Creationists and IDists v. BioLogos

This post is a little complicated, but it is important concerning the "evolution wars," and I've edited a few times to make it as clear as I can. To start, BioLogos is a group of people who are committed to "Theistic Evolution" (TE). TE is the premise that animals and humans developed by evolution helped along by God. Theoretically this help could come directly, such as if He intervened in the genes of an embryo to be therefore born slightly different than its parents. This approach does have the problem of people coming from animals. Or, in the version pushed by BioLogos, God could have acted in a Divine Hands-off manner (also known as Deism). This scenario supposes that God somehow caused evolution to happen in a pre-planned way that would LOOK to us as random.

There are several problems with this Deism view. One problem is that on a physical level it correlates exactly with any secular or atheist’s view of evolution, what we call neo-Darwinian evolution. Secularists look at evolution as random (the random genetic mutation element means the basis of evolution is random even though there is a non-random element called selection). Another problem with this view is that there is a logical fallacy in saying life LOOKS LIKE it was brought about in a random way because biological structures do NOT LOOK random. Our bodies have trillions of cells working together to give us life. A cell is a basic unit of biology. Proteins, which are the working molecules of the cell, are very specifically constructed for what they do. The DNA inside the cell acts as a code to make the proteins, and therefore must also be very specific. These molecules do not look random.

So we have a group of people (BioLogos), many of whom are scientists, who tell us God somehow created animals and plants and people, but we are supposed to go by the book of all secularist and atheist scientists. In contrast there are other groups of people who are actively questioning the secular view and secular-like TE view put forth by BioLogos. One group of Intelligent Design (ID) advocates is called the Discovery Institute. These people are dedicated, among other things, to make the facts known about proteins and other biological structures and claim these structures were designed. They are using scientific methods, such as information theory, to try to prove what they are saying. Other groups are Special Creationists (believing in direct supernatural creation by God), such as Answers in Genesis and the Institute for Creation Research. These also have scientists in their ranks and are using their websites to argue their cases.

Since BioLogos backs atheistic outlooks on creation and evolution, the arguments of the Discovery Institute and Creationists are directed against both Biologos and atheists. On the Discovery Institute’s newsletter website and his own, Darwin's God, Dr. Cornelius Hunter is showing why the BioLogos arguments are wrong. A very good example is in the post "Shared Errors: BioLogos on broken genes," Darwin's God (May 31, 2016).

So a major problem with BioLogos is though they say they want to show how science and religion can be reconciled, they promote both a non-religious and non-scientific (illogical) view of evolution. They imply that God is not really needed because evolution is random anyway, and that if you want to believe in God, you still better believe in non-divine-type evolution.

The person who started BioLogos, Dr. Francis Collins, a self-professed Christian, has been instrumental in the present legal status of using human embryos in scientific research. Though the BioLogos people profess to be Christian, neo-Darwinian evolution has been the only option until recently for atheists (for a new alternative, see The Third Way of Evolution).

Casey Luskin, who worked for Discovery Institute for many years, has published a paper about the relationship between atheism and the teaching of evolution. It is Casey Luskin, "Darwin's Poisoned Tree," Trinity Law Review 21, 1 (Fall 2015): 130-233. You can find the paper description and link to a PDF file at the link in the title.

It is not unusual for Christians to be right about some things and wrong about others. This is part of growth and learning. BioLogos Christians are wrong to push their random evolution agenda. Somehow they are blinded, perhaps by some imagined promise of scientific discovery, to the amazing design in biology that is obviously seen by others as supernatural creation. Refer to the Bible in resisting intimidation by scientists who tell you we came about by chance:

Ever since the creation of the world, his invisible attributes of eternal power and divinity have been able to be understood and perceived in what he has made. As a result, they have no excuse (Romans 1:20 NABRE).

Cambrian Explosion Explodes

The latest in the regular literary output from the Intelligent Design (ID) people has made its debut. It is by Steven Meyer, Darwin’s Doubt, (HarperCollins Publishers, 2013), and he acknowledges help from fellow Discovery Institute members. These guys are pretty sharp when it comes to biology.

Even if you are a regular follower of ID theory and read the Discovery Institute website, Evolution News, the new book gives worthwhile perspective on the breadth and depth of scientific research about evolution or the lack thereof. It focuses on the so-called “Cambrian Explosion.” This describes a geological layer of rock where many animal forms have been discovered without any build-up toward their full formation in the rock layers beneath. These findings defy the tree-like description of gradual change that Charles Darwin said would be found if he were correct about evolution. He believed the Earth started with a “simple” cell-like organism which through generations of time slowly developed into various species and forms which we know now. Meyer shows how the fossil records are not what Charles Darwin predicted.

An earlier book by Stephen Meyer, Signature in the Cell, (HarperCollins Publishers, 2010) is about the origin of life. So with these two volumes you have extensive descriptions of biology and the consolidation of many facts related to the evolution debate. I think Meyer is very readable and should be understandable even to beginners. These two volumes are worth the money for anyone interested in these subjects. That is because the coverage of the issues is so extensive that the two books sufficiently teach about the history up to the very latest of science concerning life origins and evolution, both for the ID and neo-Darwinian perspectives. The books are worthy enough to be read down to the last word, and they should be valuable reference books too. However, whether or not we accept that biological life was designed, Meyer thinks we may never know all the details of how it came about.

