Fatty Acids Are Beautiful

fattyacidsarebeautiful

BY FAZALE RANA – NOVEMBER 22, 2017

Who says that fictions onely and false hair
Become a verse? Is there in truth no beauty?
Is all good structure in a winding stair?
May no lines passe, except they do their dutie
Not to a true, but painted chair?

George Herbert, “Jordan (I)”

I doubt the typical person would ever think fatty acids are a thing of beauty. In fact, most people try to do everything they can to avoid them—at least in their diets. But, as a biochemist who specializes in lipids (a class of biomolecules that includes fatty acids) and cell membranes, I am fascinated by these molecules—and by the biochemical and cellular structures they form.

I know, I know—I’m a science geek. But for me, the chemical structures and the physicochemical properties of lipids are as beautiful as an evening sunset. As an expert, I thought I knew most of what there is to know about fatty acids, so I was surprised to learn that researchers from Germany recently uncovered an elegant mathematical relationship that explains the structural makeup of fatty acids.From my vantage point, this newly revealed mathematical structure boggles my mind, providing new evidence for a Creator’s role in bringing life into existence.

Fatty Acids

To first approximation, fatty acids are relatively simple compounds, consisting of a carboxylic acid head group and a long-chain hydrocarbon tail.

fatty-acids-are-beautiful-1

Structure of two typical fatty acids
Image credit: Edgar181/Wikimedia Commons

Despite their structural simplicity, a bewildering number of fatty acid species exist. For example, the hydrocarbon chain of fatty acids can vary in length from 1 carbon atom to over 30. One or more double bonds can occur at varying positions along the chain, and the double bonds can be either cis or trans in geometry. The hydrocarbon tails can be branched and can be modified by carbonyl groups and by hydroxyl substituents at varying points along the chain. As the hydrocarbon chains become longer, the number of possible structural variants increases dramatically.

How Many Fatty Acids Exist in Nature?

This question takes on an urgency today because advances in analytical techniques now make it possible for researchers to identify and quantify the vast number of lipid species found in biological systems, birthing the discipline of lipidomics. Investigators are interested in understanding how lipid compositions vary spatially and temporally in biological systems and how these compositions change in response to altered physiological conditions and pathologies.

To process and make sense of the vast amount of data generated in lipidomics studies, biochemists need to have some understanding of the number of lipid species that are theoretically possible. Recently, researchers from Friedrich Schiller University in Germany took on this challenge—at least, in part—by attempting to calculate the number of chemical species that exist for fatty acids varying in size from 1 to 30 atoms.

Fatty Acids and Fibonacci Numbers

To accomplish this objective, the German researchers developed mathematical equations that relate the number of carbon atoms in fatty acids to the number of structural variants (isomers). They discovered that this relationship conforms to the Fibonacci series, with the number of possible fatty acid species increasing by a factor of 1.618—the golden mean—for each carbon atom added to the fatty acid. Though not immediately evident when first examining the wide array of fatty acids found in nature, deeper analysis reveals that a beautiful yet simple mathematical structure underlies the seemingly incomprehensible structural diversity of these biomolecules.

This discovery indicates it is unlikely that the fatty acid compositions found in nature reflect the haphazard outcome of an undirected, historically contingent evolutionary history, as many biochemists are prone to think. Instead, the fatty acids found throughout the biological realm appear to be fundamentally dictated by the tenets of nature. It is provocative to me that the fatty acid diversity produced by the laws of nature is precisely the isomers needed to for life to be possible—a fitness to purpose, if you will.

Understanding this mathematical relationship and knowing the theoretical number of fatty acid species will certainly aid biochemists working in lipidomics. But for me, the real significance of these results lies in the philosophical and theological arenas.

The Mathematical Beauty of Fatty Acids

The golden mean occurs throughout nature, describing the spiral patterns found in snail shells and the flowers and leaves of plants, as examples, highlighting the pervasiveness of mathematical structures and patterns that describe many aspects of the world in which we live.

But there is more. As it turns out, we perceive the golden mean to be a thing of beauty. In fact, architects and artists often make use of the golden mean in their work because of its deeply aesthetic qualities.

