. I am now working on getting a copyright. The copyright office is not your grandfather's copyright office! There are all kinds of downloads for forms and I had to update my Adobe ® reader to get what I needed. It's neat because you can fill in the form by computer and then print it all out. You mail in the print-out and the process is supposed to be faster than before. My last book was quite a while ago and I got the notice through snail mail. It didn't take that long , but it's always nice to know you have it.

I'm writing this Thursday, and tonight I'm going to a Muskegon Cafe Scientifique meeting in the GVSU/AWRI building on Muskegon Lake. It's a research facility of Grand Valley State University. The program is by Dr. Keith Crandall who is Professor of Biology and Curator of Crustacea at Brigham Young University. After the presentation, discussion and questions are allowed in an informal setting. It's a very good idea, I think, for students and community members. I used to want to belong to a discussion group when I was in veterinary school at University of Pennsylvania, but 1) I didn't have time and 2) there weren't any--not like this anyway. So I look forward to going sometimes, especially when the topic concerns evolution, religion or both as this one does.

Tuesday, October 21, 2008

Printer

I won't take too long to write this post because I hope to go to the printer today with my book file. I had written a book 9 years ago which was a Christian adventure story. (As I told you, I'm a slow writer, but not that slow! In the meantime I earned a certificate of theology and wrote 2 booklets.) At that time there were no printers that I am aware of in this area which did digital printing of books. I took it to a regular printer and got a lot of copies in order to spread the cost. It took months to get it back and I still have books in the basement.

Now, I've found a printer who does digital printing and they told me it would only take a week or so. And, I can get less copies and still stay fairly economical. I'd like to put my book on the Internet as an e-book also. So, I better get going and soon I'll tell you all about my book!

Friday, October 17, 2008

World Blogger Day

My mother has come and gone and we had a nice visit. She has never been in Michigan in October and enjoyed the colored leaves and scenery. So, it’s time to get back to work with my book, blog and teaching plans.

One of the blogs I enjoy is Tim’s El Salvador blog which you can access at http://luterano.blogspot.com/. He has been a very faithful blogger and publishes information about El Salvador and its people. My husband and I sponsor two children in El Salvador through the agency CFCA (Christian Foundation for Children and Aging), and we were there a few years ago. Tim's blog helps me keep up to date on the happenings there.

I just noticed he has posted that October 15, 2008 was world blogger day. Apparently bloggers from all over the world blog on one subject and this year was poverty. Though this is two days late, I will feel I've added a little by telling you about our sponsored chilren and linking to CFCA HERE. They have done a marvelous job at connecting persons in the US with poor children and aging over the world. They encourage communication by letters from both the sponsor and recipient. One gets to know the family and some of their culture and situation. They also encourage visits. I've been to Mexico and El Salvador through these group "mission awareness trips." It is a way to make a genuine difference in the world.

My husband and I are watching baseball playoffs. I am from Pennsylvania and used to go to Phillies games once in a while. I’m still a fan, so I am routing for them. Although I won’t be upset if the Rays win. They seem to have character as a team. And alas, I am a graduate of Penn State and my husband graduated from University of Michigan. Need I say more?

Tuesday, October 14, 2008

Muskegonmemories

My husband has had a website for several years called "Muskegon Memories." He made a template from software we had on our computer and posted it on a server. However, our computer had a temporary crash the other day and the template would have to be re-done from scratch. I've been wanting him to move to blogging for a while and convinced him this was the time. I set up the blog for him and he is now starting. The address is http://muskegonmemories.blogspot.com/ . He grew up in Muskegon and has worked here a good part of his life. He enjoys local history and volunteers in the archive department of our Muskegon County Museum. For months he has been scanning old pictures to be put in their digital library. Now you have on-line access to old pictures that have been gathered by the museum. If you are from this area and/or enjoy histories of various localities, give it a try!


As for the rest of the week, my mother is coming to visit from Ohio, so I have to get ready. I'm not the greatest housekeeper (not the worst either, I hope), so I've got to get out the vacuum and dustcloth. I'd like to get some things done around the house, but when you're trying to get a book out by Christmas shopping season, the rest just has to wait. Maybe someday I'll get those new curtains and re-paint the bathroom.