As I’ve said before, I’ve moved from this particular point of view (ID) to Direct Biological Creationism. I’m open-minded about the age of the Earth, but ID holds that it is billions of years old. The proponents also do not want to combine the science with religion, which I think is a mistake. When faith is first, true science falls into place, even when we don’t have all the answers. Research can go on to new heights, but we will also respect life in a new light. This should not be a problem in our country because America was formed in order to give people religious freedom. The problem is with the people who interpret the Constitution in the wrong way. I’m not saying you should read Scripture in public school, because I don’t want literature from all religions read in school. But there must certainly be ways to work out the freedom to say, within the confines of a public school building, that you believe God made biological cells.

The Apostle Paul advises "be renewed in the spirit of your minds, and put on the new self, created in God's way in righteousness and holiness of Truth (Ephesians 4:23-24 NABRE). When a person becomes Christian he or she sheds the old self and becomes new. When this happens, faith, not science, is first. You do not have to be a believer to be an Intelligent Design advocate. But when you become a believer, faith is the first priority even in reason, and all logic follows in line.

Science and Culture

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

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

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

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

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

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

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

For it is written:

“I will destroy the wisdom of the wise,

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

(1 Corinthians 1:19 NABRE)

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

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

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

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

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

IC--Irreducibly Connected

The Indiana Senate passed a bill, SB 89, to allow the instruction of Creationism into the classroom (AP article on Fox News HERE). The Discovery Institute, which is the foremost think tank for Intelligent Design Theory (sometimes known as ID), condemns the bill, reported by Robert Crowther II, HERE. The ID proponents think evolution should be taught, but also that persons should be allowed to bring up flaws in the theory. The Creation in question is probably that called Young Earth Creationism, in which some people believe God created the Earth around 6 to 14 thousand years ago.

I disagree with the Discovery Institute. I think we should have long ago come to the realization there are irreconcilable differences between Americans when it comes to our various religions (or lack thereof) and science.

Though the Discovery Institute has been the victim of abuse by the leaders of today's scientific community, they are willing to heap abuse on an even more vilified group, the Young Earth Creationists. They may not intend to be demeaning, and perhaps are even trying to help. But they are not very farsighted if this is the plan.

Our country is based on freedom of religion. We are getting far afield, acting as though we believe it was founded on scientific political correctness. Please remember, not all scientific theories are right. Albert Einstein at one time believed the universe had been eternal, without a beginning. He even fudged a calculation to make his math fit his theory. But he was proven wrong by astronomers, primarily Edwin Hubble, who confirmed that the Universe is expanding and therefore had a beginning, now called the Big Bang. Why is this a lesson that never seems to sink in?

If the Discovery Institute had been around when Einstein theorized the Universe was infinite, are they saying children had to be taught that's the way it is because Albert Einstein said so? This is when the Creationist children would have believed the Universe had not been infinite, but they would be faced by authority figures who taught something against their own faith. And then later Einstein was proven wrong. Are we to say evolution is right, except it's OK to question it? The people at the Design Institute are themselves pandering to the politically correct scientific culture. If evolution is only one of various theories, it should be presented as such and the beliefs of others should be acknowledged from the start.

Though I talk here of whether a theory is correct, it is a separate but even more important matter that some Americans believe it is correct. As long as the religion of the person includes Creationism, it is a matter of freedom of religion. Catholic bishops are recently incensed over an attempt by the government to impose insurance rulings on Church institutions. They say it goes against religious freedom. But where are they when the government has walked all over other denominations in demanding that evolution and only evolution be taught in the nation's public schools?

The Discovery Institute often presents the argument that the Supreme Court has already decided that Creationism is to be kept from the classroom. But there are hundreds of thousands of people marching every year in Washington DC to reverse the Supreme Court decision of Roe v. Wade in which abortion has been made legal. Writers from the Discovery Institute grouse regularly over the decision of US District Judge John Jones in the Dover PA trial about introducing ID into classrooms (TalkOrigins description HERE) but hold as unchangeable the Supreme Court decision to keep Creationism out. Maybe they have their reasons in their own agendas. They regularly talk about the Old Earth and fossils of millions of years old. Perhaps they are unwilling to stretch their abilities in order to consider others with different points of view, such as Young Earth Creationists.

"Irreducible complexity" is a phrase coined by one of Intelligent Design's proponents, Michael Behe. It is time to recognize that many people's belief systems are irreducibly connected to science. Faith forms our biology theories as it forms our laws and political systems. Young Earth Creationists unabashedly start right from their Sacred Text and go from there, as at Answers in Genesis website HERE. This is something the laws must reconcile, and not just collapse under the pressure of anti-religion groups who claim this teaching would be unconstitutional. The government enforces anti-religious views on students in the classroom--those whose mothers are unable to home-school them, that is. This is a large part of our population which is treated thus.

I know that to bring Creation Science into the classroom would be messy. People don't like it when they have to cope with other people's conceptions of truth. For example, those who believe in evolution don't want to think about design. But who are the intelligent ones? The persons who can understand only one point of view, or those who can see a variety of possibilities? Isn't that what scientific exploration is about?

Studies in Heaven?

When I first started this blog, I said there were three things I am especially interested in. They were: 1) Latin America and the Spanish language; 2) women's rights, especially in the Church, and; 3) creationism and ID theory.

I find that as time goes on, my interests have shifted almost primarily to the third, as it concerns biology, evolution and creation. That has probably been reflected in the number of entries devoted to this subject from early on.

Biology is so fascinating that I can't tear myself from it even when I try. Of course, biology is crucial in understanding things like medicine and even psychology. But I am not involved in these endeavors and my interest is mainly from a perspective of being awed by God's abilities.

