Tag: proteins

Discovery of Intron Function Interrupts Evolutionary Paradigm

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BY FAZALE RANA – MARCH 6, 2019

Nobody likes to be interrupted when they are talking. It feels disrespectful and can be frustrating. Interruptions derail the flow of a conversation.

The editors tell me that I need to interrupt this lead to provide a “tease” for what is to come. So, here goes: Interruptions happen in biochemical systems, too. Life scientists long thought that these interruptions disrupted the flow of biochemical information. But, it turns out these interruptions serve an important function, offering a rejoinder a common argument against intelligent design.

Now back to the lead.

Perhaps it is no surprise that some psychologists study interruptions1 with the hope of discovering answers to questions such as:

  • Why do people interrupt?
  • Who is most likely to interrupt?
  • Do we all perceive interruptions in the same way?

While there is still much to learn about the science of interruptions, psychologists have discovered that men interrupt more often than women. Ironically, men often view women who interrupt as ruder and less intelligent than men who interrupt during conversations.

Researchers have also found that a person’s cultural background influences the likelihood that he or she will interrupt during a discourse. Personality also plays a role. Some people are more sensitive to pauses in conversation and, therefore, find themselves interrupting more often than those who are less uncomfortable with periods of silence.

Psychologists have learned that not all interruptions are the same. Some people interrupt because they want the “floor.” These people are called intrusive interrupters. Cooperativeinterrupters help move the conversation along by agreeing with the speaker and finishing the speaker’s thoughts.

Interruptions are not confined to conversations. They are a part of life, including the biochemical operations that take place inside the cell.

In fact, biochemists have discovered that the information harbored in genes, which contains the instructions to build proteins—the workhorse molecules of the cell—experience interruptions in their coding sequences. These intrusive interruptions would disrupt the flow of information in the cell during the process of protein synthesis if the interrupting sequences weren’t removed by the cell’s machinery.

Molecular biologists have long viewed these genetic “interruptions” (called introns) as serving no useful purpose for the cell, with introns comprising a portion of the junk DNA found in the genomes of eukaryotic organisms. But it turns out that introns—like cooperative interruptions during a conversation—serve a useful purpose, according to the recent work of two independent teams of molecular biologists.

Introns Are Abundant

Noncoding regions within genes, introns consist of DNA sequences that interrupt the coding regions (called exons) of a gene. Introns are pervasive in genomes of eukaryotic organisms. For example, 90 percent of genes in mammals consists of introns, with an average of 8 per gene.

After the information stored in a gene is copied into messenger RNA, the intron sequences are excised, and the exons spliced together by a protein-RNA complex known as a spliceosome.

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Figure 1: Drawing of pre-mRNA to mRNA. Image credit: Wikipedia

Molecular biologists have long wondered why eukaryotic genes would be riddled with introns. Introns seemingly make the structure and expression of eukaryotic genes unnecessarily complicated. What possible purpose could introns serve? Researchers also thought that once the introns were spliced out of the messenger RNA sequences, they were discarded as genetic debris.

Introns Serve a Functional Purpose

But recent work by two independent research teams from Sherbrooke University in Quebec, Canada, and MIT, respectively, indicates that molecular biologists have been wrong about introns. They have learned that once spliced from messenger RNA, these fragments play a role in helping cells respond to stress.

Both research teams studied baker’s yeast. One advantage of using yeast as a model organism relates to the relatively small number of introns (295) in its genome.

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Figure 2: A depiction of baker’s yeast. Image credit: Shutterstock

Taking advantage of the limited number of introns in baker’s yeast, the team from Sherbrooke University created hundreds of yeast strains—each one missing just one of its introns. When grown under normal conditions with a ready supply of available nutrients, the strains missing a single intron grew normally—suggesting that introns aren’t of much importance. But when the researchers grew the yeast cells under conditions of food scarcity, the yeast with the deleted introns frequently died.2

The MIT team observed something similar. They noticed that during the stationary phase of growth (when nutrients become depleted, slowing down growth), introns spliced from RNA accumulated in the growth medium. The researchers deleted the specific introns that they found in the growth medium from the baker’s yeast genome and discovered that the resulting yeast strains struggled to survive under nutrient-poor conditions.3

At this point, it isn’t clear how introns help cells respond to stress caused by a lack of nutrients, but they have some clues. The Sherbrooke University team thinks that the spliced-out introns play a role in repressing the production of proteins that help form ribosomes. These biochemical machines manufacture proteins. Because protein synthesis requires building block materials and energy, during periods when nutrients are scarce, protein production slows down in cells. Ratcheting down protein synthesis impedes cell growth but affords them a better chance to survive a lack of nutrients. One way cells can achieve this objective is to stop making ribosomes.

The MIT team thinks that some spliced-out introns interact with spliceosomes, preventing them from splicing out other introns. When this disruption happens, it slows down protein synthesis.