Friday, October 10, 2008

Catholic Interests


Along with Latin American studies and Intelligent Design theory, I'm interested in the Catholic Church in general, in unity of Christians, and in women's issues. I like to read Catholic news and opinion and it is nice to be able to access a whole variety online. I was just reading Catholic Online here about the Pope's comments concerning our economic crisis. He is heading a synod of bishops right now for study of the Bible. I've added links to Catholic Online and Catholic News Service on the right column.

I am glad the Pope is speaking on the topic of materialism. It is easy to forget in our everyday life that money is not the bedrock of our existence. We try to assure our own security, but in the end we can't. Trusting in God is in a different dimension than trusting in money. Sure, we work in whatever profession we decide upon or have the opportunity to do and we try to be good stewards. But along with that is a deeper stream of "handing things over" to the Lord. It is allowing His will to be done. In that way we are not swept away with the winds of economic crisis. We look to the Lord for our well-being.

Adding this later: I found a bishop's pastoral statement on the economy from the blog, Whispers in the Loggia. It sympathizes with those who have lost a great deal in this economic crisis and reminds other Christians to be charitable. It is well-put.

Tuesday, October 7, 2008

Latin America

One thing I'm interested in besides ID theory is Latin American studies and the Hispanic population of our country. I watch the Hispanic news on Univision channel on cable. A pet peeve of mine is the lack of news coverage of Latin America on our own news stations. You would think the other countries in this hemisphere did not exist. I am very glad to understand enough Spanish to watch "las noticias" (news) and a few "novelas" (soap operas). We only get one Spanish-speaking station, but to me it is worth the whole cable channel price. (My husband likes the sports.) I took 4 years of Spanish in high school and one semester not that long ago at our city's Community College. Since then, I volunteered for English as a Second Language (ESL), and had a wonderful time with my "student." We learned a lot from each other and are now good friends.

I find the Spanish stations extremely good. I will go into more details later, I hope. Today is busy because there's a lot of college football on. Penn State is my alma mater and Michigan is my husband's. (It's Saturday--I often write ahead and the posts come out Tuesdays and Fridays.)

Then we are going to a Buster Keaton film retrospective. His fan club meets in Muskegon every year because the actor spent time here as a youth, and they found there are many local residents interested in him also. They show his old movies at their yearly meetings which are open to the public on a Saturday night. It is a good place for Tom & I to celebrate our 20th anniversary of being engaged.

Friday, October 3, 2008

Kay at Blog, Anniversary

Now that the short history of science and religion is complete, I'd like to write about various subjects in addition to Intelligent Design. Though I have enjoyed learning about ID for the past few years and would like to teach people about it, I am a writer and interested in other things as well! I've been working on a fictional mystery with Catholic themes which I am typesetting now and hope to get to the printer soon. It is a challenge to write, print and market our own book, but with the new opportunities that digital printing and the Internet provide, I am glad to try.

I'd like to use the blog to put my thoughts in column form, which will be linked under the Topic, "Kay at Blog" and sometimes the subject at hand. I'm interested in many things, and these can swirl around in my head as probably happens with other writers. Writing can help one think and focus toward learning more.

I want to wish my wonderful husband a very happy anniversary. We got engaged 20 years ago this week. We were at a CROP walk, which raises funds for good causes both at home and throughout the world. A good start for our relationship! Our CROP walk is this weekend, and we will supply a half-bushel of apples for the "end-of-the-walk" refreshments. This shows our appreciation to those who do so much work of organizing and raising money through sponsors. Tom has been more than I could have ever asked in a life companion. I hope we have 20 or 40 more years to spend together!

Tuesday, September 30, 2008

Short History 6


In the late 1800’s and early 1900’s a large effort was being put forth by scientists to understand the atom. Many scientists even at this time rejected the concept of atoms. It was only in 1911, 2500 years after the Greek atomists, that Ernest Rutherford convincingly experimented to show that atoms exist with a negative particle encircling a positive center.

The Church’s conception of a beginning for creation has endured scientific challenge. Albert Einstein calculated his general theory of relativity with the assumption that the universe is eternal. Then in 1929, Edwin Hubble recognized that distant galaxies are moving away from each other, confirming predictions of a “Big Bang,” or initial beginning point. The “cosmological constant” with which Einstein “fudged” his numbers to agree with an eternal universe was by his own assessment his greatest mistake.[i]

It is important to note in this brief description of history that neither the church nor science is automatically right or wrong about the physical nature of the world. We must realize scientists go through many stages to get to the truth of nature. It is not wrong to use imagination to make theory—it may take years for experiments to be conducted. And our expectations should not limit our conclusions—a negative result can be as informative as a positive. In a way, every negative finding for one theory is a positive finding for a different theory. We continue to work to understand the relationships between nature and faith. Persons can use the reason God gave them to sort fact and literary metaphor in the Bible—both are there!