Everywhere we look in nature—whether the spiral arms of galaxies, the shell of a snail, or the petals of a flower—we see a grandeur so great that we are often moved to our very core. This grandeur is not confined to the elements of nature we perceive with our senses; it also exists in the underlying mathematical structure of nature, such the widespread occurrence of the Fibonacci sequence and the golden mean. And it is remarkable that this beautiful mathematical structure even extends to the relationship between the number of carbon atoms in a fatty acid and the number of isomers.

As a Christian, nature’s beauty—including the elegance exemplified by the mathematically dictated composition of fatty acids—prompts me to worship the Creator. But this beauty also points to the reality of God’s existence and supports the biblical view of humanity. If God created the universe, then it is reasonable to expect it to be a beautiful universe. Yet, if the universe came into existence through mechanism alone, there is no reason to think it would display beauty. In other words, the beauty in the world around us signifies the Divine.

Furthermore, if the universe originated through uncaused physical mechanisms, there is no reason to think that humans would possess an aesthetic sense. But if human beings are made in God’s image, as Scripture teaches, we should be able to discern and appreciate the universe’s beauty, made by our Creator to reveal his glory and majesty.

Resources to Dig Deeper

Endnotes

  1. Stefan Schuster, Maximilian Fichtner, and Severin Sasso, “Use of Fibonacci Numbers in Lipidomics—Enumerating Various Classes of Fatty Acids,” Scientific Reports 7 (January 2017): 39821, doi:10.1038/srep39821.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/11/22/fatty-acids-are-beautiful

Ribosomes: Manufactured by Design, Part 2

ribosomesmanufacturedbydesign

BY FAZALE RANA – NOVEMBER 8, 2017

“I hope there are no creationists in the audience, but it would be a miracle if a strand of RNA ever appeared on the primitive Earth.”1

Hugh Ross and I witnessed the late origin-of-life researcher, Leslie Orgel, make this shocking proclamation at the end of a lecture he presented at the 13th International Conference on the Origin of Life (ISSOL 2002).

Orgel was one of the originators of the RNA world hypothesis. And because of his prominence in the origin-of-life research community, the conference organizers granted Orgel the honor of opening ISSOL 2002 with a plenary lecture on the status of the RNA world hypothesis. During his presentation, Orgel described problem after problem with the leading origin-of-life explanation, reaching the tongue-in-cheek conclusion that it would require a miracle for this evolutionary scenario to yield RNA, let alone the first life-forms. (For a detailed discussion of the problems with the RNA world hypothesis, see my book Creating Life in the Lab.)

Despite these problems, many origin-of-life researchers—including Leslie Orgel (while he was alive)—remain convinced that the RNA world scenario must be the explanation for the emergence of life via chemical evolution. Why? For one key reason: the intermediary role RNA plays in protein synthesis.

The RNA World Hypothesis

The RNA world hypothesis posits that biochemistry was initially organized exclusively around RNA and only later did evolutionary processes transform the RNA world into the familiar DNA-protein world of contemporary organisms. If this model is correct, then the DNA-protein world represents the historically contingent outworking of evolutionary history. To put it another way, contemporary biochemistry has been cobbled together by unguided evolutionary forces and the role RNA plays in protein synthesis is an accidental outcome.

The discovery of ribozymes in the 1980s provided initial support for the RNA world scenario. These RNA molecules possess functional capabilities, behaving just like enzymes. In other words, RNA not only harbors information like DNA, it also carries out cellular functions like proteins. Origin-of-life researchers take RNA’s dual capacities as evidence that life could have been organized around RNA biochemistry. These same researchers presume that evolutionary processes later apportioned RNA’s twofold capabilities between DNA (information storage) and proteins (function). Origin-of-life researchers often point to RNA’s intermediary role in protein synthesis as evidence for the RNA world hypothesis. Again, RNA’s reduced role in contemporary biochemical systems stands as a vestige of evolutionary history, with RNA viewed as a sort of molecular fossil.