But sometimes I wonder, will biology be relevant in heaven? Will God reveal the history of his creative steps on Earth to us? Paul had said that our bodies will be different after death, and one wonders to what extent that will be. There is description in the Bible in 1 Corinthians 15 about this. Will we no longer care about the details of how our bodies work here?

I suppose those who have devoted their lives to study of these subjects may have hold-overs in heaven. They'd like to finally find out about confusing fossils, or which biological characteristics may have developed on their own and which had been affected directly by God. And perhaps with increased understanding we may be able to follow more of the systems of biology and see how it all works together. The earthly body is so remarkable that it would make good subject matter even in heaven.

The above Bible chapter is a powerful one in that at the end, Paul says we should stand firm and work for the Lord. God gives victory over death through Jesus Christ. As far as a person's interests go, this should be the priority, an organizing factor for which all other interests fall in their rightful place. It can be a little hard for each of us to discern how to do this best, but it is what I will try to do from now on.

Design v. Non-design

Most people are familiar with atoms. They have a center made of positive and neutral particles, called the nucleus, with a cloud of negative electrons encircling it. It is amazing to me that the number of these particles make such a big difference in the way the atoms combine with each other to make the huge variety of things we see in the world, including the world itself. These atoms move in a zigzag way which we call "random" and they combine with each other depending on their qualities, but also where they happen to be near each other "by chance."

Many people assume that randomness is the same as non-design, and order is the same as design. I do not believe this is correct, and I think it causes some confusion when we talk about design in nature, especially what we see in biological systems. Yet chemistry does have a predictable behavior, under what is called the Law of Mass Action (Wikipedia description HERE). Even so, an underlying characteristic in this physical law is probabilistic behaviors of atoms and molecules. So we are not getting away from randomness when we move from individual atoms and molecules to groups of them.

As I said before, the random movement of atoms is important for certain things. It helps mix the molecules in our atmosphere so we can breathe. Imagine walking into a pocket of air that has no oxygen. Where would we run to find it? Without random movements, we couldn't have mixtures of liquids with two or more things. They would otherwise stay separated, like water and oil but worse.

Therefore, if God made everything, the random movements of the atoms were also part of the design. Randomness is not opposite design. Genesis 1:2 tells us (NABRE): "the earth was a formless wasteland, and darkness covered the abyss, while a mighty wind swept over the waters." Leaving aside the word "waters," the opposite of design seems to be a dark abyss--nothingness or the void. Perhaps "waters" is metaphorical. That goes along with our Nicene Creed in which we say we believe God is the Creator of all things seen and unseen.

It is a feature of Intelligent Design Theory to see design in the workings of DNA and proteins in the cell. The trouble is, ID proponents compare it to randomness, when this is also design. So they are not proving design, just the discrepancy between biological and non-biological formations. Now this discrepancy is important, but it does not define design.

That is why faith is really more important than science. If you believe, it sets the groundwork for studying the rest of God's creation. All things are designed, and science is the study of created physical objects.

Comparitive Genetics

There have been several long comment lists to posts about evolution and Intelligent Design at the First Thoughts blog of the magazine, First Things. I was happy to be able to contribute some comments. The first post is Joe Carter, "A Walk to the Moon," First Thoughts (Jan. 5, 2010). Then more opinion and comments were presented in a subsequent post by Dr. Stephen Barr, "Re: A Walk to the Moon," First Thoughts (Jan. 7, 2010). Many have been related to the new discoveries being found in comparative genomics.

I had followed many of the "design of nature" arguments in the pages of First Things when Christoph Cardinal Schönborn and Dr. Stephen Barr were exchanging their thoughts. A partial summary and rebuttal is in one of the articles, Christoph Cardinal Schönborn, "The Designs of Science," First Things (Jan. 2006) with a link to another Barr commentary.

The exciting part about the new genomics is that it allows us to compare organisms at the level of the gene. Eugene Koonin, director of the National Center for Biotechnology Information (NCBI) has been writing for the past few years about the discoveries being made. One of the most startling discoveries is this, from an article by Koonin, "The Biological Big Bang Model for the major transitions in evolution," Biology Direct 2, 21 (2007):

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable.

Why has this discovery not been heralded from the rooftops? With any transition of understanding, it takes time. It took hundreds of years for the whole of humanity to assimilate and accept the change of view that Copernicus brought about. The switch from an Earth-centered solar system to sun-centered involved religious as well as scientific understandings. Also, science is complicated and not everyone can or will take the time to study the specific underlying mechanisms. On the other hand, today we have almost instantaneous communication and educational systems in place. I hope people will soon realize the implications.

Koonin himself is oriented toward describing all phenomena in terms of scientific materialism. Therefore he proposes a "Big Bang" model for these unexplained transitions in life. It includes very fast evolution mechanisms. However, slow evolution is hard enough to explain, much less fast evolution. He says it all when he starts his speculations with "I propose..."

Since one lifetime does not last hundreds of years, we can't wait that long to make our own decisions about whether we think science shows us there is a God. Scientific knowledge changes, but God has given us other ways to know about Himself. He has revealed Himself through His Word. The majesty of the universe suggests there is much more going on than just ourselves and our own accomplishments.

Yet sometimes we discover things that really do point the way to Him. When we see these things, it is nice to share them with others and help them understand. I hope I have been doing that here and that I can continue. After all, He is a Master beyond any master craftsman.

