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

Rabbit Burrowing Churns Claims about Neanderthal Burials

rabbitburrowingchurns

BY FAZALE RANA – FEBRUARY 7, 2018

As a kid, watching cartoons was one of the highlights of my afternoons. As soon as I arrived home from school, I would plop down in front of the TV. Among my favorites were the short features produced by Warner Brothers. What a wonderful cast of characters: Daffy Duck, Sylvester and Tweety, Yosemite Sam, the Tasmanian Devil, the Road Runner and Wile E. Coyote. As much as I loved to watch their shenanigans, none of them compared to the indomitable Bugs Bunny. That “wascally wabbit” (to quote Elmer Fudd) always seemed to create an upheaval everywhere he went.

Recently, a research team from France has come to realize that Bugs Bunny isn’t the only rabbit to make a mess of things. These investigators learned that burrowing rabbits have created an upheaval—literally—at Neanderthal archaeological sites, casting doubt on claims that the hominins displayed advanced sophisticated cognitive abilities.1

Researchers from France unearthed this problem while studying the Regourdou Neanderthal site in Dordogne. Neanderthal bones and stone artifacts, along with animal remains, were recovered from this cave site in 1954. Unfortunately, the removal of the remains by archaeologists was done in a nonscientific manner—by today’s standards.

Based on the arrangement of the Neanderthal remains, lithic artifacts, and cave bear bones at the site, anthropologists initially concluded that one of the Neanderthals found at Regourdou was deliberately buried, indicating that these hominids must have engaged in complex funerary practices. Many anthropologists consider complex funeral activities to reflect one of the most sophisticated examples of symbolic behavior. If so, then Neanderthals must have possessed similar cognitive abilities to modern humans, undermining the scientific case for human exceptionalism and, along with it, casting aspersions on the biblical view of humanity.

Questions about Neanderthal Burials

Yet, more recent analysis of the Regourdou site has raised questions about Neanderthal burial practices. One piece of evidence cited by anthropologists for the funerary burial at this French cave site was the recovery of bear remains associated with a nearly complete Neanderthal specimen. Some anthropologists argued that Neanderthals used the cave bear bones to construct a funerary structure.

But anthropologists have started to question this interpretation. Evidence mounts that this cave site functioned primarily as a den for cave bears, with the accumulation of cave bear bones largely stemming from attritional mortality—not the deliberate activity of Neanderthals.

Rabbits at Regourdou

Anthropologists have also recovered a large quantity of rabbit remains at the Regourdou site. At first, these rabbit bones were taken as evidence that the hominids had the cognitive capacity to hunt and trap small game—something only modern humans were thought to be able to do.

One species found at the Regourdou cave site is the European rabbit (Ochotona cuniculus). These rabbits dig interconnected burrows (called a warren) to avoid predation and harsh climatic conditions. Depending on the sediment, the warren architecture can be deep and complex.

Because the researchers discovered over 10,000 rabbit bones at the Regourdou site, they became concerned that the burrowing behavior of these creatures may have compromised the integrity of the site. To address this issue, they used radiocarbon dating to age-date the rabbit remains. They discovered that the rabbit bones were significantly younger than the sediments harboring them. They also noted that the skeletal parts, breakage pattern of the bones, and surface modification of the rabbit remains indicate that these creatures died within the warrens due to natural causes, negating the claim that Neanderthals hunted small game. This set of observations indicates that the rabbits burrowed and lived in warrens in the Regourdou site, well after the cave deposits formed.

Perhaps of greatest concern associated with this finding is the uncertainty it creates about the integrity of sedimentary layers, because the rabbit burrows cross and perturb several layers, resulting in the mixing of bones and artifacts from one layer to the next. This bioturbation appears to have transported artifacts and bones from the upper layers to the lower layers.

Upheaval of the cave layers caused by the rabbits means that grave goods associated with Neanderthal skeletons may not have been intentionally placed with the body at the time of death. Instead, they may just have happened to wind up next to the hominin remains due to burrowing activity.

Such tumult may not be limited to the Regourdou cave site. These creatures live throughout France and the Iberian Peninsula, raising questions about the influence that the rabbits may have had on the integrity of other archaeological cave sites in France and Spain. For example, it is not hard to envision scenarios in which rabbit burrowing caused mixing at other cave sites, resulting in the accidental association of Neanderthal remains with artifacts initially deposited in upper cave layers made by modern humans who occupied the cave sites after Neanderthals. If so, this association could mistakenly lead anthropologists to conclude that Neanderthals had advanced cognitive abilities, when in fact they did not. While Bugs Bunny’s antics may amuse us, it is no laughing matter to consider the possible impact rabbits may have had on scientific findings.

Only Human Beings Are Exceptional

Even though some anthropologists assert that Neanderthals possessed advanced cognitive abilities like those of modern humans, ongoing scientific scrutiny of the archaeological evidence consistently fails to substantiate those claims. This failure is clearly the case with the Regourdou burial. No doubt, Neanderthals were fascinating creatures. But there is no compelling scientific reason to think that their behavioral capacity threatens human exceptionalism and the notion that human beings were created to bear God’s image.

Resources

Endnotes

  1. Maxime Pelletier et al., “Rabbits in the Grave! Consequences of Bioturbation on the Neandertal ‘Burial’ at Regourdou (Montignac-sur-Vezérè, Dordogne)” Journal of Human Evolution 110 (September 2017): 1–17, doi:10.1016/j.jhevol.2017.04.001.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/02/07/rabbit-burrowing-churns-claims-about-neanderthal-burials

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.

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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