Ribosomes serve as a prime illustration of RNA’s role as a go-between in protein synthesis. As subcellular particles, ribosomes catalyze (assist) the chemical reactions that form the bonds between the amino acid subunits of the proteins. Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins, and the SSU consists of a single rRNA molecule and over 30 different proteins.

The rRNA molecules function as scaffolding, organizing the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids. In other words, the ribosome is a ribozyme. At the ISSOL 2002 meeting, I heard Orgel adamantly insist that the RNA world hypothesis must be valid because rRNA catalyzes protein bond formation.

Orgel’s perspective gains support considering the inefficiency of ribozymes as catalysts. Protein enzymes are much more efficient than ribozymes. In other words, it seemingly would be better and more efficient to design ribosomes so that proteins catalyzed bond formation between amino acids, not rRNA. This reason convinces origin-of-life researchers that the role rRNAs play in protein synthesis is a haphazard consequence of life’s historically contingent evolutionary history.

But recent work by scientists from Harvard and Uppsala Universities paints a different picture of the compositional makeup of ribosomes, and in doing so, undermines what many origin-of-life researchers believe to be the most compelling evidence for the RNA world hypothesis. These researchers demonstrate that the compositional makeup of ribosomes does not appear to be the accidental outworking of an unguided, contingent process. Instead, an exquisite molecular logic accounts for the composition and structural properties of the protein and rRNA components of ribosomes.2

Is There a Rationale for Ribosome Structure?

As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

  1. Why are ribosomes made up of so many proteins?
  2. Why are ribosomal proteins nearly the same size?
  3. Why are ribosomal proteins smaller than typical proteins?
  4. Why are ribosomes made up of so few rRNA molecules?
  5. Why are rRNA molecules so large?
  6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

Ribosomes Make Ribosomes

Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, ribosomes need to manufacture enough proteins to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

Ribosome Composition is Optimal for Efficient Production of Ribosomes

As discussed in an earlier blog post, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were large, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner. They also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature. In short, the composition of these sub cellular complexes appears to be undergirded by an elegant molecular rationale.

As part of their mathematical modeling study, these researchers also provided an explanation for why ribosomes are made up of large RNA molecules. Because the number of steps involved in rRNA production is fewer than the steps required for protein manufacture, rRNA molecules can be made more rapidly than proteins. This being the case, ribosome production is more efficient when these organelles are built using fewer and larger rRNA molecules as opposed to smaller, more numerous ones.

The research team learned that ribosomes containing more rRNA can be built faster than ribosomes made up of more proteins. This fact helps explain why rRNA operates as the catalytic portion of ribosomes (linking amino acids together to construct proteins), though less efficient as a catalyst than proteins.

These insights also explain the compositional differences among ribosomes found in bacteria, eukaryotic cells, and mitochondria. Bacteria, which typically replicate faster than eukaryotic cells, possess ribosomes that contain proportionally more rRNA and fewer proteins than ribosomes found in eukaryotic cells. Mitochondria—organelles found in eukaryotic cells—possess ribosomes with a much greater ratio of proteins to rRNA than eukaryotic cells. This observation makes sense because ribosomes in mitochondria don’t produce themselves.

It Would Be a Miracle if a Strand of RNA Appeared on the Primitive Earth

An exquisite molecular rationale undergirds the number and size of rRNA molecules in ribosomes and accounts for why the ribosome is a ribozyme. The work of the Harvard and Uppsala University scientists undermines the view that ribosomes were cobbled together as a result of the evolutionary transition from the RNA world to the DNA/protein world. If the presence and role of RNA molecules in ribosomes were simply vestiges of life’s origin out of an RNA world, then there should not be an elegant molecular logic that accounts for ribosome compositions in bacteria and eukaryotic organisms. In other words, it doesn’t appear as if ribosomes are the unintended outcome of an unguided evolutionary process.

This conclusion gains support from earlier work by life scientist Ian S. Dunn. As I wrote about in a previous blog post, Dunn has uncovered a molecular rationale for the intermediary role messenger RNA (mRNA) plays in protein synthesis. Again, it indicates that the intermediary role of RNA molecules in protein synthesis is a necessary design of a DNA/protein world, not a molecular vestige of life’s evolutionary origin that proceeds through an RNA world.