Negative Attitude

My previous post featured a review by David B. Hart in First Things magazine. He criticized Intelligent Design Theory (ID) as something that "can never be logically demonstrated." ID states that life is too complex to have happened by the physical and chemical laws alone. It may be that one experiment does not disprove total materialistic evolution of life. But when one after another yield negative results, one must put together the pieces.

In an example of a pre-life experiment, the scientist David Deamer dumped pre-biotic molecules into hot volcanic pools which were supposed to form higher and more plentiful molecules of life. His experiment showed that they did not only fail for form more, but disappeared themselves. This is from Chandra Shekhar,  "Chemist explores the membranous origins of the first living cell," UC Santa Cruz Currents 10, 31 (April 3-9, 2006) about his findings:

In June 2005, he [Deamer] led a team of scientists, including Russian geologist Vladimir Kompanichenko, to the Kamchatka region in eastern Russia, an area abounding in pools of water heated and sterilized by constant volcanic activity. Deamer carried with him a version of the "primordial soup"--a mixture of compounds like those a meteorite could have delivered to the early Earth, including a fatty acid, amino acids, phosphate, glycerol, and the building blocks of nucleic acids. Finding a promising-looking boiling pool on the flanks of an active volcano, he poured the mixture in and then took samples from the pool at various intervals for analysis back in the lab at UCSC.

The results were strikingly negative: life did not emerge, no membranes assembled themselves, and no amino acids combined into proteins. Instead, the added chemicals quickly vanished, mostly absorbed by clay particles in the pool. Instead of supporting life, the bubbling pool had snuffed it out before it began. Later, Deamer repeated the same experiment at Lassen Volcanic National Park in northern California, with the same negative result.

Now, would Hart say that this is not science, since the results were negative? How would you disprove anything if negative findings did not count?

To disprove (total materialistic) evolution is to prove something else is going on. There are discussions about Hart's review at Joe Carter, "A Walk to the Moon." First Things (Jan. 5, 2010) and Stephen Barr, "Re: A Walk to the Moon," First Things (Jan. 7, 2010).

First Things of 2010

Denyse O'Leary is a Catholic, Canadian writer who supports Intelligent Design Theory. She posts on William Dembski's blog, Uncommon Descent, and has lately been posing questions for commenters in contest form. In Contest 19, O'Leary has described a book review by David B. Hart in the magazine First Things. It is in the Jan. 2010 issue (no. 199) which I think will not be online for a few weeks until the Feb. issue comes out (I haven't followed FT lately but that's the way it sounds on the home page). The review is of Richard Dawkins, The Greatest Show on Earth (Free Press, 2009) about nature and evolution. This is the section of the review she quotes:

The best argument against ID theory, when all is said and done, is that it rests on a premise – irreducible complexity” – that may seem compelling at the purely intuitive level but that can never logically be demonstrated. At the end of the day, it is – as Francis Collins rightly remarks – an argument from personal incredulity. While it is true that very suggestive metaphysical arguments can be drawn from the reality of form, the intelligibility of the universe, consciousness, the laws of physics, or (most importantly) ontological contingency, the mere biological complexity of this or that organism can never amount to an irrefutable proof of anything other than the incalculable complexity of that organism’s phylogenic antecedents.

The reviewer apparently has not considered mathematical probabilities, chemical laws and physical distributions of random atoms and molecules. He has taken the word of two major biology scientists. However, we have seen an inkling from the Climategate hacking incident (Wikipedia description HERE) that scientists have their own agendas and can (allegedly) bend the facts their way, helped especially by computer-shuffled statistics. One of the problems in evolutionary biology is that scientists for years have ignored these mathematical probabilities and physical and chemical laws when it comes to origin and evolution of life. They live in an insular world where there is the assumption, not the proof, of evolution. That is why the word "evolution" constantly appears in the journals. It is time for them to answer to this non-scientific behavior.

An important article by David Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling  6, 27 (2009) says that scientific journals should no longer publish articles that propose speculations that are exceedingly implausible. If the chance of random formation of biologically sufficient molecules for a working system (like the bacterial flagellum) is less than one in all the quantum transitions a 14-year-old universe has ever experienced, any speculation that does not seriously answer that improbability should not be published. People usually accept the conclusions of scientists. What if they are false?

I hope in my posts to come, as in past ones, to help people understand. If we are not educated by others, we must educate ourselves. When scientists work harder at keeping facts from us than supplying them, we must ask why. This is especially sad when educators are involved, as in our public and university systems.

New ID Link

I've found another ID blog that discusses the latest breakthroughs in physiology research. It is "Darwin's God" by Cornelius Hunter, found HERE, and I will put it on my links in the right column.

Perhaps the ID people sound a little repetitive. That can be good, as I've said before (ha ha). For most people, complex science does not stick the first time. When I am confronted with something I've never seen and/or don't understand, I take in as much as I can. I let my brain play with it, and usually some questions come to mind. Often there will be terms I've never heard. What does this word mean? There are wonderful tools on the Internet for finding out. Though Wikipedia may not be respected as an academic reference, the descriptive language aside from technical terms is fairly understandable to the lay person. And it has links to other terms, so you can keep following it until you connect with something you can relate to. It also has pictures in many of its entries, a big help when it comes to DNA, RNA, proteins, etc.

When you have a chance to look for further and more accurate information, there's the National Center for Biotechnology Information, which even provides a section with textbooks of biology, microbiology, statistical evaluations, etc. Then there's always your local library, with real people called reference librarians who are happy to help you.

