Sunday, July 24, 2016

Undeniable by Axe

I just read the book by Dr. Douglas Axe, Undeniable: How Biology Confirms Our Intuition That Life Is Designed. Dr. Axe is a biology researcher who started in engineering and went on to study the working molecules of our cells, especially proteins. There are book reviews at Amazon, of course, which you can link to HERE. But I’d like to mention a few things about it myself because even though it is written for the non-scientist it might still stand more explanation.

The Intelligent Design (ID) movement will celebrate its 20 year anniversary this August, and Dr. Axe is among its advocates. ID advocates claim that design can be detected in biology by using strictly scientific methods. However, for the scientist working in research who talks about biological design, there is awkwardness among his/her colleagues which can lead to total exclusion. Though Dr. Axe worked at extremely prestigious institutions such as Cal Tech and Cambridge, he was intimidated and even ostracized when he shared his new ideas.

Dr. Axe doubted the scientific consensus of his day that said that proteins are easily made by chance. Proteins are specific molecules that do specific jobs in the basic unit of our bodies, the cells. Axe believed they have to be very fine-tuned in order to fold into the shapes they need to be to carry out their work. One of the best parts of this book is that Dr. Axe has drawings and descriptions of proteins. These molecules have to be seen to be appreciated and the more the general population is aware of these structures, the better. I was especially happy he described the proteins of photosynthesis, since this is one of the most crucial processes of life because it converts light energy to food. The machinery for photosynthesis would have had to be in organisms from the beginning.

Good a job as he did, the book could have been even better with more of a description of the structures of the sub-units of protein, called amino acids and the atoms which make them. Since the book had pictures anyway, this would have been a worthwhile description to give people more of a grounding of where the proteins fall in the nature of things. So, I’d like to fill in a little.

We’ll start with a protein complex Dr. Axe does describe, a molecular machine of photosynthesis called Photosystem I. This takes in photons from the sun and eventually fixes carbon into the building blocks of the cell. Keep in mind this is only one of several molecule complexes needed for photosynthesis to occur. These in turn set up molecular products and electrochemical gradients the cell needs for building the vast array of machinery it has.

Dr. Axe shows different parts of Photosystem I in his book, although the pictures there are in black and white. I have a color picture here from the National Center for Biotechnology Information (citations at bottom of image--click for larger view). Dr. Axe tells us there are 417 parts to the Photosystem I complex (many are used more than once). In this first stunning picture, different parts are marked with different colors. Not all the parts are proteins, so they are not all marked with colors.

The next image here is a chart of all the amino acids needed to make up just one protein of the 417 parts of Photosystem I. This analysis is from a cyanobacterium, a single-celled organism. The abbreviations are for the 20 different amino acids, which we will get to next. The information is from Uniprot, linked HERE.

Then, I have a picture of an amino acid here with the atoms of carbon, oxygen, nitrogen and hydrogen (the abbreviations may be the same for amino acids but are known because of context). In this example is the amino acid valine (pronounced way lean). The amino acids are partly all the same (on the top in this picture) where they combine to make a protein chain and differ (on the bottom) in their “side-chains.” These side-chains give the proteins different structures to do different jobs. The amino acids have an average of almost 20 atoms each.

Then in my last image I show the perspective of the first three images and what it takes to make up just one of the parts of Photosystem I (in the top circle) with the 755 amino acid abbreviations listed. Valine is marked by a V in each space it appears. This piece would have about 14,000 atoms—all in specific order so the larger machine can work as it should.

In the book, Dr. Axe spent a lot of time describing the possible number of images in a pixel grid using the three basic colors and all their intensities in order to describe the huge “search space” to get one specific image out of all the possibilities. It is similar to saying that we “try” a certain amount of times putting different combinations together to get what we want.

The structures for photosynthesis are amazing in the number of their amino acids and other molecules which combine for the work of photosynthesis. It would take a tremendous amount of chemical reaction “tries” to get the right atoms in the right positions under random conditions. Dr. Axe gave the idea of how large the search space is for specific proteins. We are talking about one in 10 to the power of 74 (10^74), which is a one with 74 zeroes after it, for a proteins of 150 amino acids. In a comparison, this is less than one atom in all the atoms in our galaxy. Even with the large amount of atoms to work with and even in an old Earth, we can consider the random combinations of atoms to be insufficient to put together the structures needed for photosynthesis. And it could not have happened piecemeal, because you need the whole system for photosynthesis to work.

Lastly, I want to say that in his book Dr. Axe takes a diversion from the regular ID advocates and names God as the Designer. Others in the ID world say they are only looking at the science of biology, and conclude it is designed without naming the designer. I am wondering how the other advocates will handle this conclusion, since their critics have always accused them of being Creationists underneath all the claims of science-only. But I am glad he did it, because I think all ID advocates should be up front about who they think the Designer is.

