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: .

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: .

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: .

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. .

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: .

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.