Both research groups believe that in times when nutrients are abundant, the spliced-out introns are broken down by the cell’s machinery. But when nutrients are scarce, that condition triggers intron accumulation.

At this juncture, it isn’t clear if the two research teams have uncovered distinct mechanisms that work collaboratively to slow down protein production, or if they are observing facets of the same mechanism. Regardless, it is evident that introns display functional utility. It’s a surprising insight that has important ramifications for our understanding of the structure and function of genomes. This insight has potential biomedical utility and theological implications, as well.

Intron Function and the Case for Creation

Scientists who view biology through the lens of the evolutionary paradigm are quick to conclude that the genomes of organisms reflect the outworking of evolutionary history. Their perspective causes them to see the features of genomes, such as introns, as little more than the remnants of an unguided evolutionary process. Within this framework, there is no reason to think that any particular DNA sequence element, including introns, harbors function. In fact, many life scientists regard the “evolutionary vestiges” in the genome as junk DNA. This clearly has been the case for introns.

Yet, a growing body of data indicates that virtually every category of so-called junk DNA displays function. We can now add introns—cooperative interrupters—to the list. And based on the data on hand, we can make a strong case that most of the sequence elements in genomes possess functional utility.

Could it be that scientists really don’t understand the biology of genomes? Or maybe we have the wrong paradigm?

It seems to me that science is in the midst of a revolution in our understanding of genome structure and function. Instead of being a wasteland of evolutionary debris, most of the genome appears to be functional. And the architecture and operations of genomes appear to be far more elegant and sophisticated than anyone ever imagined—at least within the confines of the evolutionary paradigm.

But what if the genome is viewed from a creation model framework?

The elegance and sophistication of genomes are features that are increasingly coming into scientific view. And this is precisely what I would expect if genomes were the product of a Mind—the handiwork of a Creator.

Now that is a discovery worth talking about.

Resources

Endnotes
  1. Teal Burrell, “The Science behind Interrupting: Gender, Nationality and Power, and the Roles They Play,” Post Magazine (March 14, 2018), https://www.scmp.com/magazines/post-magazine/long-reads/article/2137023/science-behind-interrupting-gender-nationality; Alex Shashkevich, “Why Do People Interrupt? It Depends on Whom You’re Talking To,” The Guardian (May 18, 2018), https://www.theguardian.com/lifeandstyle/2018/may/18/why-do-people-interrupt-it-depends-on-whom-youre-talking-to.
  2. Julie Parenteau et al., “Introns Are Mediators of Cell Response to Starvation,” Nature 565 (January 16, 2019): 612–17, doi:10.1038/s41586-018-0859-7.
  3. Jeffrey T. Morgan, Gerald R. Fink, and David P. Bartel, “Excised Linear Introns Regulate Growth in Yeast,” Nature 565 (January 16, 2019): 606–11, doi:10.1038/s41586-018-0828-1.

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/03/06/discovery-of-intron-function-interrupts-evolutionary-paradigm

Protein Amino Acids Form a “Just-Right” Set of Biological Building Blocks

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BY FAZALE RANA – FEBRUARY 21, 2018

Like most kids, I had a set of Lego building blocks. But, growing up in the 1960s, the Lego sets were nothing like the ones today. I am amazed at how elaborate and sophisticated Legos have become, consisting of interlocking blocks of various shapes and sizes, gears, specialty parts, and figurines—a far cry from the square and rectangular blocks that made up the Lego sets of my youth. The most imaginative things I could ever hope to build were long walls and high towers.

It goes to show: the set of building blocks make all the difference in the world.

This truism applies to the amino acid building blocks that make up proteins. As it turns out, proteins are built from a specialty set of amino acids that have the just-right set of properties to make life possible, as recent work by researchers from Germany attests.1 From my vantage point as a biochemist and a Christian, the just-right amino acid composition of proteins evinces intelligent design and is part of the reason I think a Creator must have played a direct role in the origin and design of life.

Why is the Same Set of Twenty Amino Acids Used to Build Proteins?

It stands as one of the most important insights about protein structure discovered by biochemists: The set of amino acids used to build proteins is universal. In other words, the proteins found in every organism on Earth are made up of the same 20 amino acids.

Yet, hundreds of amino acids exist in nature. And, this abundance prompts the question: Why these 20 amino acids? From an evolutionary standpoint, the set of amino acids used to build proteins should reflect:

1) the amino acids available on early Earth, generated by prebiotic chemical reactions;

2) the historically contingent outworking of evolutionary processes.

In other words, evolutionary mechanisms would have cobbled together an amino acid set that works “just good enough” for life to survive, but nothing more. No one would expect evolutionary processes to piece together a “just-right,” optimal set of amino acids. In other words, if evolutionary processes shaped the amino acid set used to build proteins, these biochemical building blocks should be much like the unsophisticated Lego sets little kids played with in the 1960s.