Monday, July 18, 2016

Science in US Schools

There is a very interesting article at Answers in Genesis about the history of teaching creationism and evolution in US schools. Answers in Genesis is a group associated with the teaching of Special Creationism, the belief that God created humans and animals directly in a supernatural way. The article tells about certain judgments in the courts that have turned teaching in classrooms toward evolution and away from creationism:

https://answersingenesis.org/public-school/evolution-in-us-education-and-demise-of-its-public-school-system/ .

One important trial in 2005 was in Harrisburg PA over whether a textbook could have a disclaimer that introduced Intelligent Design Theory in the Dover School District. It ended in favor of the evolutionists:

https://en.wikipedia.org/wiki/Kitzmiller_v._Dover_Area_School_District .

There had been a fight in Texas in 2013 over the science textbook to be used in the classroom, and the evolutionists won so that their textbook was chosen. That link is here at Evolution News and Views (an Intelligent Design website) to give details of the story:

http://www.evolutionnews.org/2014/02/whats_wrong_wit081811.html .

The American Association for the Advancement of Science claims:

AAAS has played a prominent role in responding to efforts in Kansas, Pennsylvania and elsewhere to weaken or compromise the teaching of evolution in public school science classrooms.

http://www.aaas.org/news/evolution-front-line .

These are among the major happenings in our schools that have directed public science teaching toward evolution, although the fights continue in the states to introduce and/or follow bills for academic freedom. For example:

http://www.evolutionnews.org/2016/06/from_political102944.html .

Though many people believe evolution is the answer to our existence, many have other beliefs. There should be a way for facts to be examined in the classroom in an equitable way.


Thursday, June 30, 2016

Human Value

Every day I check out the topics going on in the Catholic Answers Forums (CAF). The link to the home page of CAF is here:

http://forums.catholic.com/ ,

At CAF I often gravitate toward discussions about abortion. My book, Biotech Swirl, is about experimentation of human life from the embryo through the fetus and even into adult human beings. It is also about how human life can be cheapened when viewed from certain perspectives. In my opinion this is too often from the sterile worldview of scientists. Of course other factors are at play, such as the unwillingness of women to go through with a pregnancy for various reasons. But where do the women get the idea that the fetus is not really human? It can be rationalized in various ways, but these days the culture of science feeds into this idea. It is ironic, because you would think they would recognize the embryo is human. But instead they want to dissect and manipulate the embryo and/or fetus either for other people who are patients (already born paying customers), or for potential parents who want perfect children, as in in-vitro-fertilization clinics.

A part of my book explains some things about the biology of our bodies, especially at the cellular level. That may seem out of place, but it is meant to show how amazing are our bodies and that we are indeed wondrously made. Cells are the basic unit of biology, and their detail can show how valuable we are. Everyone needs to be treated as precious, including embryos and fetuses. The question is, how do we get everyone to see this value?

Well, we all have our ways to work for the Lord and there are many good people working right now in Right to Life offices and other forms of the movement. I’ve tried to contribute by writing Biotech Swirl, to blog on the magnificence of our biological makeup, and to make occasional comments on CAF. I don’t know how long my part of the effort is to continue along this vein. It depends on where I discern God is calling me. I try to do my best each day wherever that way leads.

Soul on Fire

For the past few years, I've had a music video at Christmas. I didn't do it this past Christmas--I guess I didn't have time to look very far. But now, Third Day, my favorite contemporary Christian band, has come up with another hit, Soul on Fire. It also features All Sons and Daughters. I like the music quite well, although the lyrics are for those who may feel they have drifted from God. It talks about coming back to God after wandering away from Him. I don't feel I've left God since I came back a long time ago--maybe the song reminds me of that time. For any of you reading this, perhaps you feel closer to God some times more than others. In any case, I'll put this video in my blog on this last day of June. I hope you enjoy it.


Tuesday, June 14, 2016

Mary Magdalene

In this post I mostly want to give you a link to a story about the change from what is called a "Memorial Day" of Mary Magdalene to a higher honor of "Feast Day" for her in the Catholic Church. Apparently Pope Francis requested this, and it is very fitting. As the story at the link relates, the Virgin Mary had been the only woman honored by a Feast Day, while the male Apostles and some other men were given this tribute. Since St. Thomas Aquinas (13th Century), Mary Magdalene has been known as the “Apostle to the Apostles” because she had seen the Risen Lord first and was commissioned by Him to tell the Apostles of His Resurrection.

https://cruxnow.com/global-church/2016/06/10/new-feast-touts-mary-magdalene-paradigm-women/ .

It was said we should treat Mary Magdalene as a paradigm. That is what many women have been trying to do: to follow the Lord as completely as they can. Some women feel they are being called by God to service as Deacons, but Church leadership denies that call. It is heavy-handed of these leaders to think they know how God is calling all individuals. Pope Francis said in his Apostolic Exhortation, Amoris Laetitia, Section 37:
We [Church leadership] also find it hard to make room for the consciences of the faithful, who very often respond as best they can to the Gospel amid their limitations, and are capable of carrying out their own discernment in complex situations. We have been called to form consciences, not to replace them.
http://w2.vatican.va/content/francesco/en/apost_exhortations/documents/papa-francesco_esortazione-ap_20160319_amoris-laetitia.html .

