Do Plastic-Eating Bacteria Dump the Case for Creation?

doplasticeatingbacteria

BY FAZALE RANA – JULY 18, 2018

At the risk of stating the obvious: Plastics are an indispensable part of our modern world. Yet, plastic materials cause untold problems for the environment. One of the properties that makes plastics so useful also makes them harmful. Plastics don’t readily degrade.

Recently, researchers discovered a new strain of bacteria that had recently evolved the ability to degrade plastics. These microbes may help solve some of the environmental problems caused by plastics, but their evolution seemingly causes new problems for people who hold the view that a Creator is responsible for life’s origin and design. But, is this really the case? To find out, we need to break down this discovery.

One plastic in widespread use today is polyethylene terephthalate (PET). This polymer was patented in the 1940s and became widely used in the 1970s. Most people are familiar with PET because it is used to make drinking bottles.

This material is produced by reacting ethylene glycol with terephthalic acid (both produced from petroleum). Crystalline in nature, this plastic is a durable material that is difficult to break down, because of the inaccessibility of the ester linkages that form between the terephthalic acid and ethylene glycol subunits that make up the polymer backbone.

PET can be recycled, thereby mitigating its harmful effects on the environment. A significant portion of PET is mechanically recycled by converting it into fibers used to manufacture carpets.

In principle, PET could be recycled by chemically breaking the ester linkages holding the polymer together. When the ester linkages are cleaved, ethylene glycol and terephthalic acid are the breakdown products. These recovered starting materials could be reused to make more PET. Unfortunately, chemical recycling of PET is expensive and difficult to carry out because of the inaccessibility of the ester linkages. In fact, it is cheaper to produce PET from petroleum products than from the recycled monomers.

Can Bacteria Recycle PET?

An interesting advance took place in 2016 that has important implications for PET recycling. A team of Japanese researchers discovered a strain of the bacterium Ideonella sakaiensis that could break down PET into terephthalic acid and ethylene glycol.1 This strain was discovered by screening wastewater, soil, sediments, and sludge from a PET recycling facility. The microbe produces two enzymes, dubbed PETase and MHETase, that work in tandem to convert PET into its constituent monomers.

Evolution in Action

Researchers think that this microbe acquired DNA from the environment or another microbe via horizontal gene transfer. Presumably, this DNA fragment harbored the genes for cutinase, an enzyme that breaks down ester linkages. Once the I. sakaiensis strain picked up the DNA and incorporated it into its genome, the cutinase gene must have evolved so that it now encodes the information to produce two enzymes with the capacity to break down PET. Plus, this new capability must have evolved rather quickly, over the span of a few decades.

PETase Structure and Evolution

In an attempt to understand how PETase and MHETase evolved and how these two enzymes might be engineered for recycling and bioremediation purposes, a team of investigators from the University of Plymouth determined the structure of PETase with atomic level detail.2 They learned that this enzyme has the structural components characteristic of a family of enzymes called alpha/beta hydrolases. Based on the amino acid sequence of the PETase, the researchers concluded that its closest match to any existing enzyme is to a cutinase produced by the bacterium Thermobifida fusca. One of the most significant differences between these two enzymes is found at their active sites. (The active site is the location on the enzyme surface that binds the compounds that the enzyme chemically alters.) The active site of the PETase is broader than the T. fusca cutinase, allowing it to accommodate PET polymers.

As researchers sought to understand how PETase evolved from cutinase, they engineered amino acid changes in PETase, hoping to revert it to a cutinase. To their surprise, the resulting enzyme was even more effective at degrading PET than the PETase found in nature.

This insight does not help explain the evolutionary origin of PETase, but the serendipitous discovery does point the way to using engineered PETases for recycling and bioremediation. One could envision spraying this enzyme (or the bacterium I. sakaiensis) onto a landfill or in patches of plastics floating in the Earth’s oceans. Or alternatively using this enzyme at recycling facilities to generate the PET monomers.

As a Christian, I find this discovery exciting. Advances such as these will help us do a better job as planetary caretakers and as stewards of God’s creation, in accord with the mandate given to us in Genesis 1.