An Optimal Set of Amino Acids

But, contrary to this expectation, in the early 1980s biochemists discovered that an exquisite molecular rationale undergirds the amino acid set used to make proteins. Every aspect of the amino acid structure has to be precisely the way it is for life to be possible. On top of that, researchers from the University of Hawaii have conducted a quantitative comparison of the range of chemical and physical properties possessed by the 20 protein-building amino acids versus random sets of amino acids that could have been selected from early Earth’s hypothetical prebiotic soup.2 They concluded that the set of 20 amino acids is optimal. It turns out that the set of amino acids found in biological systems possesses the “just-right” properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity. They also showed that the amino acids selected for proteins are a “highly unusual set of 20 amino acids; a maximum of 0.03% random sets outperformed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously.”3

A New Perspective on the 20 Protein Amino Acids

Beyond charge, size, and hydrophobicity, the German researchers wondered if quantum mechanical effects play a role in dictating the universal set of 20 protein amino acids. To address this question, they examined the gap between the HOMO (highest occupied molecular orbital) and the LUMO (lowest unoccupied molecular orbital) for the protein amino acids. The HOMO-LUMO gap is one of the quantum mechanical determinants of chemical reactivity. More reactive molecules have smaller HOMO-LUMO gaps than molecules that are relatively nonreactive.

The German biochemists discovered that the HOMO-LUMO gap was small for 7 of the 20 amino acids (histidine, phenylalanine cysteine, methionine, tyrosine, and tryptophan), and hence, these molecules display a high level of chemical activity. Interestingly, some biochemists think that these 7 amino acids are not necessary to build proteins. Previous studies have demonstrated that a wide range of foldable, functional proteins can be built from only 13 amino acids (glycine, alanine, valine, leucine, isoleucine, proline, serine, threonine, aspartic acid, glutamic acid, asparagine, lysine, and arginine). As it turns out, this subset of 13 amino acids has a relatively large HOMO-LUMO gap and, therefore, is relatively unreactive. This suggests that the reactivity of histidine, phenylalanine cysteine, methionine, tyrosine, and tryptophan may be part of the reason for the inclusion of the 7 amino acids in the universal set of 20.

As it turns out, these amino acids readily react with the peroxy free radical, a highly corrosive chemical species that forms when oxygen is present in the atmosphere. The German biochemists believe that when these 7 amino acids reside on the surface of proteins, they play a protective role, keeping the proteins from oxidative damage.

As I discussed in a previous article, these 7 amino acids contribute in specific ways to protein structure and function. And they contribute to the optimal set of chemical and physical properties displayed by the universal set of 20 amino acids. And now, based on the latest work by the German researchers, it seems that the amino acids’ newly recognized protective role against oxidative damage adds to their functional and structural significance in proteins.

Interestingly, because of the universal nature of biochemistry, these 7 amino acids must have been present in the proteins of the last universal common ancestor (LUCA) of all life on Earth. And yet, there was little or no oxygen present on early Earth, rendering the protective effect of these amino acids unnecessary. The importance of the small HOMO-LUMO gaps for these amino acids would not have become realized until much later in life’s history when oxygen levels became elevated in Earth’s atmosphere. In other words, inclusion of these amino acids in the universal set at life’s start seemingly anticipates future events in Earth’s history.

Protein Amino Acids Chosen by a Creator

The optimality, foresight, and molecular rationale undergirding the universal set of protein amino acids is not expected if life had an evolutionary origin. But, it is exactly what I would expect if life stems from a Creator’s handiwork. As I discuss in The Cell’s Design, objects and systems created and produced by human designers are typically well thought out and optimized. Both are indicative of intelligent design. In human designs, optimization is achieved through foresight and planning. Optimization requires inordinate attention to detail and careful craftsmanship. By analogy, the optimized biochemistry, epitomized by the amino acid set that makes up proteins, rationally points to the work of a Creator.

Resources

Endnotes

  1. Matthias Granhold et al., “Modern Diversification of the Amino Acid Repertoire Driven by Oxygen,” Proceedings of the National Academy of Sciences USA 115 (January 2, 2018): 41–46, doi:10.1073/pnas.1717100115.
  2. Gayle K. Philip and Stephen J. Freeland, “Did Evolution Select a Nonrandom ‘Alphabet’ of Amino Acids?” Astrobiology 11 (April 2011): 235–40, doi:10.1089/ast.2010.0567.
  3. Philip and Freeland, “Did Evolution Select,” 235–40.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/02/21/protein-amino-acids-form-a-just-right-set-of-biological-building-blocks

Is the Laminin “Cross” Evidence for a Creator?

