Protein-Binding Sites ENCODEd into the Design of the Human Genome

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BY FAZALE RANA – MARCH 15, 2017

At last year’s AMP Conference, I delivered a talk titled: “How the Greatest Challenges Can Become the Greatest Opportunities for the Gospel.” I illustrated this point by describing three scientific concepts related to the origin of humanity that 20 years ago stood as insurmountable challenges to the traditional biblical view of human origins. But, thanks to scientific advances, these concepts have been replaced with new insights that turn these challenges into evidence for the Christian faith.

The Challenge of Junk DNA

One of the challenges I discussed centered on junk DNA—nonfunctional DNA littering the genomes of most organisms. Presumably, these nonfunctional DNA sequences arose through random biochemical, chemical, and physical events, with functional DNA converted into useless junk, in some instances. In fact, when the scientific community declared the human genome sequence completed in 2003, estimates at that time indicated that around 95 percent of the human genome consist of junk sequences.

Since I have been involved in apologetics (around 20 years), skeptics (and believers) have regarded the high percentages of junk DNA in genomes as a significant problem for intelligent design and creation models. Why would an all-powerful, all-knowing, and all-good God create organisms with so much junk in their genomes? The shared junk DNA sequences found among the genomes of humans and the great apes compounds this challenge. For many, these shared sequences serve as compelling evidence for common ancestry among humans and the other primates. Why would a Creator introduce nonfunctional DNA sequences into corresponding locations in genomes of humans and the great apes?

But what if the junk DNA sequences are functional? It would undermine the case for common descent, because these shared sequences could reasonably be interpreted as evidence for common design.

The ENCODE Project

In recent years, numerous discoveries indicate that virtually every class of junk DNA displays function, providing mounting support for a common-design interpretation of junk DNA. (For a summary, see the expanded and updated edition of Who Was Adam?) Perhaps the most significant advance toward that end came in the fall of 2012 with the publication of phase II results of the ENCODE project—a program carried out by a consortium of scientists with the goal of identifying the functional DNA sequence elements in the human genome.

To the surprise of many, the ENCODE project reported that around 80 percent of the human genome displays function, with the expectation that this percentage should increase with phase III of the project. Many of the newly recognized functional elements play a central role in regulating gene expression. Others serve critical roles in establishing and maintaining the three-dimensional hierarchical structure of chromosomes.

If valid, the ENCODE results would force a radical revision of the way scientists view the human genome. Instead of a wasteland littered with junk DNA sequences, the human genome (and the genome of other organisms) would have to be viewed as replete with functional elements, pointing to a system far more complex and sophisticated than ever imagined—befitting a Creator’s handiwork. (See the articles listed in the Resources section below for more details.)

ENCODE Skeptics

Within hours of the publication of the phase II results, evolutionary biologists condemned the ENCODE project, citing a number of technical issues with the way the study was designed and the way the results were interpreted. (For a response to these complaints go herehere, and here.)

These technical complaints continue today, igniting the junk DNA war between evolutionary biologists and genomics scientists. Though the concerns expressed by evolutionary biologists are technical, some scientists have suggested the real motivation behind the criticisms of the ENCODE project are philosophical—even theological—in nature. For example, molecular biologists John Mattick and Marcel Dinger write:

There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase ‘evolution-free gospel’ in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins2006). This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011).1

Is DNA-Binding Activity Functional?

Even though there may be nonscientific reasons for the complaints leveled against the ENCODE project, it is important to address the technical concerns. One relates to how biochemical function was determined by the ENCODE project. Critics argued that ENCODE scientists conflated biochemical activity with function. As a case in point, three of the assays employed by the ENCODE consortium measure binding of proteins to the genome, with the assumption that binding of transcription factors and histones to DNA indicated a functional role for the target sequences. On the other hand, ENCODE skeptics argue that most of the measured protein binding to the genome was random.

Most DNA-binding proteins recognize and bind to short stretches of DNA (4 to 10 base pairs in length) comprised of highly specific nucleotide sequences. But given the massive size of the human genome (3.2 billion genetic letters), nonfunctional binding sites will randomly occur throughout the genome, for statistical reasons alone. To illustrate: Many DNA-binding proteins target roughly between 1 and 100 sites in the genome. Yet, the genome potentially harbors between 1 million and 1 billion binding sites. The hundreds of sites that are slight variants of the target sequence will have a strong affinity to the DNA-binding proteins, with thousands more having weaker affinities. Hence, the ENCODE critics maintain that much of the protein binding measured by the ENCODE team was random and nonfunctional. To put it differently, much of the protein binding measured in the ENCODE assays merely is a consequence of random biochemical activity.