But, this discovery does raise a question: Does the evolution of a PET-eating bacterium prove that evolution is true? Does this discovery undermine the case for creation? After all, it is evolution happening right before our eyes.

Is Evolution in Action Evidence for Evolution?

To answer this question, we need to recognize that the term “evolution” can take on a variety of meanings. Each one reflects a different type of biological transformation (or presumed transformation).

It is true that organisms can change as their environment changes. This occurs through mutations to the genetic material. In rare circumstances, these mutations can create new biochemical and biological traits, such as the ones that produced the strain of I. sakaiensis that can degrade PET. If these new traits help the organism survive, it will reproduce more effectively than organisms lacking the trait. Over time, this new trait will take hold in the population, causing a transformation of the species.

And this is precisely what happened with I. sakaiensis. However, microbial evolution is not controversial. Most creationists and intelligent design proponents acknowledge evolution at this scale. In a sense, it is not surprising that single-celled microbes can evolve, given their extremely large population sizes and capacity to take up large pieces of DNA from their surroundings and incorporate it into their genomes.

Yet, I. sakaiensis is still I. sakaiensis. In fact, the similarity between PETase and cutinases indicates that only a few amino acid changes can explain the evolutionary origin of new enzymes. Along these lines, it is important to note that both cutinase and PETase cleave ester linkages. The difference between these two enzymes involves subtle structural differences triggered by altering a few amino acids. In other words, the evolution of a PET-degrading bacterium is easy to accomplish through a form of biochemical microevolution.

But just because microbes can undergo limited evolution at a biochemical level does not mean that evolutionary mechanisms can account for the origin of biochemical systems and the origin of life. That is an unwarranted leap. This study is evidence for microbial evolution, nothing more.

Though this advance can help us in our planetary stewardship role, this study does not provide the type of evidence needed to explain the origin of biochemistry and, hence, the origin of life through evolutionary means. Nor does it provide the type of evidence needed to explain the evolutionary origin of life’s major groups. Evolutionary biologists must develop appropriate evidence for these putative transformations, and so far, they haven’t.

Evidence of microbial evolution in action is not evidence for the evolutionary paradigm.

Resources:

Endnotes

  1. Shosuke Yoshida et al., “A Bacterium that Degrades and Assimilates Poly(ethylene terephthalate)” Science 351 (March 11, 2016): 1196–99, doi:10.1126/science.aad6359.
  2. Harry P. Austin, et al., “Characterization and Engineering of a Plastic-Degrading Aromatic Polyesterase,” Proceedings of the National Academy of Sciences, USA (April 17, 2018): preprint, doi:10.1073/pnas.1718804115.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/07/18/do-plastic-eating-bacteria-dump-the-case-for-creation

Mitochondria’s Deviant Genetic Code: Evolution or Creation?

mitochondriasdeviantgeneticcode

BY FAZALE RANA – APRIL 18, 2018

When I was in high school, I had the well-deserved reputation of being a wise guy—though the people who knew me then might have preferred to call me a wise—, instead. Either way, for being a wise guy, I sure didn’t display much wisdom during my teenage years.

I would like to think that I am wiser today. But, the little wisdom I do possess didn’t come easy. To quote singer and songwriter, Helen Reddy, “It’s wisdom born of pain.”

Life’s hardships sure have a way of teaching you lessons. But, I also learned that there is a shortcut to gaining wisdom—if you are wise enough to recognize it. (See what I did there?) It is better to solicit the advice of wise people than to gain wisdom through life’s bitter experiences. And, perhaps there was no wiser person ever than Solomon. Thankfully, Solomon’s wisdom was captured in the book of Proverbs. Many of life’s difficulties can be sidestepped if we are willing to heed Solomon’s advice.

Solomon gained his wisdom through observation and careful reflection. But, his wisdom also came through divine inspiration, and according to Solomon, it was through wisdom that God created the world in which we live (Proverbs 8:22–31). And, it is out of this wisdom that the Holy Spirit inspired Solomon to offer the insights found in the Proverbs.

In Psalm 104, the Psalmist (presumably David) echoes the same idea as Solomon: God created our world through wisdom. The Psalmist writes:

How many are your works, Lord!