You may even want to go to a talk or take a class about Intelligent Design Theory. The more experts there are in the field, the more of these that will be available. They can help you learn the facts of science that you don't normally hear from regular scientists, especially as they are quoted in the media. Some facts just don't come to light in our culture and you have to dig for them.

Intelligent Design Theory is controversial, and people should become informed about controversial issues. Don't be afraid of facts. You don't have to take a test each time you try to learn something new. The world is fascinating, and the more you learn, the more you will want to know.

The Wrong Dance

In a previous post, I talked about the 1857 Supreme Court decision concerning a slave named Dred Scott. It is known as Dred Scott v. Sandford (Wikipedia description HERE). Scott claimed:

his presence and residence in free territories required his emancipation. Scott's lawyers argued the same for Scott's wife, and further claimed that Eliza Scott's birth on a steamboat between a free state and a free territory had made her free upon birth.

Scott lost and the results can be read at the Wikipedia link above. Among them is the ruling that African-Americans could not ever be considered US citizens (since overruled by the 14th Amendment).

The ruling in this case is so bad that at first it deflects consideration of the argument. Scott's lawyers worked within the confines of the mindset of the day. Laws allowing slavery in some states were accepted, and in others they were not. The argument "danced" around these laws. The thinking was that because Scott resided in free territories for a time, he should be emancipated.

But this argument was wrong. Scott should have been freed from slavery because no one should have been a slave in the first place.

I think the same can be said for the situation in US classrooms and the way the theory of evolution is handled. We are making the wrong arguments and dancing the wrong dance. Though atheists may have their rights in the classroom, so do believers. No child should be made to answer to a government institution against his or her religious beliefs. The Intelligent Design movement tries to dance around the rules against teaching creationism in the classroom by saying it is OK to teach evolution as the working theory but we should be allowed to look at the weaknesses of it. Instead they should demand that Darwinian Evolution Theory not be forced upon children at all.

Though many scientists want Darwinian evolution to be their working theory, that does not mean they should enforce it upon everyone. Some scientific theories impinge on the religious beliefs of certain segments of the population. American scientists and educators may not want to trouble themselves with thinking of others, but they live in a country with many different kinds of religions and they need to face that fact. There are soldiers willing to die for the right of freedom in this country, and many of these soldiers have beliefs that are contrary to philosophical materialists. When one thinks of the toll taken by the efforts to correct the scourge of slavery, it is asking little of educators to make the effort to teach scientific methods in a way that does not impinge on individual beliefs. For believers, science is the study of designed physical entities.

The ID people should realize that for a believer, design doesn't have to be proven. It is already understood that God made everything. Science itself can be defined as the study of created physical entities. Science is how we learn about these entities.

A Creationist is someone who believes God created the world--not just someone who thinks He did it exactly 10,000 years ago. It is time to claim back the word "Creationist" for all believers and to unite for what is right.

Of course, Creationists also need to respect the rights of others. There has got to be some way we can work this out.

Cambrian Explosion

There is a new video out from Illustra Media, the same people who made Unraveling the Mystery of Life and The Privileged Planet. It is called Darwin's Dilemma and is about the Cambrian Explosion, a geological period in which many original forms of animals appeared fully formed in the fossil record. I've never copied a video to my blog, and I don't know 1) how to do it and 2) whether it is within the Upload Terms of Google to do it with commercial previews. So, I'll just show you the above picture which is on their website and link to the video HERE, where you can see the trailer for Darwin's Dilemma.

The Cambrian Explosion (Wikipedia entry HERE), when so many full-fledged animals without intermediates started appearing, is estimated at about 530 million years ago. When you compare the graphs of what Darwin expected for fossil development and what has actually been found, it looks like these graphs by Art Battson from the Veritas Forum (accessed Sept. 2009):


Darwin predicted a gradual appearance of simple forms in the fossil record which would diversify and become more complex (graph on left). Instead, you have the abrupt appearance of many complex forms at one time (right).

I look forward to seeing this film. I haven't seen Illustra Media's other films since I felt I've read a great deal concerning their subjects, but this one is a little different because it contains information about fossils over the entire Earth. I know something about fossils, but could use more education on them. What I've heard about this film makes me look forward to seeing it.

2019 Update:

The link to Veritas Forum above now goes to a similar discussion of evolution but with slightly different-looking charts. A similar chart is found in the book by Stephen C. Meyer, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (HarperCollins, 2008), 35.

Also, many people believe the abrupt fossil appearances are due to a world-wide flood that occurred several thousands of years ago.

Ben Stein Removed

Ben Stein was recently let go from the New York Times as a columnist. He credits several reasons. One was his tendency to criticize Obama policies. The other was his role in the 2008 pro-Intelligent Design movie, Expelled: No Intelligence Allowed (Rampant Films, 2008). At the American Spectator, Aug. 10, 2009, he says:

Expelled was a plea for open discussion of the possibility that life might have started with an Intelligent Designer. This idea, that freedom of academic discussion on an issue as to which there is avid scientific disagreement has value, seems obvious to me. But it drives the atheists and neo-Darwinists crazy and they responded viciously.

This is the type of hostility there is in the cultural wars. I saw a Gallup poll recently that said only 14% of Americans believe that God had nothing to do with evolution. The rest believe He either created us directly or guided the process. But, as I thought at the time I saw the poll, those 14% have an inordinate grip of power over education and media.

That is our challenge. 

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Image credit: Wikimedia Commons, Bensteinol.jpg , work of US gov.