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BY FAZALE RANA – JANUARY 31, 2018

As I interact with people on social media and travel around the country to speak on the biochemical evidence for a Creator, I am frequently asked to comment on laminin.1 The people who mention this protein are usually quite excited, convinced that its structure provides powerful scientific evidence for the Christian faith. Unfortunately, I don’t agree.

Motivating this unusual question is the popularized claim of a well-known Christian pastor that laminin’s structure provides physical evidence that the God of the Bible created human beings and also sustains our lives. While I wholeheartedly believe God did create and does sustain human life, laminin’s apparent cross-shape does not make the case.

Laminin is one of the key components of the basal lamina, a thin sheet-like structure that surrounds cells in animal tissue. The basal lamina is part of the extracellular matrix (ECM). This structure consists of a meshwork of fibrous proteins and polysaccharides secreted by the cells. It forms the space between cells in animal tissue. The ECM carries out a wide range of functions that include providing anchor points and support for cells.

Laminin is a relatively large protein made of three different protein subunits that combine to form a t-shaped structure when the flexible rod-like regions of laminin are fully extended. Each of the four “arms” of laminin contains sites that allow this biomolecule to bind to other laminin molecules, other proteins (like collagen), and large polysaccharides. Laminin also provides a binding site for proteins called integrins, which are located in the cell membrane.

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Figure: The structure of laminin. Image credit: Wikipedia

Laminin’s architecture and binding sites make this protein ideally suited to interact with other proteins and polysaccharides to form a network called the basal reticulum and to anchor cells to its biochemical scaffolding. The basal reticulum helps hold cells together to form tissues and, in turn, helps cement that tissue to connective tissues.

The cross-like shape of laminin and the role it plays in holding tissues together has prompted the claim that this biomolecule provides scientific support for passages such as Colossians 1:15–17 and shows how the God of the Bible must have made humans and continues to sustain them.

I would caution Christians against using this “argument.” I see a number of problems with it. (And so do many skeptics.)

First, the cross shape is a simple structure found throughout nature. So, it’s probably not a good idea to attach too much significance to laminin’s shape. The t configuration makes laminin ideally suited to connect proteins to each other and cells to the basal reticulum. This is undoubtedly the reason for its structure.

Secondly, the cross shape of laminin is an idealized illustration of the molecule. Portraying complex biomolecules in simplified ways is a common practice among biochemists. Depicting laminin in this extended form helps scientists visualize and catalog the binding sites along its four arms. This configuration should not be interpreted to represent its actual shape in biological systems. In the basal reticulum, laminin adopts all sorts of shapes that bear no resemblance to a cross. In fact, it’s much more common to observe laminin in a swastika configuration than in a cross-like one. Even electron micrographs of isolated laminin molecules that appear cross-shaped may be misleading. Their shape is likely an artifact of sample preparation. I have seen other electron micrographs that show laminin adopting a variety of twisted shapes that, again, bear no resemblance to a cross.

Finally, laminin is not the only molecule “holding things together.” A number of other proteins and polysaccharides are also indispensable components of the basal reticulum. None of these molecules is cross-shaped.

As I argue in my book, The Cell’s Design, the structure and operation of biochemical systems provide some of the most potent support for a Creator’s role in fabricating living systems. Instead of pointing to superficial features of biomolecules such as the “cross-shaped” architecture of laminin, there are many more substantive ways to use biochemistry to argue for the necessity of a Creator and for the value he places on human life. As a case in point, the salient characteristics of biochemical systems identically match those features we would recognize immediately as evidence for the work of a human design engineer. The close similarity between biochemical systems and the devices produced by human designers logically compels this conclusion: life’s most fundamental processes and structures stem from the work of an intelligent, intentional Agent.

When Christians invest the effort to construct a careful case for the Creator, skeptics and seekers find it difficult to deny the powerful evidence from biochemistry and other areas of science for God’s existence.

Resources:

Endnotes

  1. This article was originally published in the April 1, 2009, edition of New Reasons to Believe.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/01/31/is-the-laminin-cross-evidence-for-a-creator

Ribosomes: Manufactured by Design, Part 1

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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

DNA Replication Winds Up the Case for Intelligent Design

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BY FAZALE RANA – AUGUST 8, 2017

One of my classmates and friends in high school was a kid we nicknamed “Radar.” He was a cool kid who had special needs. He was mentally challenged. He was also funny and as good-hearted as they come, never causing any real problems—other than playing hooky from school, for days on end. Radar hated going to school.

When he eventually showed up, he would be sent to the principal’s office to explain his unexcused absences to Mr. Reynolds. And each time, Radar would offer the same excuse: his grandmother died. But Mr. Reynolds didn’t buy it—for obvious reasons. It didn’t require much investigation on the principal’s part to know that Radar was lying.