[i] Ronald Clark, Einstein (NY: Avon, 1971), 268-270.

Friday, September 26, 2008

Short History 5

The short history of science and religion continues:

The philosophers of the 1600’s & 1700’s promoted a movement called the “Enlightenment.” They influenced a shift in philosophy from a God-created universe to the concept that nature consists only of matter. This outlook is called philosophical naturalism.[i]

In the 18th century, a geologist named James Hutton suspected that the Earth was older than the Biblical interpretation of 6000 years. He believed that rocks slowly formed over time, a theory called uniformitarianism. Though now accepted by geologists, it was rejected by science at the time.

William Paley in 1802 wrote Natural Theology in which he saw the wonder of design in nature. Much of his book describes anatomy, but it also includes the famous “watchmaker” argument. If someone were walking over a heath and saw a watch on a stone, he says, they would immediately recognize the timepiece as made by a designer. When Paley finds intricate marvels with important functions, such as the mechanical muscular system in animals, he concludes they could only be made by a designer with intelligence. One could appreciate nature yet see it as God’s design.

Then in 1859, Charles Darwin introduced The Origin of Species which described his theory of evolution. He believed all species derived from one or a few original organisms. The following generations of offspring changed through the combination of random variation and natural selection. The laws of genetic inheritance had not yet been worked out.

These laws were presented in 1865 by a monk, Gregor Mendel, who had discovered them by careful observation in generations of plants. They were not accepted by the scientific community for some time but are now known to be true.

The 1920’s many persons worked to blend Darwin’s theory with Mendel’s genetic laws. The names of Morgan, Mayr and Dobzhansky are prominent in the formation of what is now called neo-Darwinism. This new synthesis, however, was taken by some to be more than a scientific theory. It has been used as a reason to reject any possibility of supernatural intervention.

[i] Del Ratzsch, Science and its Limits (Downers Grove, IL: InterVarsity Press, 2000), 180, footnote 10 from page 122.

Tuesday, September 23, 2008

Short History 4

We continue our (very) short history of the relationships between science and religion.

After Christ's life on Earth, Christianity spread throughout Europe, Africa and Asia Minor. Other world religions thrived: Hinduism, Confucianism, Buddhism. Mohammed, originator of Islam, was born in 570 AD.

Roger Bacon (c.1214-1292) was a British Franciscan (friar of the order of St. Francis) who is credited with the grounding of science in experiment. He conducted some experiments of his own and promoted optics, mathematics and language as keys to the sciences. Persons in the church, however, became suspicious of him and he was imprisoned for a time.[i]

Also in the 1200’s, Thomas Aquinas took a new look at Aristotle. Europe had seemed to lose interest in him, but Aristotle was preserved in the Arab world and now was being revived in Europe. Aquinas wrote the famous Summa Theologica. His first premise was that humans need both reason and revelation from God for full knowledge.[ii]

Nicolaus Copernicus (1473-1543) was both a scientist and churchman. His belief in the heliocentric (sun-centered) solar system was reinforced by Galileo (1564-1642). Many know of Galileo’s clash with religious authority of his day. He was condemned two times by the Catholic Church, but later exonerated by other scientists. In 1992, Pope John Paul II apologized on behalf of the Church.[iii]

Francis Bacon (1561-1626) encouraged the “inductive” method of science. He said science should be conducted only through observation and experiment. He was reacting against the mixture of knowledge of nature with spiritual speculation of the day. For example, investigators of chemistry often included alchemy and magic in their reasoning.

[i] New Catholic Encyclopedia, Second ed., s.v. “Roger Bacon.”
[ii] Thomas Aquinas, Summa Theologica Part I, Question 1, Article 1.
[iii] Smith, A. Mark, “Galileo,” 11/15/06, http://www.nasa.gov/worldbook/galileo_worldbook.html#wbtop .

Friday, September 19, 2008

Short History 3

From Old Testament times, prophets predicted a Messiah for the Jewish people. They expected a political liberator who would bring in a new age where Israel would be triumphant and rule over enemies.