Given these new insights and the intractable problems with the RNA world scenario, I must agree with Leslie Orgel. It would be a miracle if a strand of RNA appeared on the primitive Earth—unless a Creator intervened.

Resources to Dig Deeper

Endnotes

  1. Fazale Rana, Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator(Grand Rapids, MI: Baker Books, 2011), 161.
  2. Shlomi Reuveni, Måns Ehrenberg, and Johan Paulsson, “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–7, doi:10.1038/nature22998.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/11/08/ribosomes-manufactured-by-design-part-2

Ribosomes: Manufactured by Design, Part 1

ribosomesmanufacturedbydesign1

BY FAZALE RANA – NOVEMBER 1, 2017

Before joining Reasons to Believe in 1999, I spent seven years working in R&D at a Fortune 500 company, which meant that I spent most of my time in a chemistry laboratory alongside my colleagues trying to develop new technologies with the hope that one day our ideas would become a reality, making their way onto store shelves.

From time to time, my work would be interrupted by an urgent call from one of our manufacturing plants. Inevitably, there was some crisis requiring my expertise as a chemist to troubleshoot. Often, I could solve the plant’s problem over the phone, or by analyzing a few samples sent to my lab. But, occasionally, the crisis necessitated a trip to the plant. These trips weren’t much fun. They were high pressure, stressful situations, because the longer the plant was offline, the more money it cost the company.

But, once the crisis abated, we could breathe easier. And that usually afforded us an opportunity to tour the plant.

It was a thrill to see working assembly lines manufacturing our products. These manufacturing operations were engineering marvels to behold, efficiently producing high-quality products at unimaginable speeds.

The Cell as a Factory

Inside each cell, an ensemble of manufacturing operations exists, more remarkable than any assembly line designed by human engineers. Perhaps one of the most astounding is the biochemical process that produces proteins—the workhorse molecules of life. These large complex molecules work collaboratively to carry out every cellular operation and contribute to the formation of all the structures within the cell.

Subcellular particles called ribosomes produce proteins through an assembly-line-like operation, replete with sophisticated quality control checkpoints. (As discussed in The Cell’s Design, the similarity between the assembly-line production of proteins and human manufacturing operations bolsters the Watchmaker argument for God’s existence.)

Ribosomes

About 23 nanometers in diameter, ribosomes play a central role in protein synthesis by catalyzing (assisting) the chemical reactions that form the bonds between the amino acidsubunits of proteins. A human cell may contain up to half a million ribosomes. A typical bacterium possesses about 20,000 of these subcellular structures, comprising one-fourth the total bacterial mass.

Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins and the SSU consists of a single rRNA molecule and over 30 different proteins. The rRNAs act as scaffolding that organizes the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids.

Ribosomes Make Ribosomes

Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, the cell’s machinery needs to manufacture enough ribosomes to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

Is There a Rationale for Ribosome Structure?

Clearly, ribosomes are complex subcellular particles. But, is there any rhyme or reason for their structure? Or are ribosomes the product of a historically contingent evolutionary history?

New work by researchers from Harvard University and Uppsala University in Sweden provides key insight into the compositional make up of ribosomes, and, in doing so, help answer these questions.1

As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

  1. Why are ribosomes made up of so many proteins?
  2. Why are ribosomal proteins nearly the same size?
  3. Why are ribosomal proteins smaller than typical proteins?
  4. Why are ribosomes made up of so few rRNA molecules?
  5. Why are rRNA molecules are so large?
  6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

Ribosome Composition Is Optimal for Efficient Production of Ribosomes

Using mathematical modeling, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were larger, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner.

These researchers also learned that if the ribosomal proteins were any shorter, inefficient ribosome production also results. This inefficiency stems from biochemical events needed to initiate protein production. If proteins are too short, then the initiation events take longer than the elongation processes that build the protein chains.

The bottom line: The mathematical modeling work by the Harvard and Uppsala University research team indicates that the sizes of ribosomal proteins are optimal to ensure the most rapid and efficient production of ribosomes. The mathematical modeling also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature.