Skeptics have something in common with my friend Radar. They use the same tired excuse when presented with compelling evidence for design from biochemistry. Inevitably, they dismiss the case for a Creator by pointing out all the “flawed” designs in biochemical systems. But this excuse never sticks. Upon further investigation, claimed instances of bad designs turn out to be elegant, in virtually every instance, as recent work by scientists from UC Davis illustrates.

These researchers accomplished an important scientific milestone by using single molecule techniques to observe the replication of a single molecule of DNA.1 Their unexpected insights have bearing on how we understand this key biochemical operation. The work also has important implications for the case for biochemical design.

For those familiar with DNA’s structure and replication process, you can skip the next two sections. But for those of you who are not, a little background information is necessary to appreciate the research team’s findings and their relevance to the creation-evolution debate.

DNA’s Structure

DNA consists of two molecular chains (called “polynucleotides”) aligned in an antiparallel fashion. (The two strands are arranged parallel to one another with the starting point of one strand of the polynucleotide duplex located next to the ending point of the other strand and vice versa.) The paired molecular chains twist around each other forming the well-known DNA double helix. The cell’s machinery generates the polynucleotide chains using four different nucleotides: adenosine, guanosine, cytidine, and thymidine, abbreviated as A, G, C, and T, respectively.

A special relationship exists between the nucleotide sequences of the two DNA strands. Biochemists say the DNA sequences of the two strands are complementary. When the DNA strands align, the adenine (A) side chains of one strand always pair with thymine (T) side chains from the other strand. Likewise, the guanine (G) side chains from one DNA strand always pair with cytosine (C) side chains from the other strand. Biochemists refer to these relationships as “base-pairing rules.” Consequently, if biochemists know the sequence of one DNA strand, they can readily determine the sequence of the other strand. Base-pairing plays a critical role in DNA replication.

 

Image 1: DNA’s Structure

DNA Replication

Biochemists refer to DNA replication as a “template-directed, semiconservative process.” By “template-directed,” biochemists mean that the nucleotide sequences of the “parent” DNA molecule function as a template, directing the assembly of the DNA strands of the two “daughter” molecules using the base-pairing rules. By “semiconservative,” biochemists mean that after replication, each daughter DNA molecule contains one newly formed DNA strand and one strand from the parent molecule.

 

Image 2: Semiconservative DNA Replication

Conceptually, template-directed, semiconservative DNA replication entails the separation of the parent DNA double helix into two single strands. By using the base-pairing rules, each strand serves as a template for the cell’s machinery to use when it forms a new DNA strand with a nucleotide sequence complementary to the parent strand. Because each strand of the parent DNA molecule directs the production of a new DNA strand, two daughter molecules result. Each one possesses an original strand from the parent molecule and a newly formed DNA strand produced by a template-directed synthetic process.

DNA replication begins at specific sites along the DNA double helix, called “replication origins.” Typically, prokaryotic cells have only a single origin of replication. More complex eukaryotic cells have multiple origins of replication.

The DNA double helix unwinds locally at the origin of replication to produce what biochemists call a “replication bubble.” During the course of replication, the bubble expands in both directions from the origin. Once the individual strands of the DNA double helix unwind and are exposed within the replication bubble, they are available to direct the production of the daughter strand. The site where the DNA double helix continuously unwinds is called the “replication fork.” Because DNA replication proceeds in both directions away from the origin, there are two replication forks within each bubble.

 

Image 3: DNA Replication Bubble

DNA replication can only proceed in a single direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed with the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand, in the top-to-bottom direction. For this strand—referred to as the “leading strand”—DNA replication proceeds rapidly and continuously in the direction of the advancing replication fork.

DNA replication cannot proceed along the strand with the top-to-bottom orientation until the replication bubble has expanded enough to expose a sizable stretch of DNA. When this happens, DNA replication moves away from the advancing replication fork. DNA replication can only proceed a short distance for the top-to-bottom-oriented strand before the replication process has to stop and wait for more of the parent DNA strand to be exposed. When a sufficient length of the parent DNA template is exposed a second time, DNA replication can proceed again, but only briefly before it has to stop again and wait for more DNA to be exposed. The process of discontinuous DNA replication takes place repeatedly until the entire strand is replicated. Each time DNA replication starts and stops, a small fragment of DNA is produced.

Biochemists refer to these pieces of DNA (that will eventually compose the daughter strand) as “Okazaki fragments”—after the biochemist who discovered them. Biochemists call the strand produced discontinuously the “lagging strand” because DNA replication for this strand lags behind the more rapidly produced leading strand. One additional point: the leading strand at one replication fork is the lagging strand at the other replication fork since the replication forks at the two ends of the replication bubble advance in opposite directions.

An ensemble of proteins is needed to carry out DNA replication. Once the origin recognition complex (which consists of several different proteins) identifies the replication origin, a protein called “helicase” unwinds the DNA double helix to form the replication fork.