In wisdom you made them all;

Based on Proverbs 8 and Psalm 104, I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency but also display undeniable wisdom. In my view, that wisdom should be reflected in the elegance, cleverness, and ingenuity of the designs seen throughout nature. Designs that reflect an underlying purpose. And these features are exactly what we observe when we study the biological realm—as demonstrated by recent work on aquatic mammal body size conducted by investigators from Stanford University.1

Body Sizes of Aquatic Mammals

Though the majority of the world’s mammals live in terrestrial habitats, the most massive members of this group reside in Earth’s oceans. For evolutionary biologists, common wisdom has it that the larger size of aquatic mammals reflects fewer evolutionary constraints on their body size because they live in the ocean. After all, the ocean habitat is more expansive than those found on land, and aquatic animals don’t need to support their weight because they are buoyed by the ocean.

As it turns out, common wisdom is wrong in this case. Through the use of mathematical modeling (employing body mass data from about 3,800 living species of aquatic mammals and around 3,000 fossil species), the research team from Stanford learned that living in an aquatic setting imposes tight constraints on body size, much more so than when animals live on land. In fact, they discovered (all things being equal) that the optimal body mass for aquatic mammals is around 1,000 pounds. Interestingly, the body mass distributions for members of the order Sirenia (dugongs and manatees), and the clades Cetacea (whales and dolphins), and Pinnipeds (sea lions and seals) cluster near 1,000 pounds.

Scientists have learned that the optimal body mass of aquatic mammals displays an underlying biological rationale and logic. It reflects a trade-off between two opposing demands: heat retention and caloric intake. Because the water temperatures of the oceans are below mammals’ body temperatures, heat retention becomes a real problem. Mammals with smaller bodies can’t consume enough food to compensate for heat loss to the oceans, and they don’t have the mass to retain body heat. The way around this problem is to increase their body mass. Larger bodies do a much better job at retaining heat than do smaller bodies. But, the increase in body mass can’t go unchecked. Maintaining a large body requires calories. At some point, metabolic demands outpace the capacity for aquatic mammals to feed, so body mass has to be capped (near 1,000 pounds).

The researchers noted a few exceptions to this newly discovered “rule.” Baleen whales have a body mass that is much greater than 1,000 pounds. But, as the researchers noted, these creatures employ a unique feeding mechanism that allows them to consume calories needed to support their massive body sizes. Filter feeding is a more efficient way to consume calories than hunting prey. The other exception is creatures such as otters. The researchers believe that their small size reflects a lifestyle that exploits both aquatic and terrestrial habitats.

Argument for God’s Existence from Wisdom

The discovery that the body mass of aquatic mammals has been optimized is one more example of the many elegant designs found in biological systems—designs worthy to be called the Creator’s handiwork. However, from my perspective, this optimization also reflects the Creator’s sagacity as he designed mammals for the purpose of living in the earth’s oceans.

But, instead of relying on intuition alone to make a case for a Creator, I want to present a formal argument for God’s existence based on the wisdom of biology’s designs. To make this argument, I follow after philosopher Richard Swinburne’s case for God’s existence based on beauty. Swinburne argues, “If God creates a universe, as a good workman he will create a beautiful universe. On the other hand, if the universe came into existence without being created by God, there is no reason to suppose that it would be a beautiful universe.”2 In other words, the beauty in the world around us signifies the Divine.

In like manner, if God created the universe, including the biological realm, we should expect to see wisdom permeating the designs in nature. On the other hand, if the universe came into being without God’s involvement, then there is no reason to think that the designs in nature would display a cleverness and ingenuity that affords a purpose—a sagacity, if you will. In fact, evolutionary biologists are quick to assert that most biological designs are flawed in some way. They argue that there is no purpose that undergirds biological systems. Why? Because evolutionary processes do not produce biological systems from scratch, but from preexisting systems that are co-opted through a process dubbed exaptation (by the late evolutionary biologist Stephen Jay Gould), and then modified by natural selection to produce new designs.3 According to biologist Ken Miller:

“Evolution . . . does not produce perfection. The fact that every intermediate stage in the development of an organ must confer a selective advantage means that the simplest and most elegant design for an organ cannot always be produced by evolution. In fact, the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification.”4

And yet we see designs in biology that are not just optimized, but characterized by elegance, cleverness, and ingenuity—wisdom.