Though Pope Francis was referring to married couples in his Exhortation, his statement applies to leadership and laypersons in general.

A letter just came out from the Congregation of the Doctrine of the Church in which the interaction between Church hierarchy and particular movements of the laity are discussed. It says the Bishops should not squash the charisms of the laypersons in which they feel moved by God for certain works in the Church. On the other hand, the laypersons are supposed to respect the hierarchy in what they do. The link for this article is here:

http://forums.catholic.com/showthread.php?t=1014267  .

It takes wise leaders to get the right balance and that is about impossible except with God's help. Discernment should be done together, not separately.

Perhaps as Church leaders realize Mary Magdalene is deserving of a Feast Day, they will recognize women are deserving of being heard.

Friday, June 3, 2016

Supernatural Creation

I believe that Creation has had direct supernatural intervention (called Special Creation), both at the beginning of life and along the way from simple organisms to human beings. I don’t know if the “days” mentioned in Genesis 1-2 lasted 24 hours or were long ages, but I believe there was a direct supernatural element in the formation of humans.

So why do I believe this? I have a tendency to think of biology. With biology there are vast numbers to consider. The first in this vein is the number of our cells, the basic unit of biology. I’ve seen estimates that humans have about 10 to 100 trillion cells, all working together. How big is a trillion? A trillion is one million (already a big number) times one thousand times another thousand. So take all that times 10 to 100 and you have the number of cells of an adult human being. We’ll say 50 trillion as a rounded number for discussion. More information on the cell is here:

http://creationwiki.org/Cell_biology .

These 50 trillion cells all start with one cell from union of a sperm (from the male) and an egg (from the female) that meet through sexual intercourse. Now this first cell is already a wonder. It contains molecules inside—made of atoms which combine in specific ways. A central molecule is DNA, which is in the form of a code to make other molecules. DNA looks like a ladder twisted along its long axis and the steps or rungs are composed of smaller molecules that follow a precise order. Parts of the DNA are known as "genes." More information and pictures of DNA are here:

http://creationwiki.org/Deoxyribonucleic_acid .

At specific times, these rungs separate in the middle and are copied for the code in order to make other working molecules and more cells. The rungs of the ladder, more officially known as “bases,” in the human number 3.2 billion in each cell. Yet the average cell is only about 10 to 100 microns long. This equals about 1/250th to 1/2500th of an inch long.

So 3.2 billion DNA bases (the rungs) are active in almost all new cells that come from the division of the first cell and the next and the next etc. The DNA has to be copied in the right way for differentiation into the right kind of cells as they come about during the divisions. The cell products have the effect of making the right cells for eyes, ears, nose, bones, muscles, inner organs, skin, and everything else that makes our physical bodies.

The organization of the growing human in the womb, baby, child and adult must be regulated by genes which are made up by the DNA. Some regulation comes from the DNA and some from the egg cell to form the body orientation.

All the while, cells need to be able to use food to make the right kind of energy for them to keep growing and dividing. As mentioned before, the DNA has genes, and these make proteins that do the work of the cell, such as copying DNA.

These are among the facts that make me believe humans needed direct supernatural intervention to be formed. I hope you will consider these numbers too. Don’t let others tell you they would be easy to come about. Neo-Darwinian evolution involves chance—just atoms that happen to come together with no guidance. Though evolutionists invoke natural selection of the fittest, there has to be something from which to select if you are to have neo-Darwinian evolution at all.

I don't believe the original DNA sequences needed for life came about by chance. I don't think we'd have the tiniest cell, much less a human, if it were not for the direct intervention of God.

Monday, May 30, 2016

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. 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. Many people believe this, but it 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 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 advocates is called the Discovery Institute. These people are dedicated 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, Dr. Cornelius Hunter is showing why the BioLogos arguments of Dr. Dennis Venema are wrong. In the links below there are articles that point out faults and also go to other references which cover enlightening insights of several ongoing arguments. Though Creationists and Intelligent Design advocates are accused of being anti-science, the irony is that in matters of biological complexity they are more precisely scientific than BioLogos.

http://darwins-god.blogspot.com/2016/05/shared-errors-biologos-on-broken-genes.html .

http://darwins-god.blogspot.com/2016/06/biologos-broken-genes-and-urate-oxidase.html#comment-form .

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 (see The Third Way of Evolution) for atheists. Casey Luskin, who worked for Discovery Institute for many years, has published a paper called Darwin's Poisoned Tree in the Trinity Law Review about the relationship between the teaching of evolution and atheism. You can find the paper at this link:

http://www.discovery.org/a/25273 .

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 Romans 1:20 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. (USCCB, NABRE).