 

Image 4: DNA Replication Proteins

Once the replication fork is established and stabilized, DNA replication can begin. Before the newly formed daughter strands can be produced, a small RNA primer must be produced. The protein that synthesizes new DNA by reading the parent DNA template strand—DNA polymerase—can’t start production from scratch. It must be primed. A massive protein complex, called the “primosome,” which consists of over 15 different proteins, produces the RNA primer needed by DNA polymerase.

Once primed, DNA polymerase will continuously produce DNA along the leading strand. However, for the lagging strand, DNA polymerase can only generate DNA in spurts to produce Okazaki fragments. Each time DNA polymerase generates an Okazaki fragment, the primosome complex must produce a new RNA primer.

Once DNA replication is completed, the RNA primers are removed from the continuous DNA of the leading strand and from the Okazaki fragments that make up the lagging strand. A protein called a “3’-5’ exonuclease” removes the RNA primers. A different DNA polymerase fills in the gaps created by the removal of the RNA primers. Finally, a protein called a “ligase” connects all the Okazaki fragments together to form a continuous piece of DNA out of the lagging strand.

Are Leading and Lagging Strand Polymerases Coordinated?

Biochemists had long assumed that the activities of the leading and lagging strand DNA polymerase enzymes were coordinated. If not, then DNA replication of one strand would get too far ahead of the other, increasing the likelihood of mutations.

As it turns out, the research team from UC Davis discovered that the activities of the two polymerases are not coordinated. Instead, the leading and lagging strand DNA polymerase enzymes replicate DNA autonomously. To the researchers’ surprise, they learned that the leading strand DNA polymerase replicated DNA in bursts, suddenly stopping and starting. And when it did replicate DNA, the rate of production varied by a factor of ten. On the other hand, the researchers discovered that the rate of DNA replication on the lagging strand depended on the rate of RNA primer formation.

The researchers point out that if not for single molecule techniques—in which replication is characterized for individual DNA molecules—the autonomous behavior of leading and lagging strand DNA polymerases would not have been detected. Up to this point, biochemists have studied the replication process using a relatively large number of DNA molecules. These samples yield average replication rates for leading and lagging strand replication, giving the sense that replication of both strands is coordinated.

According to the researchers, this discovery is a “real paradigm shift, and undermines a great deal of what’s in the textbooks.”2 Because the DNA polymerase activity is not coordinated but autonomous, they conclude that the DNA replication process is a flawed design, driven by stochastic (random) events. Also, the lack of coordination between the leading and lagging strands means that leading strand replication can get ahead of the lagging strand, yielding long stretches of vulnerable single-stranded DNA.

Diminished Design or Displaced Design?

Even though this latest insight appears to undermine the elegance of the DNA replication process, other observations made by the UC Davis research team indicate that the evidence for design isn’t diminished, just displaced.

These investigators discovered that the activity of helicase—the enzyme that unwinds the double helix at the replication fork—somehow senses the activity of the DNA polymerase on the leading strand. When the DNA polymerase stalls, the activity of the helicase slows down by a factor of five until the DNA polymerase catches up. The researchers believe that another protein (called the “tau protein”) mediates the interaction between the helicase and DNA polymerase molecules. In other words, the interaction between DNA polymerase and the helicase compensates for the stochastic behavior of the leading strand polymerase, pointing to a well-designed process.

As already noted, the research team also learned that the rate of lagging strand replication depends on primer production. They determined that the rate of primer production exceeds the rate of DNA replication on the leading strand. This fortuitous coincidence ensures that as soon as enough of the bubble opens for lagging strand replication to continue, the primase can immediately lay down the RNA primer, restarting the process. It turns out that the rate of primer production is controlled by the primosome concentration in the cell, with primer production increasing as the number of primosome copies increase. The primosome concentration appears to be fine-tuned. If the concentration of this protein complex is too large, the replication process becomes “gummed up”; if too small, the disparity between leading and lagging strand replication becomes too great, exposing single-stranded DNA. Again, the fine-tuning of primosome concentration highlights the design of this cellular operation.

It is remarkable how two people can see things so differently. For scientists influenced by the evolutionary paradigm, the tendency is to dismiss evidence for design and, instead of seeing elegance, become conditioned to see flaws. Though DNA replication takes place in a haphazard manner, other features of the replication process appear to be engineered to compensate for the stochastic behavior of the DNA polymerases and, in the process, elevate the evidence for design.

And, that’s no lie.