Jesus Christ was born about 4 BC According to the Christian religion, Jesus was and is the Messiah, but His leadership was not what the Jews were expecting. Christians believe He is the Son of God and came to redeem and free the human race from sin. He died around 30 AD (the exact year can only be approximated).[i]

Shortly afterward Paul, a disciple of Jesus, wrote regarding knowledge of God through nature: “For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made…so that they are without excuse” (Rom. 1:20).

In 30 AD, Galen, a Greek physician, was born. He wrote books which influenced the way medicine was practiced for about 1500 years, even though it was very limited. For example, he did not know that blood circulated in the body.

Also, Ptolemy, an Egyptian (probably Greek immigrant parents) living at 100 AD, drew an elaborate planetary system in which the Earth was center. It agreed with Aristotle’s view and continued to be accepted in the Middle East and Europe.

St. Augustine, a great theologian, lived in about 400 AD. In “The Literal Meaning of Genesis,” he warned Christians that unbelievers know facts about physical elements of earth and sky. If Christians try to teach Scripture in terms of false facts, they would detract from the true spiritual messages.[ii] However, Augustine himself did not hesitate to proclaim that the initial Creation is God’s handiwork.[iii]

This short history of relationships between science and religion will be continued.

[i] New Catholic Encyclopedia, Second ed., s.v. “Jesus Christ.”
[ii] Cf. St. Augustine, the Literal Meaning of Genesis Sec. 38-39, Ancient Christian Writers. trans. John Hammond Taylor (NY: Paulist, 1982), search “augustine-genesis” at: http://www.holycross.edu/search.html .
[iii] Cf. St. Augustine, City of God, Book XI, Ch. 1-8,

Tuesday, September 16, 2008

Short History 2

Continuing in the historical relationship between religion and science, Abraham lived at about 2000 BC. He believed in one God, and that God promised he would be very fruitful, the ancestor of kings and nations (cf. Gen. 17:4). He was the great-grandfather of the twelve tribes of Israel and is listed in the genealogy of Jesus Christ.

Various groups of peoples lived in the Americas from the times before Christ. The Olmecs were developing calendars and language in Mexico. They were polytheistic, worshipping, for example, gods of sun and rain.
[i]

Ancient Greeks worked on understanding nature. Pythagoras (circa 582-507) wove ideas about mathematics and philosophy. Around 500 BC, “atomists” believed in tiny building blocks for the structure of nature. Anaxagoras, himself an atomist, thought a cosmic “Mind” had intervened to bring order from chaos, thereby perhaps anticipating Intelligent Design Theory (picture from Wikipedia s.v. Anaxagoras).

One of the greatest philosophers, Aristotle, was born in 384 BC. He believed in a God who sustained an infinite universe, with the Earth in the center. He thought God had little to do personally with human beings. Aristotle classified nature as he observed it and developed formal logic.

The theory that the Earth was the center of the universe, therefore, was not just from the Bible. In ancient times, philosophy, science and theology were intertwined in various forms. Philosophy literally meant a “pursuit of wisdom” which in that day included knowledge of the natural world.

To be continued.

[i]
World Book Encyclopedia, 2006 ed., s.v. “Mexico.”

Friday, September 12, 2008

Short History 1

People throughout the ages have had both a yearning for God and a curiosity about nature. It may be helpful to look at a very short summary of science and religion history to give perspective for today's comparisons.

Many civilizations of the Earth in these early times believed in multiple gods. The Sumerians by 2500 BC worshipped Mother Goddess Innin and son Tammuz. Egypt in 2000 BC had Isis (picture from Wikipedia s.v. Isis) and Osiris.[i]

The vast times of history before 2000 BC are dim. But in one of the earliest scientific endeavors, Egyptians developed a 300-day calendar with 12 30-day months, then eventually one with 365 days regulated by the sun, moon and stars.[ii]

Also before 2000 BC, Sumerians (who lived in present-day Iraq) were writing on clay tablets with pictograph signs. Egyptians and Sumerians were using copper alloys.[iii]

The Old Testament of the Bible is in part a history of the Jewish people. The book of Genesis proclaims the creation of Heaven and Earth and the first people, Adam and Eve. A man named Tubalcain was the seventh generation after Adam. He was “an instructor of every artificer in brass and iron” (Gen. 4:22, KJV).

To be continued.