Truly, God is a wise guy.

Resources

Endnotes

  1. William Gearty, Craig R. McClain, and Jonathan L. Payne, “Energetic Tradeoffs Control the Size Distribution of Aquatic Mammals,” Proceedings of the National Academy of Sciences USA (March 2018): doi:10.1073/pnas.1712629115.
  2. Richard Swinburne, The Existence of God, 2nd ed. (New York: Oxford University Press, 2004), 190–91.
  3. Stephen Jay Gould and Elizabeth S. Vrba, “Exaptation: A Missing Term in the Science of Form,” Paleobiology8 (January 1, 1982): 4–15, doi:10.1017/S0094837300004310.
  4. Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994): 24–32.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/04/11/mitochondria-s-deviant-genetic-code-evolution-or-creation

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

proteinaminoacids

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

Love Is in the Air and It Smells Like Intelligent Design

loveisintheair

BY FAZALE RANA – FEBRUARY 14, 2018

Being the hopeless romantic, I worked hard last year to come up with just the right thing to say to my wife on Valentine’s Day. I decided to let my lovely bride know that I really liked her signaling traits. Sadly, that didn’t go over so well.

This year, I think I am going to tell my wife that I like the way she smells.

I don’t know how Amy will receive my romantic overture, but I do know that scientific research explains the preference I have for my wife’s odors—it reflects the composition of a key component of her immune system, specifically her major histocompatibility complex. And, my wife’s immune system really turns me on.

Odor Preference and Immune System Composition

Why am I so attracted to my wife’s scents, and hence, the composition of her immune system? Several studies help explain the connection.

In a highly cited study, researchers had men sleep in the same T-shirt for several nights in a row. Then, they asked women to rank the T-shirts according to odor preference. As it turns out, women had the greatest preference for the odor of T-shirts worn by men who had MHC genes that were the most dissimilar to theirs.

In another oft-cited study, researchers had 121 men and women rank the pleasantness of T-shirt odors and found that the ones they most preferred displayed odors that were most similar to those of their partners. Based on the results of another related study, it appears that this odor preference reflects dissimilarities in immune systems. Researchers discovered that the genetic differences in the MHC genes for 90 married couples were far more extensive than for 152 couples made up by randomly combining partners.

Body Odor and the Immune System

So, how does odor reflect the composition of the MHC genes? Researchers believe that the breakdown products from the MHC during the normal turnover of cellular components serves as the connection between the immune system and body odors.

The MHC is a protein complex that resides on the cell surface. This protein complex binds proteins derived from pathogens after these organisms have infected the host cell and, in turn, displays them on the cell surface for recognition by the cells of the immune system.

 

love-is-in-the-air-and-it-smells-like-intelligent-design

Association of Pathogen Proteins with MHCs

Image credit: By Scray (Own work) [CC BY-SA 3.0 (https://creativecommons.org.licenses/by-sa/3.0)], via Wikimedia Commons

Organisms possess a large number of MHC variants, making the genes that code the MHCs some of the most diverse in the human genome. Because the MHCs bind proteins derived from pathogens, the greater the diversity of MHC genes, the greater the capacity to respond to infectious agents.

As part of the normal turnover of cellular components, the MHCs are constantly being broken down and replaced. When this happens, protein fragments from the MHCs become dispersed throughout the body, winding up in the blood, saliva, and urine. Some researchers think that the microbes in the mouth and on the skin surface lining body cavities metabolize the MHC breakdown products leading to the production of odorants. And these odors tell us something about the immune system of our potential partners.

Advantages of Having a Partner with Dissimilar MHC Genes

When men and women with dissimilar MHC genes pair up, it provides a significant advantage to their children. Why? Because parental MHC gene dissimilarity translates into the maximal genetic diversity for the MHC genes of their children. And, as already noted, the more diverse the MHC genes, the greater the resistance to pathogens and parasites.