Nonfunctional Protein Binding to DNA Is Rare

This challenge does have some merit. But, this criticism may not be valid. In an earlier response to this challenge, I acknowledged that some protein binding in genomes will be random and nonfunctional. Yet, based on my intuition as a biochemist, I argued that random binding of proteins throughout the genome would be disruptive to DNA metabolism, and, from an evolutionary perspective would have been eliminated by natural selection. (From an intelligent design/creation model vantage point, it is reasonable to expect that a Creator would design genomes with minimal nonfunctional protein-binding sites.)

As it happens, new work by researchers from NYU affirms my assessment.2 These investigators demonstrated that protein binding in genomes is not random but highly specific. As a corollary, the human genome (and genomes of other organisms) contains very few nonfunctional protein-binding sites.

To reach this conclusion, these researchers looked for nonfunctional protein-binding sites in the genomes of 75 organisms, representative of nearly every major biological group, and assessed the strength of their interaction with DNA-binding proteins. The researchers began their project by measuring the binding affinity for a sample of regulatory proteins (from humans, mice, fruit flies, and yeast) with every possible 8 base pair sequence combination (32,896). Based on the binding affinity data, the NYU scientists discovered that nonfunctional binding sites with a high affinity for DNA binding proteins occurred infrequently in genomes. To use scientific jargon to describe their findings: The researchers discovered a negative correlation between protein-binding affinity and the frequency of nonfunctional binding sites in genomes. Using statistical methods, they demonstrated that this pattern holds for all 75 genomes in their study.

They attempted to account for the frequency of nonfunctional binding sequences in genomes by modeling the evolutionary process, assuming neutral evolution in which random mutations accrue over time free from the influence of natural selection. They discovered that this modeling failed to account for the sequence distributions they observed in the genomes, concluding that natural selection must have weeded high affinity nonfunctional binding sites in genomes.

These results make sense. The NYU scientists point out that protein mis-binding would be catastrophic for two reasons: (1) it would interfere with several key processes, such as transcription, gene regulation, replication, and DNA repair (the interference effect); and (2) it would create inefficiencies by rendering DNA-binding proteins unavailable to bind at functional sites (the titration effect). Though these problems may be insignificant for a given DNA-binding protein, the cumulative effects would be devastating because there are 100 to 1,000 DNA-binding proteins per genome with 10 to 10,000 copies of each protein.

The Human Genome Is ENCODEd for Design

Though the NYU researchers conducted their work from an evolutionary perspective, their results also make sense from an intelligent design/creation model vantage point. If genome sequences are truly the product of a Creator’s handiwork, then it is reasonable to think that the sequences comprising genomes would be optimized—in this case, to minimize protein mis-binding. Though evolutionary biologists maintain that natural selection shaped genomes for optimal protein binding, as a creationist, it is my contention that the genomes were shaped by an intelligent Agent—a Creator.

These results also have important implications for how we interpret the results of the ENCODE project. Given that the NYU researchers discovered that high affinity nonfunctional binding sites rarely occur in genomes (and provided a rationale for why that is the case), it is difficult for critics of the ENCODE project to argue that transcription factor and histone binding assays were measuring mostly random binding. Considering this recent work, it makes most sense to interpret the protein-binding activity in the human genome as functionally significant, bolstering the original conclusion of the ENCODE project—namely, that most of the human genome consists of functional DNA sequence elements. It goes without saying: If the original conclusion of the ENCODE project stands, the best evidence for the evolutionary paradigm unravels.

Our understanding of genomes is in its infancy. Forced by their commitment to the evolutionary paradigm, many biologists see genomes as the cobbled-together product of an unguided evolutionary history. But as this recent study attests, the more we learn about the structure and function of genomes, the more elegant and sophisticated they appear to be. And the more reasons we have to believe that genomes are the handiwork of our Creator.

Resources

Endnotes

  1. John S. Mattick and Marcel E. Dinger, “The Extent of Functionality in the Human Genome,” The HUGO Journal 7 (July 2013): doi:10.1186/1877-6566-7-2.
  2. Long Qian and Edo Kussell, “Genome-Wide Motif Statistics Are Shaped by DNA Binding Proteins over Evolutionary Time Scales,” Physical Review X 6 (October–December 2016): id. 041009, doi:10.1103/PhysRevX.6.041009.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/03/15/protein-binding-sites-encoded-into-the-design-of-the-human-genome

Hagfish Slime Expands the Case for a Creator

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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

Earwax Discovery Gives New Hearing to the Case for Intelligent Design

earwaxdiscoverygivesnew

BY FAZALE RANA – FEBRUARY 22, 2017

If you are like most people, you probably haven’t devoted much thought to earwax, unless it relates to the safest way to clean it out of your ears.