[i] Bernard Grun, The Timetables of History, New third rev. ed. (NY: Simon and Schuster, 1991), 2.
[ii] Grun, 3.
[iii] Grun, 2.

Tuesday, September 9, 2008

Cosmological Model

Picture from Hubble Space Craft, NASA.


Another of Eugene Koonin's articles published last year, "The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life," takes unsolved aspects of evolution to a higher level. The numbers of combinations that atoms can make randomly show us that biological life by random chance is so improbable as to be impossible. Genes can flow, drift, move horizontally or vertically or double, triple or quadruple but they just can't overcome these probability numbers. That is because the extreme improbability encompasses all the movements and chemical reactions of the so-called pre-biotic elements. Though scientists are trying to find chemistry which produces the present organization, they haven't found a set of answers which can explain the complexity of life.

What has been found on the cosmological level is an anthropic fine-tuning of physical laws that had to be as they are to make the universe livable for humans (anthropic). So Koonin blends the high improbabilities of life into the anthropic principle. He says, "In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable."

Koonin says that in this scenario, the RNA world may never have existed. The universe we live in is, in this theory, fine-tuned not only for physical laws but biological origin and evolution. It has only become that way, however, by chance because an infinite number of universes would cover everything.

This is a scientific article published by a scientific journal. Yet many believe evolution is a fact, not a theory.

The infinite universe theory is as un-falsifiable as they accuse Intelligent Design of being. It seems to me that if the multiverse wipes out biological probabilities, it would wipe out physical ones as well--the ones used to understand quantum physics in the first place. It is quantum physics that underlies the multiverse claim--a quantum fluctuation somewhere in space (see references in Koonin article for more information). And quantum physics was first described by Max Planck based on probabilities of energy radiating from light at various frequencies.

New microbiological scientific data does not coincide with past evolutionary data and theory. If new facts fell into the expected place, it would be different. Scientists should evaluate where we are now no matter what they hope for the future. It is important for citizens such as judges and school board members to know the truth. As of now, though there may be micro-evolution where species can make small changes, macro-evolution of all species, one from another, is not a fact.

I talked a while ago about doing some posts on the history of science and religion. I haven't gotten very far but will try to do more shortly.

Friday, September 5, 2008

Exaptation


The number of possible combinations of amino acids in proteins is directly related to the number of combinations of sections of DNA called "nucleotides." The central rungs of the "ladder" in DNA as seen in the picture on left and the August 19 post are composed of a sub-unit called a nitrogenous base. Every set of three of these rungs is coded for one of the 20 amino acids used in proteins. So you need the right order of 4 possible nucleotides to get the right order of amino acids in the protein. The four nucleotides contain cytosine, thymine, guanine and adenine, designated c, t, g or a. It seems a little easier to talk about 20 amino acids than the codes of 3 nucleotides from combinations of 4. In the last post I said it is estimated that about 1 in 10^65 proteins are specifically functional. This was estimated for proteins of about 100 amino acids in length. Therefore, 300 nucleotides would have to be in correct order for the proteins to have 100 amino acids in correct order. It gets a little complicated because some sets of nucleotides can code for the same amino acid. But this gives us at least an idea of the numbers we are talking about.

I put all this in to comment on the theory of the "RNA world" that many are touting as the answer to origin of life. It wasn't protein, they say, that had to form by chance, but RNA. Well, RNA still has to overcome the numbers just like protein. The RNA nucleotides have to be in the right place to do the work it is supposed to and to "evolve" to the right molecules that we find in the bacteria and archaea. (RNA has one different nitrogenous base from DNA--uracil for thymine).

Another concept that some scientists insist is the answer to all our questions about evolution is "exaptation." So what if the flagellum of the bacteria is a complicated machine made of 25 types of proteins? All we have to do is realize that these proteins had other jobs on their way to evolving a flagellum. The Cyanobacteria DNA polymerase protein has over 900 amino acids. That is a total of 10^1200 possible combinations of 20 amino acids for the molecule. How long before it falls into the configuration that copies Cyanobacteria DNA? What about the other 3,100 or so proteins of Cyanobacteria (as reported by Kaneko et al.)? And what about the hundreds of amino acids that are not found in protein?