The attraction between mates with dissimilar immune genes is not limited to human beings. This phenomenon has been observed throughout the animal kingdom. And from studying mate attraction of animals, we can come to appreciate the importance of MHC gene diversity. For example, one study demonstrated that salmon raised in hatcheries displayed a much more limited genetic diversity for their MHC genes than salmon that live in the wild. As it turns out, hatchery-raised salmon are four times more likely to be infected with pathogens than those found in the wild.

Is Love Nothing More than Biochemistry?

Does the role odor preference plays in mate selection mean that love is merely an outworking of physiological mechanisms? Does it mean that there is not a spiritual dimension to the love we feel toward our partners? Does it mean that human beings are merely physical creatures? If so, does this type of discovery undermine the biblical view of humanity?

Hardly. In fact, this discovery makes perfect sense within a Christian worldview.

In his book The Biology of Sin, neuroscientist Matthew Stanford presents a model that helps make sense of these types of discoveries. Stanford points out that Scripture teaches that human beings are created as both material and immaterial beings, possessing a physical body and nonphysical mind and spirit. Instead of being a “ghost in the machine,” our material and immaterial natures are intertwined, interacting with each other. It is through our bodies (including our brain), that we interact with the physical world around us. The activities of our brain influence the activities of our mind (where our thoughts, feelings, and emotions are housed), and vice versa. It is through our spirit that we have union with God. Spiritual transformation can influence our brain’s activities and how we think; also, how and what we think can influence our spirit.

So, in light of Stanford’s model, we can make sense of how love can be both a physical and spiritual experience while preserving the biblical view of human nature.

Smells Like Intelligent Design

Clearly, the attraction between two people extends beyond body odor and other physical processes and features. Still, the connection between body odor and the composition of the MHC genes presents itself as an ingenious, elegant way to ensure that animal populations (and human beings) are best positioned to withstand the assaults of pathogens. As an old-earth creationist, this insight is exactly what I would expect, attracting me to the view that life on Earth, including human life, is the product of Divine handiwork.

Now, I am off to the chocolatier to get my wife a box of her favorite chocolates for Valentine’s Day. I don’t want her to decide that I stink as a husband.

Resources

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/02/14/love-is-in-the-air-and-it-smells-like-intelligent-design

Is the Laminin “Cross” Evidence for a Creator?

isthelaminincrossevidence

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.

is-the-laminin-cross-evidence-for-a-creator

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

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 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

DNA Replication Winds Up the Case for Intelligent Design

dnareplicationwindsup
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: adenosineguanosinecytidine, 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.”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

DNA Wired for Design

dnawiredfordesign
BY FAZALE RANA – JUNE 20, 2017

Though this be madness, yet there is method
in’t.

Hamlet (Act II, scene II)

Was Hamlet crazy? Or was he feigning madness so he could investigate the murder of his father without raising suspicion?

In my senior year of high school, Mrs. Hodges assigned our class these questions as the topic for the first essay we wrote for honors English. I made the case that Hamlet was perfectly sane. Indeed, there was method to his madness.

I wound up with a B- on the assignment. Mrs. Hodges wasn’t impressed with my reasoning, writing on my paper in red ink, “You aren’t qualified to comment on Hamlet’s sanity. You are not a psychologist!” When she returned my paper, I muttered, “Of course, I’m not a psychologist. I’m a high school student. You were the one who asked me to speculate on his sanity. And then when I do . . .”

I was reminded of this high school memory a few days ago while contemplating the structure and function of DNA. This biomolecule’s design is “crazy.” Yet every detail of DNA’s structure is crucial for the role it plays as an information storage system in the cell. You might say there is biochemical method to DNA’s madness when it comes to its properties. One of DNA’s “insane” features is its capacity to conduct electrical current through the interior of the double helix.

DNA Wires

Caltech chemist Jacqueline Barton discovered this phenomenon in the early 1990s. Barton and her collaborators attached different chemical groups to the two ends of the DNA double helix. Both compounds possessed redox centers (metal atoms that can give off and take up electrons). When they blasted one of the redox centers with a pulse of light, it ejected an electron that was taken up by the redox center attached to the opposite end of the DNA molecule, causing the compound to emit a flash of light. The researchers concluded that the ejected electron must have travelled through the interior of the double helix from one redox center to the other.

