Saturday, June 30, 2018

The Inspirational Design & Presence of Phosphate

This entry summarizes four YouTube Videos by Reasons to Believe, conversations between Barrie Winn and Fazale Rana about phosphates, found here: https://www.youtube.com/user/ReasonsToBelieve1/videos

Some information also comes from The Inspirational Design of DNA, by Fazale R. Rana, PhD, published in Chapter 3 of Building Bridges, 2018 by Reasons to Believe.

Phosphate is indispensable for life.  It is uniquely designed to be used in a variety of applications in living organisms; no other substance has the chemistry to accomplish this wide range of functions. You will find phosphates in cell membranes, DNA, RNA, ATP, ADP, as well as the teeth and bones of vertebrates.

Phosphate is best able to ionize in the same pH range (around 7) in which cell reactions operate; this is crucial for phosphate to retain a negative charge while bonding with two sugars in the deoxyribose nucleic acid (DNA) backbone. This negative charge stabilizes the DNA backbone by preventing water molecules from breaking it up while also insuring that the DNA stays within the cell membrane.  Phosphate chemical analogs cannot bond to both sugars in the same manner. Phosphite and sulfate can form two bonds but would do so without the necessary negative charge remaining. Arsenate is not able to form bonds with organic materials and bonds to nitrate would not be stable.

In addition to being perfect in DNA, phosphate is also the best molecule to provide energy for metabolic functions. All organisms, from the simplest bacteria to humans, use adenosine triphosphate (ATP) as their primary energy currency. Phosphate is also found as part of the calcium apatite crystal structure in bones and teeth of vertebrates.

Phosphate is obviously crucial for life on earth. It is a component of vertebrate backbones as well as the backbone of DNA; it is also the basis for the physiology of every organism. For it to be used in so many applications, it should have been easy to access on the early earth as the first life emerged, but it wasn’t; this is known as “The Phosphate Problem”. Phosphorus doesn’t exist in a stable gas form or even as a stable liquid element or compound. Given that all the other major elements necessary for life (carbon, nitrogen, oxygen, and hydrogen) exist in the gaseous phase as stable substances, it is almost impossible to see how phosphorus could have participated in reactions with the other necessary elements. Phosphorus was probably present on the early earth as apatite or phosphide compounds, but both of these are extremely insoluble solids. To make them soluble requires conditions (like a very low pH or a very high temperature) that would not support other reactions required to make the molecules necessary for life.  What is necessary to make phosphates available to reactions in solution would undermine any other kind of chemical evolution. 

We have found some pathways and conditions that can increase the solubility of phosphorus compounds in other solutions, such as urea, but all of these require intense human intervention.  It is highly unlikely that these pathways existed on early earth without a mind intervening. 

As we continue to do research, the origin and concentration of phosphorus on earth is looking more and more like a miracle.  Phosphides are found in meteorites, but it is difficult to get these to become phosphates under the conditions of early earth; these reactions also require attentive lab intervention; requiring a mind to make sure they occur. The trendline of research confirms the increasingly difficult task of finding a chemical pathway necessary for phosphate to be available on the early earth.

Even the presence of phosphorus on earth in a relatively large concentration looks as if a mind was required. Phosphorus is produced by nucleosynthesis and is spread throughout the universe when a star explodes. Recent research is finding that phosphorus creation is inconsistent in supernovae; it is found in some explosions but not in others! Even though phosphorus is not ubiquitous in the universe; the earth seems to have an exceptionally high concentration and it seems that it was delivered in a “geological instant”.  The earth’s crust is relatively abundant in phosphorus; much of it delivered by meteorites in a relatively short  period of time.  We were either exceptionally lucky, or the phosphorus on earth is another example of the incredible design we are discovering as we investigate the universe.

It is reasonable to conclude that the presence and amount of phosphorus on earth was designed.  Not only does it look as if the presence of phosphorus is unusual, but only a mind could take something that would be hard to access and make it a major component necessary for life. Phosphate provides us with another example of nature declaring the glory of God.

Friday, June 15, 2018

The Inspirational Design of DNA

This entry is a summary of The Inspirational Design of DNA, by Fazale R. Rana, PhD, published in Chapter 3 of Building Bridges, 2018 by Reasons to Believe.

DNA design is elegant, ingenious, and optimally designed for its role in the cell as a molecular-scale information storage system.  Biochemists believe that DNA approaches the theoretical maximum in terms of its digital storage capacity.

There are several key structural features of DNA that are responsible for its optimal data storage properties. Emerging data indicates that the components that make up the nucleotides appear to have been chosen carefully with every detail of DNA’s structure critically factored into this molecule information-storage role.  The components must give the DNA maximum stability while still allowing for protein binding to occur.

Phosphate is perfectly suited to form the stable backbone. Phosphate can form bonds with two sugars at the same time to bridge two nucleotides, while still maintaining a negative charge.  This negative charge imparts the DNA backbone with stability that prevents reactive water molecules from cleaving it.  The charge also serves as a protein binding site.  Both phosphite and sulfate (chemical analogs to phosphate) can form two bonds, but would do so without the necessary negative charge remaining. Arsenate (also a chemical analog) is not able to form bonds with organic materials.

The specific nature of the phosphate to sugar bonds is also optimized. The 5’ to 3’ phosphodiester linkage is a maximally stable bond; stability being one of the requirements to effectively store information. The sugar itself, deoxyribose (which lacks an OH group on the #2 carbon), also provides stability.  Ribose (the sugar in RNA), however, has this #2 OH group, which can catalyze the cleavage of the backbone. While DNA needs to be stable to store information, RNA needs to possess a certain measure of instability to keep extra proteins from cluttering up the cell.  The use of thymine (instead of uracil) in DNA, along with the antiparallel arrangement of the nucleotide strands both lead to the increased stability of DNA over RNA.

Research has shown that deoxyribose is the only sugar that could fulfill the role it does in DNA. When other sugars instead of deoxyribose are used, the DNA does not have all the properties necessary to operate in the cell.  Some of the analogs don’t form a double helix, in others the interaction between the nucleotide strands is too strong or too weak.  Still others can assume multiple structural conformations – which keeps the cells machinery from operating on the DNA as it should.

The nucleobases adenine, guanine, cytosine, thymine, and uracil appear to be the best possible choices as well. This set of nucleobases display ideal photophysical properties; minimizing the damage caused by ultraviolet radiation by absorbing light at exactly the same wavelengths that are most effectively shielded by ozone! Also, the chemical structure of these nucleobases cause the UV radiation to be radiated away after absorption, limiting the damage.

One kilogram of DNA can store all the digital data that currently exists. This exquisite optimization of DNA’s structure indicates that it is not the outworking of a historically contingent evolutionary process; instead extreme optimization points to a creator. Computer scientists and molecular biologists have come to realize that the cells machinery, which manipulates DNA, literally functions like a computer system at its most basic level of operation. How could humans have designed a system that operates exactly like the information computing system that operates inside a cell?  The most rational answer is that since we were created by God, we think in a similar way as our creator.