With information theory, Hubert Yockey gives us the number of 1 in 10^65 amino acid combinations (of the 20 biological amino acids) is functional for a specific job. That's a 1 with 65 zeroes after it. With the kinds of numbers of intermediates, exaptation means little. Who can think of all the other functions these proteins would need to take on the way to becoming what they are? What would carry on the work of replication while we waited? And many of the "one in 10^65" combinations for DNA polymerase would not even have folds which proteins need for function. These unfolded proteins as well as folded on their way to the right use would be hanging around looking for a place to work like the jobless at an employment agency.

Tuesday, September 2, 2008

Biological Big Bang

It is an exciting time in biology. Last year, several articles about origin of life (OOL) and evolution were published by Eugene Koonin from the National Center f0r Biotechnology Information, National Institutes of Health, Bethesda, MD. Though I don't agree with his theories, Koonin does the best job in summarizing the state of OOL and evolution that I have seen. One article was called "The Biological Big Bang model for the major transitions in evolution." It discusses the areas in biology that show "the sudden emergence of diverse forms at a new level of complexity." These areas typically co-exist with the old forms rather than replace them as is predicted in Darwin's theory.

Koonin lists six areas of transition that are unexplained: Origin of protein folds; Origin of Viruses; Origin of cells; Origin of the major branches (phyla) of bacteria and archaea; Origin of the major branches (supergroups) of eukaryotes (true cells); Origin of animal phyla.

Several very interesting facts emerge from the text. One is that two of the principle cell types that exits, bacteria and archaea (one-celled organisms) have, among other things, "non-homologous core DNA replication enzymes." This means that the proteins of bacteria are distinctly different from another group of simple cells, the archaea (to see examples, scroll down or hit DNA label below or on right under topics). Some scientists had expected the archaea to be the evolutionary precursors of the bacteria, but they are not. The DNA polymerase molecule of the Cyanobacteria which has over 900 amino acids is different than the molecule that replicates DNA in one of the archaea species which has 882 amino acids as reported in Uniprot (Q2JWV2 and P26811).

Now, this does show that different molecules can do the same thing. But, as Koonin says, "This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria..." Two different molecules with the same specific job came from a tremendously large pool of possible combinations. After all, I've shown you molecules that do very different jobs within the cells, so the amino acid sequence is crucial to function. Koonin proposes alternate solutions, still hoping for that common ancestor. But let's look at the numbers. For Cyanobacteria, just one protein, the DNA polymerase, has about 10^1200 combinations of 20 specific amino acids. The number of events (including chemical reactions) in the universe, if it is about 14 billion years old, has been less than 10^150. This discrepency is obvious.

Hubert Yockey used Information Theory to estimate that in a protein of 100 amino acids, only about 1 in 10^65 are functional for a specific job. I can imagine that a longer protein would have even less chance to be functional enough to replicate DNA in conjunction with other equally complex molecules. To determine the exact proportion of functional combinations would be a great project for proponents of Intelligent Design (it has not yet been done that I know). That area of study is being stifled in universities, as reported in various places such as Discovery Institute (link on right column of this blog). It is the subject of the movie "Expelled" with Ben Stein that was shown over the summer.

Assuming reactions between potential proteins, with 1 in 10^65 proteins being specifically functional, the probability that 3 functional ones would meet together would be about 1 in 10^195. Less than one chance in all the events of the universe for the combination of 3 proteins to function as they need. And even 3 specific, functional proteins are not enough for DNA replication for one organism.

Friday, August 29, 2008

DNA Polymerase


In the picture of DNA replication from August 19, we skip to the left a few molecules along the top and find DNA polymerase. This is the molecule which is necessary for copies of genes (DNA) to be made. DNA replicates in order to produce the next generation of organisms and, in plants and animals, for cell reproduction. We are talking now about Archaea and Cyanobacteria since they were among the first organisms on Earth. The DNA polymerase (pronounced po-LIM-er-ace) has a complex job and we will not go into all the details. I want to show you the pictures of those from a species of Archaea and Cyanobacteria. At the top is a computer structure from Swiss Model RepositoryDNA polymerase from Archea. Details are reported at Uniprot P26811. It has 882 amino acids.

The Cyanobacteria DNA polymerase pictured above has 928 amino acids as reported at Uniprot Q2JWV2. It is shaped in a way that it can work on the DNA molecule to manipulate the chemical reactions needed. It is made by other molecules which can carry out reactions that copy the DNA genes and transform the code of the DNA to proteins. One of those molecules is RNA polymerase, which is pictured in the right column of the blog.