Design Drifting

After a few months of taking a vacation from Intelligent Design Theory (ID), I feel myself drifting back. This spring I needed some time away from ID. I was a little burned out and felt I was at the point where further study would take on a higher degree of technical knowledge, such as computer programming. But, I slowly learn more as I read more, and I'm resolved to enjoy it as I go and not expect myself to ever comprehend it all. I don't think any human ever can, or even all of us put together, which says much for the genius of our God.

I've just read Stephen Meyer's new book, Signature in the Cell (HarperCollins Publishers, 2009). I knew this would be a much-discussed book, so I couldn't leave it alone. I gave a review of it in a previous post. He talks quite a bit about Information Theory, since that is what is being used to evaluate DNA and its products. I had read about Information Theory a long time ago, with the writings of Hubert Yockey, a physicist who evaluated proteins in that way. But it was a new concept for me then and I was more interested at the time in other facets of biology. Now as I see more papers coming out on Information Theory as it relates to biology, I'd like to learn more about it.

The person considered the founder of this discipline is Claude Shannon. He is a fascinating person and you can read about him HERE at Wikipedia. I was surprised to learn he was born in Michigan. He went to University of Michigan and then on to MIT. His master's degree paper is considered one of the most important in history. It sets up the theoretical basis for the digital computer.


And yet, this is not the total of Shannon's work. Information theory is above and beyond that which he worked out in his master's paper. It relates information to uncertainty, which in turn relates to probabilities. It works with communication channels and the sending of information over electrical systems.

I did well in high school and college math classes, but I studied biology before the days that this kind of mathematical application to genetics was widely known or taught. Fortunately, my husband is a retired engineer and has been a big help in my efforts. However, after I started this seminal article, C.E. Shannon, "A Mathematical Theory of Communication," The Bell System Technical Journal 27 (July, Oct. 1948): 379-423, 623-656, I realized lot of it is over my head. I read it anyway. Roger Penrose, an award-winning mathematical physicist (Wikipedia biography HERE), has said we should read through mathematics even if we don't understand it, because we can still get a feel for what's going on. I did that with two of Penrose's books and learned quite a bit about quantum physics even though there was much I did not get.

And so I'll be reading more about ID and of course commenting sometimes about it here. It is too fascinating to ignore, that is for sure.

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Image credit: statue of Claude Shannon at University of Michigan campus, from flickr by hyperboreal, some rights reserved.

Meyer's Signature

We are back from vacation to Ohio and Baltimore, MD. We had a nice time visiting relatives and friends. It’s good to be back.

While we were away, Stephen Meyer’s new book, Signature in the Cell, (HarperCollins Publishers, 2009) came out. I bought it and have read it. I know I said I am moving onto other subjects beside Intelligent Design Theory, but this book will probably be one of the classics of ID and I want to make some comments about it. It is long but very readable and includes many previous points made about ID. Meyer goes through the history of discoveries made in biology. He provides pictures of the important elements of the cell that lead to the conclusions of the theory. Therefore, it is a very good book to read if you want to learn about the theory.

This book is closely related to the work of another ID proponent, William Dembski, but Meyer does it in a much more understandable manner than Dembski did in his book, The Design Inference (Cambridge University Press, 2006). Meyer focuses on the code of DNA and the origin of the cell, a good strategy. He demonstrates the fact that this code is incompatible with the laws of physics and chemistry as we now know them. He analyzes DNA by way of Information Theory, a mathematical approach to communication channels shown by Claude Shannon in the late 1940’s. Meyer modifies this theory to reveal functional information in the cell. He shows that the recent discoveries about DNA point to computer program-like actions, such as operators acting on other areas of gene code in a hierarchy. These operators have been found in the parts of DNA that were previously thought to be "junk." Meyer points out that the only way we know that computer-like programming can be formed is by design by an intelligent agent.

I think Meyer’s book is very exciting. However, one problem is his insistence that ID Theory has nothing to do with religion. He is only partially right. It is correct that a person does not have to be religious to see that the code of DNA is better understood as a conveyor of information than an accident of evolution. However, Meyer wants to compartmentalize that understanding to allow for further scientific questioning but not the questions which come from philosophical logic. Though he says the theory is not a “science-stopper” as critics claim, he wants us to stop short of asking who the designer is. This is not a fair, or even possible, rule. Any theory should and does bring on the logical next questions. If only intelligence could create DNA, and humans were not around at the time, who had this intelligence? The only alternatives are God, aliens, or some other “force.” And when a person is a believer, the answer is ultimately God.

So, Meyer wants non-ID proponents to see his side, but does not see theirs. This is one of the main problems with the ID movement today. The thing is, in my opinion, the ID Theory is scientifically correct. If the non-ID people refuse to accept it, as is currently the case on the grounds that it is “not science,” they will never really understand the origin of the cell. For a long time people have wanted to keep religion out of scientific thinking. This separation goes back to the time when alchemy and myth detracted from science. But keeping the Whole Truth out of science is now showing itself to also be a hindrance to understanding. The strictly factual evidence points to the major possibility that God supernaturally created the cell on Earth.

Many people today want to keep reason concerning nature (natural philosophy) and that concerning religion (theology) separate. But when St. Thomas Aquinas wrote his proofs for the existence of God from material things in Summa Theologica, Part I, Question 2, Article 3 (New Advent link HERE), he went from one domain to another. The discoveries about the cell lead us on the same path.