Shortly after this discovery, Barton and her team learned that electrical charges  move through DNA only when the double helix is intact. Electrical current won’t flow through single-stranded DNA, nor will it flow if the DNA double helix is distorted, due to damage or misincorporation of DNA subunits during replication.

These (and other) observations indicate that the conductance of electrical charge through the DNA molecule stems from π-π stacking interactions of the nucleobases in the double helix interior. These interactions produce a molecular orbital that spans the length of the double helix. In effect, the molecular orbital functions like a wire running through DNA’s interior.

DNA Wires and Nanoelectronics

Charge conductance through the DNA double helix occurs more rapidly than it does through “standard” molecular wires made from inorganic materials. These “insane” transport speeds have inspired researchers to explore the possibility of using DNA as molecular scale wiring in nanoelectronic devices. In fact, some researchers think that DNA wires might become an integral feature for the next generation of medical diagnostic equipment.

Does DNA Function as a Wire in the Cell?

While the charge conductance through the DNA double helix is an interesting and potentially useful property, biochemists have long wondered if DNA functions as a nanowire in the cell.

In 2009, Barton and her team discovered the answer to this question. DNA’s capacity to transmit electrical charges along the length of the double helix plays a key role in the DNA repair process, and recently Barton’s collaborators have demonstrated that DNA’s wire property plays an important role in the initiation of DNA replication. Both processes are important for DNA to function as an information storage system. Repairing damage to DNA insures the integrity of the information it houses. And DNA replication makes it possible to pass this information on to the next generation. There is a purpose to every aspect of DNA’s properties—a method to the madness.

Detecting Damage to DNA

Damage to DNA distorts the double helix. In a process called base excision repair, the cell’s machinery recognizes and removes the damaged portion of the DNA molecule, replacing it with the correct DNA subunits.

For some time, biochemists puzzled over how the DNA repair enzymes located the damaged regions. In the bacteria E. coli, two repair enzymes, dubbed EndoIII and MutY, occur at low levels. (E. coli is a model organism often used by biochemists to study cellular processes.) Biochemists estimate that less than 500 copies of EndoIII exist in the cell and around 30 copies of MutY. These are low numbers considering the task at hand. These repair enzymes bear the responsibility of surveying the E. coli genome for damage—a genome that consists of over 4.6 million base pairs (genetic letters).

Barton and her team discovered that the two repair enzymes possess a redox center consisting of an iron-sulfur cluster (4Fe4S) that has no enzymatic activity.1 They speculated and then demonstrated that the 4Fe4S cluster functions just like the compounds they attached to the DNA double helix in their original experiment in the 1990s.

It turns out Barton and her team were right. These repair proteins bind to DNA. Once bound, they send an electron from the 4Fe4S redox center through the interior of the double helix, which establishes a current through the DNA molecule. Once the repair protein loses an electron, it cannot dissociate from the DNA double helix. Other repair proteins bound to the DNA pick up the electrons from the DNA’s interior at their iron-sulfur redox center. When they do, they dissociate from the DNA and resume their migration along the double helix. Eventually, the migrating repair protein will bind to the DNA again, sending an electron through the DNA’s interior.

This process is repeated, over and over again. However, if the DNA becomes damaged and the double helix distorted, then the DNA wire breaks, interrupting the flow of electrons. When this happens, the repair proteins remain attached to the DNA close to the location of the damage—thus, initiating the repair process.

Initiating DNA Replication

Recently, Barton and her team discovered that charge conductance through DNA also plays a critical role in the early stages of DNA replication.DNA replication—the process of generating two “daughter molecules” identical to the “parent” molecule—serves an essential life function.

DNA replication begins at specific sites along the double helix, called replication origins. Typically, prokaryotic cells, such as E. coli, have only a single origin of replication.

The replication machinery locally unwinds the DNA double helix at the origin of replication to produce a replication bubble. 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.

Before the newly formed daughter strands can be produced, a small RNA primer must be produced. DNA polymerase—the protein that synthesizes new DNA by reading the parent template strand—can’t start production from scratch. It must be primed. The primosome, a massive protein complex that consists of over 15 different proteins (including the enzyme primase), produces the RNA primer. From there, DNA polymerase takes over and begins synthesizing the daughter DNA strand.