I could go on with showing you the rest of the molecules that are pictured on the DNA replication picture as well as some which are not. There are sub-units of DNA polymerase which repair DNA when it is broken. There are some which attach short molecules at first that have to be replaced later for the DNA replication to be complete. I think, however, that by now you see the vast complexity of even the very first organisms.

There is much to be said about this complexity and I will discuss implications in posts to come. I want to link you to some articles from mainstream scientific journals that help us see that this complexity is a very significant obstacle to the notion of random, materialistic origin of life and total random, materialistic evolution (total-natural evolution) to explain all life.

Tuesday, August 26, 2008

DNA Primase

Organisms called Archaea were discovered in fossils dating, according to accepted radiometric methods, from about 3.8 billion years ago (bya). I've shown some of the molecules from the first of bacteria, found in fossils from 2 bya, Cyanobacteria (and will show one of Archaea soon). Another molecule to add to the list is DNA Primase which you can read about in the link to Wikipedia. The primase helps the helicase make the DNA ready for replication. A picture of one is here.


This protien molecule has 646 amino acids as reported by UniprotKB/trEMBL here. The amino acids are shown and described in the previous post. This is a different protein than the helicase and topoisomerase which I showed in previous pictures (use DNA link under topics and label or scroll down). The molecules are each shaped uniquely to give them the ability to do specific jobs, just like a toaster and coffee-maker are shaped differently, with different shapes and arrangements of parts.

Friday, August 22, 2008

Helicase


The DNA molecule as seen in my previous entry (and at DNA label below) is undergoing reproduction. There I showed the first molecule which affects the DNA to prepare it for the process of replication. Now we come to another molecule, called a helicase. These take apart the pairs of nucleotide units which make up the DNA. Above and at the link is a picture of one from Swiss-Model Repository from a Cyanobacterial species. This molecule is made of 773 amino acids, as reported in the research reference in Uniprot Q8DG65. To remind you, there are 20 types of amino acids in proteins, as opposed to hundreds found throughout nature. I am adding pictures of the 20. They are made of atoms like Oxygen, hydrogen and nitrogen. The corners of the lines are understood to have the atom Carbon. The Amino Acid--Creationwiki link at right takes you to a better view if you want it.






These are the units which make up the proteins. There were over 900 amino acids in the first molecule we needed to loosen up the DNA so it would be ready to replicate. This molecule with over 700 amino acids is needed to take apart the DNA so it can be copied to make more cells and organisms. The amino acids have to be in enough of a specific order to allow for the protein to form the way it should. Some of the amino acids may be substituted by a limited amount of others, since there are several groups which have similar properties. But experimentally, some amino acid placements have been found to be absolutely necessary or a protein will not work. Just one difference will completely leave the protein without function.

Tuesday, August 19, 2008

Topoisomerase



Every cell that has DNA needs a set of tools for copying it so the cell can reproduce. We turn over most cells in our bodies, so new ones have to be made. Also, when the organism reproduces, DNA must be replicated.


Last time I talked about Archaea and Cyanobacteria, since they are some of the first organisms to be seen in fossilized form on the Earth. We will see some of the microscopic tools these ancient organisms must have had from the start. To begin, they needed the DNA itself, shown at top. In my previous post I had a picture of the molecules which make up the rungs and sides of the DNA (which is shaped like a twisted ladder). Though scientists speculate that molecules evolved from RNA, these organisms all need DNA. Some of the DNA is stored in circular form, but it needs to be copied for reproduction and production of cell products, the proteins.


The molecule at the right in the top picture is called "topoisomerase." This molecule is necessary in the process of copying DNA. In circular DNA, it loosens the DNA which is packed tightly. A picture of a topoisomerase acting on a DNA strand is at left. The molecule in one species of Cyanobacteria has 933 amino acids, as shown in Uniprot Q2JJ84. The atoms of this molecule have to be arranged in an order that will do the job of systematically working on the DNA to prepare it for reproduction.

Each of the 933 amino acids themselves must be in correct order of atoms, since the order determines the arrangement of charges which hold the topoisomerase molecule together. The 933 amino acids first are connected in a straight line, but then they must attract each other in just a way to make folds that make a working machine.