Resources

Endnotes

  1. James E. Graham et al., “Independent and Stochastic Action of DNA Polymerases in the Replisome,” Cell 169 (June 2017): 1201–13, doi:10.1016/j.cell.2017.05.041.
  2. Bec Crew, “DNA Replication Has Been Filmed for the First Time, and It’s Not What We Expected,” ScienceAlert, June 19, 2017, https://sciencealert.com/dna-replication-has-been-filmed-for-the-first-time-and-it-s-stranger-than-we-thought.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/08/08/dna-replication-winds-up-the-case-for-intelligent-design

Hagfish Slime Expands the Case for a Creator

hagfishslimeexpands

BY FAZALE RANA – MARCH 8, 2017

The designs found in biological systems never cease to amaze me. Even something as gross and seemingly insignificant as hagfish slime displays remarkable properties, befitting the handiwork of a Creator. In fact, the design of hagfish slime is so ingenious, it is serving as the source of inspiration for researchers from the US Navy in their quest to develop new types of military technology.

What Are Hagfish?

Hagfish are ancient creatures that first appeared on Earth around 520 million years ago, with representative specimens recovered in the Cambrian fossil assemblages. These eel-like creatures are about 20 inches in length with loose fitting skin that varies in color from pink to blue-gray, depending on the species.

The hagfish are jawless but have a mineralized encasement around their skull (cranium). With eyespots instead of true eyes, these creatures have no vision. Hagfish are bottom-dwellers. To explore their environment, they make use of whisker-like structures. As scavengers, hagfish consume dead and dying creatures by burrowing into their bodies and ingesting the remains from the inside out. Remarkably, hagfish absorb nutrients through their skin and gills, in addition to feeding with their mouths. In fact, researchers estimate that close to half their nutrient intake comes through absorption.

Hagfish Slime

When disturbed or attacked by predators, hagfish secrete a slime from about 100 glands that line the flanks of their bodies. (This behavior explains why hagfish are sometimes called slime eels.) Produced by epithelial and gland thread cells, the slime rapidly expands to 10,000 times its original volume. A single hagfish can generate around 5.5 gallons of slime each time it’s disturbed. Once secreted, the slime coats the gills of attacking fish, suffocating the predator. With the predator distracted, the hagfish performs this defensive maneuver that allows it to escape, while scrapping the slime off its body to prevent self-suffocation.

Two different types of proteins comprise hagfish slime. One of the components, mucin, is a large protein found widely throughout nature, serving as the primary component of mucus. Secreted by epithelial cells, mucin interacts with water molecules, restricting their movement, contributing to the slime’s viscosity.1

Additionally, hagfish slime consists of long, thread-like proteins. These protein threads are 12 nanometers in diameter and 15 centimeters long! (That is one big molecule.) These dimensions equate to a rope that is 1 centimeter in diameter and 1.5 kilometers in length. These protein fibers are incredibly strong, equivalent to a string that is 100 times thinner than a strand of human hair, but 10 times stronger than a piece of nylon.

Inside the gland thread cells, these protein fibers are carefully packaged like a skein of yarn, held together by other proteins that serve as a type of molecular glue.2 When the secreted hagfish slime contacts seawater, the glue proteins dissolve, leading to an explosive unraveling of the protein skeins, without any of the fibers becoming tangled. The protein threads contribute to the slime’s viscoelastic properties and provide the mechanism for the rapid swelling of the slime.

Hagfish Slime Inspires Military Technologies

The unusual and ingenious properties of the slime and the slime’s thread proteins have inspired researchers from the US Navy to explore their use in military technology. For example, the remarkable durability of the protein fibers (reminiscent of Kevlar) suggests an application for them in bulletproof vests. The properties of the hagfish slime could also be used as a flame retardant and a shark repellent for Navy divers.

Other commercial labs are exploring applications that include food packaging, bungee cords, and bandages. In fact, some have gone as far as to dub the thread proteins as the ultimate biodegradable biofiber.

Biomimetics and the Case for a Creator

In recent years, engineers have routinely and systematically benefited by insights from biology to address engineering problems and to inspire new technologies by either directly copying (or mimicking) designs from biology, or using insights from biological designs to guide the engineering enterprise.

From my perspective, the use of biological designs to guide engineering efforts fits awkwardly within the evolutionary paradigm. Why? Because evolutionary biologists view biological systems as the products of an unguided, historically contingent process that co-opts preexisting systems to cobble together new ones. Evolutionary mechanisms can optimize these systems, but they are still kludges.

Given the unguided nature of evolutionary mechanisms, does it make sense for engineers to rely on biological systems to solve problems and inspire new technologies? Conversely, biomimetics and bioinspiration find a natural home in a creation model approach to biology. Using designs in nature to inspire engineering makes sense only if these designs arose from an intelligent Mind—even if they are as disgusting as the slime secreted by a bottom-dwelling scavenger.