Barton and her team discovered that the handoff between primase and DNA polymerase relies on DNA’s wire property. Both primase and DNA polymerase possess 4Fe4S redox clusters. When primase’s 4Fe4S redox center loses an electron, this protein binds to DNA to produce the RNA primer. When primase’s 4Fe4S redox center picks up an electron, the protein detaches from the DNA to end the production of the RNA primer.

When DNA polymerase binds to the DNA to begin the process of daughter strand synthesis, it sends an electron from its 4Fe4S redox center along the double helix formed by the parent DNA-RNA primer. When the electron reaches the 4Fe4S redox center of primase, it brings the production of the RNA primer to a halt.

DNA Wires and the Case for a Creator

The work by Barton and her colleagues highlights the elegant and sophisticated design of biochemical systems. DNA’s wire property is so remarkable that it serves as inspiration for the design of the next generation of electronic devices—at the nanoscale. The use of biological designs to drive technological advance is one of the most exciting areas in engineering. This area of study—called biomimetics and bioinspiration—presents us with new reasons to believe that life stems from a Creator. It paves the way for a new type of design argument I dub the converse Watchmaker argument: If biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models and, otherwise, inspire the development of new technologies.

The converse Watchmaker argument complements William Paley’s classical Watchmaker argument for God’s existence. In my book The Cell’s Design, I describe how recent advances in biochemistry revitalize this classical argument. Over the last few decades, one of the most astounding insights from biochemistry is the recognition that many biochemical systems display the same properties as human designs. This similarity can be used to argue that life must come from the work of a Mind.

The Watchmaker Prediction

In conjunction with my presentation of the revitalized Watchmaker argument in The Cell’s Design, I proposed the Watchmaker prediction. I contend that many of the cell’s molecular systems currently go unrecognized as analogs to human designs because the corresponding technology has yet to be developed. That is, the Watchmaker argument may well become stronger in the future, and its conclusion more certain, as human technology advances.

The possibility that advances in human technology will ultimately mirror the molecular technology that already exists as an integral part of biochemical systems leads to the Watchmaker prediction: As human designers develop new technologies, examples of these technologies, which previously went unrecognized, will become evident in the operation of the cell’s molecular systems. In other words, if the Watchmaker analogy truly serves as evidence for the Creator’s existence, then it is reasonable to expect that life’s biochemical machinery anticipates human technological advances.

The Watchmaker Prediction, Satisfied

The discovery that DNA’s wire properties are critical for DNA repair and the initiation of DNA replication fulfills the Watchmaker prediction. Barton and her team recognized the physiological importance of DNA charge conductance a year after The Cell’s Design was published.

Nanoscientists have been working to develop molecular-scale nanowires for the last couple of decades. The discovery of DNA’s wire properties occurred in this context. In other words, as new technology emerged—in this case, nanoelectronics—we have discovered its existence inside the cell.

Considering the wire properties of DNA, it is not madness to think that a Creator exists and played a role in life’s genesis.

Resources

Endnotes

  1. Amie K. Boal et al., “Redox Signaling between DNA Repair Proteins for Efficient Lesion Detection,” Proceedings of the National Academy of Sciences, USA 106 (September 8, 2009): 15237–42, doi:10.1073/pnas.0908059106Pamel A. Sontz et al., “DNA Charge Transport as a First Step in Coordinating the Detection of Lesions by Repair Proteins,” Proceedings of the National Academy of Sciences, USA 109 (February 7, 2012): 1856–61, doi:10.1073/pnas.1120063109; Michael A. Grodick, Natalie B. Muren, and Jacqueline K. Barton, “DNA Charge Transport within the Cell,” Biochemistry 54 (February 3, 2015): 962–73, doi:10.1021/bi501520w.
  2. Elizabeth O’Brien et al., “The [4Fe4S] Cluster of Human DNA Primase Functions as a Redox Switch Using DNA Charge Transport,” Science 355 (February 24, 2017): doi:10.1126/science.aag1789.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/06/20/dna-wired-for-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