But earwax is worth thinking about, because it is a remarkable substance with extraordinary properties, as recent work by engineers from Georgia Institute of Technology (GIT) attests.1 In fact, the GIT researchers think that they can use their new insight about earwax to develop specialized filters for electronic devices that must perform in dusty environments.

By using earwax as an inspiration for new technology, these researchers have unwittingly provided more evidence for intelligent design, while at the same time raising a powerful challenge to the evolutionary explanation for the history and the design of life.

What Is Earwax?

This substance is an eclectic mixture of fatty acids, fatty alcohols, cholesterol, and squalene formed from secretions of the sebaceous and the ceruminous glands that line the outer portion of the ear canal. Earwax also consists of shed epithelial cells and hair.

Earwax is produced by all mammals, including humans. Two different types of earwax are found in humans, referred to as wet and dry. Honey brown in color, wet earwax contains a higher concentration of lipids and pigments than dry earwax. A single genetic change converts wet earwax (which is the genetically dominant form) into dry earwax (the genetically recessive form), which is gray and flaky.

The type of earwax a person has reflects their ancestry, with people of African and European descent having the wet variety and Asian and Native American people groups having dry earwax. Anthropologists have noted a correlation between earwax type and body odor. People with wet earwax tend to be more odiferous than people with dry earwax. Anthropologists think this correlation reflects sweat production levels, with people with wet earwax sweating more profusely than people with dry earwax. Presumably, the mutation which alters the color and consistency of the earwax also impacts sweat production. Anthropologists think that reduced sweating may have offered an advantage to Asian peoples and Native Americans, and consequently, dry earwax became fixed within these populations.

What Is the Function of Earwax?

Earwax serves several functions. One is protecting the inner ear from water, dust particles, and microorganisms. Even though earwax is a solid substance, it allows air to flow through it to the inner ear. Yet, the high fat content of earwax makes it an ideal water repellent, keeping water away from the inner ear. The hair fibers in earwax serve a useful function, forming a meshwork that traps dust particles. And the acidic pH of earwax and the lysosomes from the cellular debris associated with it impart this waxy secretion with antibacterial and antifungal properties.

The fatty materials associated with earwax also help lubricate the skin of the inner ear canal as the earwax moves toward the outer ear. Earwax motion occurs via a conveyor action set up, in part, by the migration of epithelial cells toward the outer ear. These migrating cells, which move at about the same rate as fingernails grow, carry the earwax along with them. Jaw motion also helps with the earwax movement.

By comparing earwax from several animals and by video recording earwax in human ear canals, the GIT researchers discovered that earwax has special properties that make it a non-Newtonian fluid. It is solid at rest, but flows when under pressure. Apparently, the pressure exerted on the earwax from jaw movements helps it to flow toward the outer ear. This movement serves as a cleaning mechanism, carrying the debris picked up by the earwax toward the outer ear. Interestingly, the particles picked up by the earwax alter its consistency, from a waxy material, to a flaky solid that readily crumbles, making it easier to clear the outer ear, while making room for newer, cleaner earwax.

New Technology Inspired by Earwax

The GIT engineers recognized that, based on its physical properties, earwax could serve as an inspiration for the design of new types of filters that could protect electronics from water and dusty environments. With a bit of imagination, it is possible to conceive of ways to take advantage of shear-thinning behavior to design filters that could be readily replaced with cleaner ones, once they have trapped their limit of dust particles.

Biomimetics, Bioinspiration, and the Case for Intelligent Design

It has become rather commonplace for engineers to employ insights from biology to solve engineering problems and to inspire the invention of new technologies. This activity falls under the domain of two relatively new and exciting areas of engineering known as biomimetics and bioinspiration. As the names imply, biomimetics involves direct copying (or mimicry) of designs from biology, whereas bioinspiration relies on insights from biology to guide the engineering enterprise.

From my perspective, the use of biological designs to guide engineering efforts seems fundamentally at odds with evolutionary theory. Generally, 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, in essence.

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? Is it in alignment with evolutionary beliefs to build an entire subdiscipline of engineering upon mimicking biological designs? I would argue that these engineering subdisciplines do not fit with the evolutionary paradigm. On the other hand, biomimetics and bioinspiration naturally flow out of a creation model approach to biology. Using designs in nature to inspire engineering only makes sense if these designs arose from an intelligent Mind.