Unique Genes

A very important research paper was published in 2008 by researchers of the National Center for Biotechnology Information (NCBI). I already discussed it back in February (HERE) when I was writing a series about biological origins. It is by Eugene Koonin and Yuri Wolf, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 1, 2008): 6688-6719.

The paper reports on the gene make-ups of bacteria and archaea. Archaea are a group of organisms that were thought to be bacteria until the 1970's, but were found too different to group in the same category.

There are reasons this paper and the research it reflects is so important. As the researchers determine the specific gene sequences in more and more organisms, they are finding a pattern, but it is not neo-Darwinian. First, there is a small core of genes that appears almost unchanged in most of the organisms (what they call "highly conserved"). Second, there is a larger amount of genes that are "moderately common." And last but not least, is a huge amount of genes that appear in one or just a few organisms (are "narrowly distributed"). However, these statistics should not be confused with the gene make-up in a particular organism. There you will find the small core of common genes, a larger set of moderately common genes, and a smaller set of unique genes (the unique genes are a larger group of genes but a smaller percentage in each individual organism).

The graph above is from the article. It is called a self-organizing map or SOM. It shows the spaces between groups of genes, called COGs (Clusters of Orthologous Groups). The "Orthologous" in that name means "coming from a common ancestor." (As an aside, similar gene sequences are assumed here to be from common ancestors, although design advocates say they could be from common design.) The spaces between the isolated clusters shows that there is no progressive, Darwinian relationship between these organisms. They are all unique in certain ways. And the gene groups themselves each had to become functional on their own--they did not inherit them from other groups in a Darwinian way. This makes the origin of life much more difficult to support by neo-Darwinian theory.

The authors of the paper and many other scientists want to quickly claim that a new phenomenon, Horizontal (or Lateral) Gene Transfer, can explain these new findings. HGT is the transfer of genes between organisms. But they are wrong to suppose that HGT can handle the vastly improbable odds of the existence of all these unique functional genes any more than gene mutation could have. First of all, you have to have functional genes before they can be transferred. I have touched upon HGT HERE. As the information about biological life increases, I hope that more and more people realize the immensity of these discoveries.

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I am now finished, for at least a while, with Intelligent Design Theory. There are surely more things I could say, but I've covered a lot. If you are interested, please see my ID link in the right column and read the past posts. I am not an expert, although I have a bachelor's degree in animal science and have been able to learn a lot on my own. I feel I can introduce the subject to others, but at this point I don't have the inclination to delve into the advanced mathematics and chemistry of the subject. I don't want to spend all my time trying to master new fields of study like biological computing and genetic algorithms. I hope the next generation will enjoy the adventure of learning more and more about God's world.

And yet, as I move onto other things, I can't give up ID completely. The physiology of biological life is startling, and each time I look at a new "Molecule of the Month" at PDB-101, I am amazed. I have given many links in the blog so you can go and discover the fabulous world of biology.

We praise God through Jesus Christ for His awesome, beautiful Creation!

2013 Update: My interest in Intelligent Design Theory has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly.

LUCA

Before the advent of gene sequencing, the theory of evolution was based on morphology (physical characteristics). Then, scientists developed methods to find the make-up of the gene. The gene is made of a set of 4 molecules which repeat, which we call nucleotides (Wikipedia entry HERE). They have names but are often nick-named A, T, C and G. These nucleotides combine in an order that acts as a code, which is read by other cell units and turned into proteins which do much of the work of the cell.

The National Center for Biotechnology Information (NCBI) is taking the sequences found by researchers all over the world and comparing them. Many of these sequences are done on small organisms of single cells. Bacteria were considered the only organisms to be of one type of cell, the prokaryote (pro-CARry-oat) type. In the 1970’s, scientists realized there was another type of prokaryote, called archaea (ar-KEY-ah). They were considered a separate domain from bacteria and a third one, eukaryotes (you-CARry-oat). The third type is the one in plants and animals, including humans. To make things more complicated, each of the domains have branches, so they need to find common ancestors to the branches for each of the 3.

Unfortunately for the advocates of Darwinian evolution, the results of the sequencing have shown anything but a clear-cut progression from an organism which can be considered the simplest to the next which is more complex and on up to human scale. I will talk more about that next week. But the point is important because it moves the search "back" to a previous ancestor that would have shared genes of all of them and been able to branch off into the 3 distinct domains we see now.

In a paper, Makarova et al., "Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea," Biology Direct 2, 33 (2007), they discuss the findings of comparitive gene studies (orthologous means genes that come from a supposed common ancestor). The conclusion for the archaeal branch is:

Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles.

They estimate it would have had to have at least 996 genes. As they say, it is almost as complex as modern organisms. And archaea are believed to have been present as long as 3.5-3.8 billion years ago. Where then does the common ancestor of all organisms fit? They are running out of back time for all the gene sequences to fall into place, because some scientists think the Earth was too hot for organisms to form until around 4 billion years ago.

Next time, for my last regular ID entry, I will talk about the NCBI results which show the end of genomic Darwinian evolution before it even begins.

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

LUCA to come

I've been really busy this week, so I'll just give you an intro into my next Intelligent Design theme, which will be related to some in the past. Of course, biological life is all intertwined, but there are distinct categories we work with.

I've had a series about "Origins" which started HERE. I talked about some of the issues of naturalistic, materialistic theories for the beginning of life. One concept I mentioned was the "Last Unknown Common Ancestor," abbreviated LUCA (HERE). Though the term does not in itself indicate a very first organism, it heads in that direction. It includes research into what genes and proteins the ancestors of present-day species would have needed in order for the organisms of today to be what they are. It considers the number of possible offspring that a certain organism could have through the generations and how much the inner workings could have changed in that time (on a natural basis).