The probability that 933 amino acids formed by chance 3.8 billion years ago so that the DNA of a Cyanobacteria could be copied is, as you might guess, infinitesimally small. It is less than 1 event in all the events of the universe so far, including chemical reactions (which is 10^150). But we have many more molecules to go to show the extent to which Cyanobacteria had probably already developed.

Many scientists think there was some way that these molecules could form naturally, such as following a law which caused arrangements that could perform these tasks. . The scientists insist life started without supernatural help from God. In the meantime, though they are far from finding the supposed way it happened, they are incensed when others are reluctant to believe a non-established theory that life somehow started by materialistic, naturalistic means.

Even many scientists who are Christian insist that it is unreasonable to look to direct supernatural intervention to explain life. Are they worried that children will not grow up with curiosity in science? I think curiosity is a human trait that comes from and through all circumstances. No one will stop wondering about science just because of Intelligent Design Theory. Some fear Intelligent Design Theory will suppress the pursuit of knowledge. I hope my blog shows that the more one pursues knowledge, the more the wonders of the biological world reveal earmarks of design.
Added 8/9/2010: I have moved from using the term "Intelligent Design Theory" to "Creationism" to describe my own stance. Though ID theory has done much to show the science of biology, the theological attitude is that the designer could be anyone. I do not agree with this. If you are a Christian, you believe that God is the creator and designer. Science cannot be separated from theology for a Christian in the way the ID advocates say.

Friday, August 15, 2008

Archaea, Cyanobacteria

The Archaea are considered one of the first forms of life. They were found in rocks that were judged by radiometric dating (r.d.) to be 3.5 billion years old. Traces of one of their molecules they contain (a lipid, which is a fat), were found in west Greenland and r.d. to 3.8 billion years ago. These organisms were found at extreme temperature environments at first, but since then have been found in almost any kind of environment.

Archaea were supposed at first to be variations of the bacteria, but were eventually found to be so different from bacteria that they were classified in a different kingdom, or domain, from bacteria and the other type of cell (eukaryote, or true cell). And so, it became apparent that the original organism that Darwinists look for had to be a common ancestor of both the archaea and bacteria. The search for this Last Unknown Common Ancestor, known as LUCA, is what is going on now in Origin of Life studies. Here's the rub: the fossils for the Archaea appear almost as soon as the Earth, after being bombarded by meteors, was cool enough to allow any life at all .

The cyanobacteria were formerly called bluegreen algae but now are considered bacteria. They have made hardened structures called Stromatolites which scientists use to date bacteria as far back as 2 billion years.
So, because the proteins of the prokaryotes such as cyanobacteria do not match closely to the proteins of the archaea, scientists are looking for a last previous common ancestor. They are running out of pre-organism time, because the structures of functional molecules in each of these types of organisms alone would take not millions or billions but trillions upon trillions of years to happen by chance. Any laws of physics or chemistry that would cause them to organize like the molecules I will be showing you would themselves be non-random laws (and therefore lead to a biologic anthropic principle). One study by Kaneko et al. from "DNA Research" tells us a certain strain of Cyanobacteria have 3.5 million base pairs in their DNA. It also estimates a total of over 3000 genes. The following picture shows a unit of the DNA. These units alone are hard to find in nature, much less put together in a way that is functional. They are made of atoms, such as oxygen, hydrogen, nitrogen and carbon which are arranged in a specific way. The unit on the left is the "backbone" of the DNA, the part that looks like the long sides of a ladder. The molecules on the right are attached where it says "Base" to the backbone. Each pairs to another, thus the name "base pairs" for description of DNA. A short one connects to a long one, always in the same A-T or C-G pairing. The Uracil is used in RNA instead of Thymine. These base pairs form the rungs of the ladder and make a genetic code that can be read to form proteins. The picture is from Wikipedia s.v. nucleotide. (The molecules on the right are also the components of spliceosomes I've had in recent posts).

Cyanobacteria are free-living because they have a system for photosynthesis, which allows them to convert light energy into a source for chemical energy (ATP). Kaneko et al. estimates 128 genes are needed for photosynthesis alone. The organisms can then make all the molecules they need for structure and metabolism. Their genes, made of the DNA, allow them to reproduce by themselves. The structures that have been suggested by some scientists as original life, such as ribozymes, have been manufactured in the laboratory and cannot do these necessary things, and cannot sustain themselves. One study by Ouzounis, et al. from "Research in Microbiology" has shown that at least 1000 genes are needed for life to exist independently.