Resources

Engineers’ Muse: The Design of Biochemical Systems” by Fazale Rana (article)
Beetles Inspire an Engineering Breakthrough” by Fazale Rana (article)

Endnotes

  1. Society for Integrative and Comparative Biology, “The Technological Potential of Earwax,” Science News(blog), ScienceDaily, January 6, 2017, www.sciencedaily.com/releases/2017/01/17016092506.htm.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/02/22/earwax-discovery-gives-new-hearing-to-the-case-for-intelligent-design

Recent Insights into Morning Sickness Bring Up New Evidence for Design

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BY FAZALE RANA – FEBRUARY 15, 2017

“A woman giving birth to a child has pain because her time has come; but when her baby is born she forgets the anguish because of her joy that a child is born into the world.”
–John 16:21
There is no end to a mother’s love. Most willingly sacrifice and even suffer for their children’s sake. And for many women, this suffering starts in the early days of their pregnancies.

Somewhere between 50% to 70% of women experience morning sickness—nausea, vomiting, and disgust toward certain foods—beginning near the onset of their pregnancies, and continuing for 2 to 3 months into the second trimester.

Interestingly, no other mammal experiences morning sickness. It is a uniquely human trait. This has prompted anthropologists and biomedical scientists to ask, why does morning sickness only occur in humans?

What Causes Morning Sickness?

As Christians, it might be tempting to view morning sickness as part of the curse—the increased pain in childbirth—described in Genesis 3:16–17.

Many anthropologists think that it is an epiphenomenon—a nonfunctional byproduct of humanity’s evolutionary origin. These scientists argue that morning sickness results from the genetic incompatibility between the mother and fetus that leads to a conflict for resources, causing the mother to become ill.

But, in recent years, scientists have identified another explanation for morning sickness, dubbed the prophylaxis hypothesis. They view nausea, vomiting, and disgust toward certain foods as a protective mechanism that keeps both mother and fetus healthy during the initial critical phase of embryonic development.

Recent work provides new support for this hypothesis,1 and, along with it, gives added insight to the biblical idea that as human beings we are fearfully and wonderfully made (Psalm 139:14). Support for the prophylaxis hypothesis also has pro-life implications.

What Is the Purpose of Morning Sickness?

The prophylaxis hypothesis gains support from several observations. First, there are correlations between morning sickness and both reduced incidences of miscarriages and elevated birth weights.

As it turns out, only certain foods trigger nausea and vomiting and serve as the objects of disgust during the first trimester of pregnancy: namely, meats, poultry, eggs, strongly flavored vegetables, and some fruit. These foods are the most likely to harbor pathogens and dietary toxins that can interfere with embryological development (teratogens). Along these lines, it is interesting that the incidence of morning sickness varies from culture to culture, most likely because of dietary differences.

The timing of morning sickness also supports the prophylaxis hypothesis. During the first trimester, the mother’s immune system is suppressed. The genetic differences between mother and fetus makes this suppression necessary. Because the fetus is only 50% genetically identical to the mother, her body treats the fetus as foreign and would otherwise attack it, if it wasn’t for the suppression of her immune system.

Immunosuppression is maximal during the first trimester, leaving both the mother and fetus vulnerable to infection. By the second trimester, the mother’s immunosuppression becomes localized to the interface between the mother and fetus. It is during this time that the developing child’s immune system begins to form. The fetus also enjoys protection from the mother’s antibodies that are transferred to the fetus via the placenta.

The first trimester is also critical because this is when organ development begins in the fetus. At this juncture in development, the fetus is highly vulnerable to infectious agents and reproductive toxins found in fruits and vegetables.

There is also another role that morning sickness and disgust toward certain foods play in the early stages of pregnancy: calorie restriction for the mother. It is counterintuitive, but limiting the caloric intake benefits the pregnancy by inhibiting tissue synthesis in the mother. When calories are few, anabolic pathways shut down. This allows nutrients to be devoted to placental formation.

Why Does Morning Sickness Only Occur in Humans?

Researchers think that morning sickness in humans stems from our wide-ranging diet. Most mammals have highly specialized diets. Because of this, their immune systems can readily target the pathogens most likely to be found in the foods they eat. They can also make use of specialized enzymes to detoxify the teratogens most likely to be found in the foods they eat. This type of specialized protection isn’t feasible in humans, in fact, it might not even be possible at all, because our diets are so wide-ranging—varying from region to region around the world. Unlike most mammal species, humans literally occupy every corner of the planet. And this capability requires us to eat all sorts of foods. Given our highly varied diet, the most efficient and effective way to protect the mother and fetus during the first trimester of pregnancy is through nausea, vomiting, and disgust toward potentially harmful foods—unpleasant as these experiences might be.