In fact, I've found some very interesting research on this, and hope to get into the details by next week.

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

Anaerobics

In the last few ID posts, I showed some proteins from cell membranes. The point was to see that the cell needs some rather complicated structures to keep charged particles and water at a balance so the cell doesn't explode or collapse. I want to tie that into the speculations of materialistic origins of life.

To the right is a protein from a bacteria named Desulfovibrio Vulgaris, NCBI taxonomy ID 882 (NCBI:txid882). I show this to you because of the evolutionary story that the first creatures on Earth were anaerobes (pronounced AN-air-robes). These creatures did not need oxygen to breathe. It is maintained that atmospheric oxygen was not available at first in sufficient quantities. The materialists believe that because if oxygen were available, it would keep organic molecules from forming, and thereby life itself could not start on its own. So the first cells were supposedly anaerobic. (I have seen speculation both ways on whether there was oxygen in the very early atmosphere but will not get into it here). The oxygen was theoretically produced by the first living organisms, and then later organisms adapted to the oxygen in the atmosphere. The protein complex at right, from Uniprot P45574 and RCSB PDB 2V4J is involved in the pathway that uses a sulfur-containing molecule instead of the ones used in oxygen-type respiration. It is made of several types of protein chains, totaling over 1800 amino acids.

One paper which speculates on the first organisms of life is by Girbaldo and Brochier-Armanet, "The Origins of Archaea: a state of the art," Philosophical Transactions B of the Royal London Society, 461, 1470 (May 9, 2006) 1007-1022. It is found in full through PubMed Central at the link in the title. Archaea are one of the 3 domains, or groups of life, based on cell construction. The other two are Bacteria and Eukaryotes. The article includes all three domains in its analysis although is mostly about Archaea. It states that though a certain type of Archaea (methanogenic) were previously thought to be the first organisms, their whole-gene sequences do not bear out that theory. Now it is thought that anaerobic bacteria which have this sulfur-type respiration were among the first (see Section 3, "How Old," in the paper). So this is why I looked up this type of organism.

Interestingly, this bacteria has the complete proteome available at Uniprot HERE. It has 3,517 proteins listed. Some of them are not complete in themselves. They have to fit together to make the protein work. This does not diminish the effect of the number, however, since some of the types of proteins are used several times in the same protein machine. For example, ATP Synthase, as pictured in a previous post has several types of subunits, some used as many as 12 times in the same structure. You will notice in the complete proteome that D. vulgaris also has an ATP synthase structure.

The type of respiration in anaerobes may be different, but the first organisms still needed complex structures for energy production, cell membrane transport and other cell activities. The picture to the left is not from D. vulgaris, but shows a Sodium-hydrogen type cell membrane protein that the organism does have. This is also made up of hundreds of amino acids in specific sequence in order for them to fall into the shape they need for function.

So, you can see that even the very "first" organisms needed complex types of proteins in order to function. It doesn't really matter whether they used oxygen or not. It may sound like an organism is simpler if it doesn't use oxygen to breathe, but it still needs many metabolic pathways in order for it to manufacture its own DNA, RNA, proteins, and other structures so that it can support life and reproduce.

Cell Membrane 3

The picture at left is a membrane transport protein known as a sodium-potassium pump. Details are found at the "Orientations of Proteins in Membranes" (OPM) site of University of Michigan. The horizontal red and blue lines represent the cell membrane outline.

This protein, or actually set of inter-working proteins, has about 2500 amino acids. It is necessary for the cell to be able to pump out positively charged sodium particles so that the cell doesn't become too attractive to water, which can move in by osmosis and explode the cell. There are many negatively charged proteins and positive particles inside the cell, and this pump keeps the positive ion level down. The action of the pump is part of what is called active transport, when particles are moved against a gradient and/or are unable to diffuse through the membrane. More information can be found at the Wikipedia site for Sodium Pump HERE.

There are other reasons for a sodium gradient, such as stimulation of nerve cells. These cells must move ions quickly in order for them to pass a charge along their membranes from one end to the next and from one cell to another. Different cells have specialized needs and the membrane proteins must be able to handle them. Muscle cells need calcium in order to contract. Cells must move food in and waste products out, and must respond to changes in levels of hormones in the bloodstream. All these take individually specialized membrane proteins, since the rest of the membrane will not allow large proteins and food in or out.

There have been discoveries of proteins which are completely different and yet have some of the same properties. They are composed of different sets of amino acids (the building blocks of proteins), yet they fold in similar ways, which allows them to do similar work. However, folding itself is rarely found in randomly arranged amino acid sequences, as reported by protein laboratories in papers such as this by Moffet and Hecht, "De Novo Proteins from Combinatorial Libraries," Chemical Reviews 101, 10 (2001): 3191-3204. (The introduction at the title link is quite interesting). "De Novo" in the title here means, basically, new proteins. The authors were trying to figure out how to make functional proteins from the vast numbers of non-functional ones.

The calculations of the proportions of functional proteins are being worked upon now by many on both the materialistic and design advocate "sides." So far the proportions are amazingly small, such as 1 in 10^65 viable for a protein of 100 amino acids calculated by Hubert Yockey (discussed in another post HERE). Many proteins are believed to be very close to the same as they were at the very start of life because they are the ones that work. (On a different note but related: many proteins are being found unique for particular species and contribute to the species-specific features.)