Resources

Endnotes

  1. Lukas Böni et al., “Hagfish Slime and Mucin Flow Properties and Their Implications for Defense,” Scientific Reports 6 (July 2016): id. 30371, doi:10.1038/srep30371.
  2. Timothy Winegard et al., “Coiling and Maturation of a High-Performance Fibre in Hagfish Slime Gland Thread Cells,” Nature Communications 5 (April 2014): id. 3534, doi:10.1038/ncomms4534; Mark A. Bernards Jr. et al., “Spontaneous Unraveling of Hagfish Slime Thread Skeins Is Mediated by a Seawater-Soluble Protein Adhesive,” Journal of Experimental Biology 217 (April 2014): 1263–68, doi:10.1242/jeb.096909.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/03/08/hagfish-slime-expands-the-case-for-a-creator

Historical Contingency and the Improbability of Protein Evolution, Part 2 (of 2)

historicalcontingencyandtheimprobability

BY FAZALE RANA – JULY 20, 2016

A few weeks ago, Kathy Emmons of WORD FM in Pittsburg interviewed me about the connection between human evolution and human trafficking. During the interview, she asked me if theological or scientific concerns drove my skepticism about human evolution. My answer is both.

I find it difficult to reconcile the idea of human evolution with passages in the Old and New Testaments that address human origins. But, I also think that there are significant scientific problems confronting the evolutionary paradigm. A recent study by scientists from the Universities of Oregon and Chicago highlights one of those scientific challenges.1

As described in a previous post, these researchers wanted to develop a better understanding of the role that chance historical events play in evolutionary processes. To do this, they reconstructed what they believe to be the evolutionary pathway that led to the emergence of the cortisol-specific glucocorticoid receptor protein, a key component of the vertebrate endocrine system. Based on their reconstruction, it appears that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol. They determined that two of the changes were permissive. That is, these changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur before any of the functional changes took place. Based on their analysis, it appears that the permissive changes were highly improbable, leading the researchers to conclude that historical contingency plays a central role in evolutionary transformations.

According to the researchers:

“If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR . . . or the vertebrate endocrine system more generally—would be substantially different.”2

Historical Contingency

The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.3 According to this idea, the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Gould envisioned historical contingency as primarily resulting from external events (such as climate change or asteroid impacts). But this latest work indicates that the intrinsic complexity of proteins also contributes to historical contingency, because of the necessity and low probability of of permissive amino acid substitutions that support functional changes.

How Widespread Is Historical Contingency?

The question then becomes: How widely applicable is this result? The research team from the Universities of Oregon and Chicago expressed uncertainty regarding this point, but other studies indicate that historical contingency must play a prominent role in molecular evolution.

For example, the long-term evolution experiment conducted by Richard Lenski’s group at Michigan State University demonstrated that the emergence of citrate metabolism in E. coliunder aerobic conditions was historically contingent, predicated on a sequence of chance molecular events. (For more information, see the articles listed under “Resources.”)

Using simulations to monitor the evolution of a protein dubbed argT, researchers from the University of Pennsylvania showed that genetic mutations selected by the evolutionary process are dependent on previous mutations, and over time it becomes increasingly difficult to reverse mutational transformations.4 In other words, an amino acid substitution that occurs in a protein today and is accepted by the evolutionary process would most likely be deleterious if it occurred in the past (because of the central role permissive substitutions play in evolutionary history). Consequently, this mutational change would be selected against by the evolutionary process. One of the researchers involved in this study, Joshua Plotkin, stated,

“There is intrinsically a huge amount of contingency in evolution. Whatever mutations happen to come first set the stage for what other later mutations are permissible. Indeed, history channels evolution down a certain path. Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.”5

A Failed Prediction of the Evolutionary Paradigm

Because the evolutionary process is historically contingent, it seems unlikely that evolutionary processes would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes have been a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, that identical evolutionary outcomes are a characteristic feature of the biological realm.6 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

I regard the widespread occurrence of convergence to one of evolution’s failed predictions, and, as I told Kathy Emmons, a justifiable reason to be skeptical of the claim that evolutionary processes can fully explain the history, diversity, and design of life.

In an upcoming blog post, I will further explore the challenge convergence poses for the evolutionary paradigm.

Stay tuned… (or set your tape player to “record.”)

 

Resources

Endnotes

  1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–07, doi:10.1038/nature13410.
  2. Ibid., 207.
  3. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  4. Premal Shah, David McCandlish, and Joshua Plotkin, “Contingency and Entrenchment in Protein Evolution under Purifying Selection,” Proceedings of the National Academy of Sciences, USA 112 (June 2015): E3226–E3235, doi: 10.1073/pnas.1412933112.
  5. University of Pennsylvania, “Evolution Is Unpredictable and Irreversible, Biologists Show,” ScienceDaily,June 8, 2015, sciencedaily.com/releases/2015/06/150608213032.htm.
  6. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/20/historical-contingency-and-the-improbability-of-protein-evolution-part-2-(of-2)