Ribosome Composition Is Optimal to Produce a Varied Population of Ribosomes

The insights of this work have bearing on the recent discovery that within cells a heterogeneous population of ribosomes exists, not a homogeneous one as biochemists have long thought.2 Instead of every ribosome in the cell being identical, capable of producing each and every protein the cell needs, a diverse ensemble of distinct ribosomes exists in the cell. Each type of ribosome manufactures characteristically distinct types of proteins. Typically, ribosomes produce proteins that work in conjunction to carry out related cellular functions. The heterogeneous makeup of ribosomes contributes to the overall efficiency of protein production, and also provides an important means to regulate protein synthesis. It wouldn’t make sense to use an assembly line to make both consumer products, such as antiperspirant sticks, and automobiles. In the same manner, it doesn’t make sense to use the same ribosomes to make the myriad proteins, performing different functions for the cell.

Because ribosomes consist of a large number of small proteins, the cell can efficiently produce heterogeneous populations of ribosomes by assembling a ribosomal core and then including and excluding specific ribosomal proteins to generate a diverse population of ribosomes.3 In other words, the protein composition of ribosomes is optimized to efficiently replicate a diverse population of these subcellular particles.

The Case for Creation

The ingenuity of biochemical systems was one of the features of the cell’s chemistry that most impressed me as a graduate student (and moved me toward the recognition that there was a Creator). And the latest work by researchers on ribosome composition from Harvard and Uppsala Universities provides another illustration of the clever way that biochemical systems are constructed. The composition of these subcellular structures doesn’t appear to be haphazard—a frozen accident of a historically contingent evolutionary process—but instead is undergirded by an elegant molecular rationale, consistent with the work of a mind.

The case for intelligent design gains reinforcement from the optimal composition of ribosomal proteins. Quite often, designs produced by human beings have been optimized, making this property a telltale signature for intelligent design. In fact, optimality is most often associated with superior designs.

As I pointed out in The Cell’s Design, ribosomes are chicken-and-egg systems. Because ribosomes are composed of proteins, proteins are needed to make proteins. As with ingenuity and optimality, this property also evinces for the work of intelligent agency. Building a system that displays this unusual type of interdependency requires, and hence, reflects the work of a mind.

On the other hand, the chicken-and-egg nature of ribosome biosynthesis serves as a potent challenge to evolutionary explanations for the origin of life.

The Challenge to Evolution

Because ribosomes are needed to make the proteins needed to make ribosomes, it becomes difficult to envision how this type of chicken-and-egg system could emerge via evolutionary processes. Protein synthesis would have to function optimally at the onset. If it did not, it would lead to a cycle of auto-destruction for the cell.

Ribosomes couldn’t begin as crudely operating protein-manufacturing machines that gradually increased in efficiency—evolving step-by-step—toward the optimal systems, characteristic of contemporary biochemistry. If error-prone, ribosomes will produce defective proteins—including ribosomal proteins. In turn, defective ribosomal proteins will form ribosomes even more prone to error, setting up the auto-destruct cycle. And in any evolutionary scheme, the first ribosomes would have been error-prone.

The compositional requirement that ribosomal proteins be of the just-right size and uniform in length only exacerbates this chicken-and-egg problem. Even if ribosomes form functional, intact proteins, if these proteins aren’t the correct number, size, or uniformity then ribosomes couldn’t be replicated fast enough to support cellular reproduction.

In short, the latest insights in the protein composition of ribosomes provides compelling reasons to think that life must stem from a Creator’s handiwork.

So does the compositional makeup of ribosomal RNA molecules, which will be the topic of my next blog post.

Resources

Endnotes

  1. Shlomi Reuveni et al., “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–97, doi:10.1038/nature22998.
  2. Zhen Shi et al., “Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-Wide,” Molecular Cell 67 (July 6, 2017): 71–83, doi:10.1016/j.molcel.2017.05.021.
  3. Jeffrey A. Hussmann et al., “Ribosomal Architecture: Constraints Imposed by the Need for Self-Production,” Current Biology 27 (August 21, 2017): R798–R800, doi:10.1016/j.cub.2017.06.080.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/11/01/ribosomes-manufactured-by-design-part-1