Morning Sickness as Evidence for the Christian Faith

Though some biologists have argued that morning sickness is an epiphenomenon that emerged as the byproduct of human evolution, the data indicates otherwise. Morning sickness and disgust toward certain foods plays a critical function in an healthy pregnancy by protecting both the mother and the developing child. As a Christian, I see morning sickness as one more elegantly designed facet of human pregnancy.

I also see it as affirming key passages of Scripture. Instead of seeing morning sickness as support for Genesis 3:16–17, I view it as deepening the meaning of passages in Psalm 139describing each of us as being fearfully and wonderfully made. This latest insight about the benefit of morning sickness also expands my perspective of the idea from Psalm 139 that God has knit each of us together in our mother’s womb.

I also see this insight relating to the command God gave us in Genesis 1 to multiply and fill the earth. To do so would require that we would be able to thrive in a wide range of habitats, demanding that we are capable of consuming a highly varied diet. And of course, this is where morning sickness plays a vital role. For humans to increase in number, while we fill the world, requires a prophylactic mechanism (such as morning sickness) to ensure healthy pregnancies.

On a side note: The prophylaxis hypothesis also points to human exceptionalism. In contrast to our the highly varied diets, Neanderthals consumed a much more limited range of food. In fact, these differences in dietary practices likely reflect differences in the cognitive capacities of modern humans and Neanderthals. It is no accident that Neanderthals had a limited biogeographical distribution, confined to Europe, Western Asia, and the Middle East. In fact, Neanderthals’ limited diet may well have contributed to their extinction.

Pro-Life Implications

This work also has implications for the pro-life debate. I have often heard pro-choice advocates argue that abortion is not murder because the fetus is like a tumor. However, the latest insights into morning sickness undermine this position. This argument would gain validity if morning sickness was, indeed, an epiphenomenon, resulting from a tug-of-war between mother and fetus. But the data says otherwise. Even though the fetus is genetically distinct from the mother, the mother’s body is designed to do everything it can to protect the fetus, including develop morning sickness and disgust toward potentially harmful foods.

Though this latest understanding about morning sickness may make evolutionary biologists and pro-choice advocates sick, it spews forth new evidence for design. (Sorry, I couldn’t resist.)

Resources

What Are the Odds of You Being You?” by Matthew McClure (article)
Placenta Optimization Shows Creator’s Handiwork” by Fazale Rana (article)
Curvaceous Anatomy of Female Spine Reveals Ingenious Obstetric Design” by Virgil Robertson (article)
Does the Childbirth Process Represent Clumsy Evolution or Good Engineering?” by Fazale Rana (article)
The Female Brain: Pregnant with Design” by Fazale Rana (article)
Dietary Differences Separate Humans from Neanderthals” by Fazale Rana (article)

Endnotes

  1. Rachel R. Huxley, “Nausea and Vomiting in Early Pregnancy: Its Role in Placental Development,” Obstetrics and Gynecology 95 (May 2000): 779–82, doi:10.1016/S0029-7844(99)00662-6; Daniel M. T. Fessler, Serena J. Eng, and C. David Navarrete, “Elevated Disgust Sensitivity in the First Trimester of Pregnancy: Evidence Supporting the Compensatory Prophylaxis Hypothesis,” Evolution and Human Behavior 26 (July 2005): 344–51, doi:10.1016/j.evolhumbehav.2004.12.001; Samuel M. Flaxman and Paul W. Sherman, “Morning Sickness: Adaptive Cause or Nonadaptive Consequence of Embryo Viability?” The American Naturalist 172 (July 2008): 54–62, doi:10.1086/588081.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/02/15/recent-insights-into-morning-sickness-bring-up-new-evidence-for-design

The Female Brain: Pregnant with Design

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BY FAZALE RANA – JANUARY 25, 2017

When Jesus saw his mother there, and the disciple whom he loved standing nearby, he said to her, “Woman, here is your son.”

–John 19:26

I’ve learned the hard way: It is best to be circumspect when offering commentary about pregnancy, especially when women are around.

So, it’s with some hesitation I bring up the latest scientific insight developed by a team of researchers from Spain. These investigators discovered that pregnancy alters a woman’s brain. In fact, pregnancy reduces her grey matter.1 (Okay Fuz. Hold your tongue. Don’t say what you’re thinking.)

But, as it turns out, the loss of grey matter is a good thing. In fact, it reveals the elegant design of the human brain and adds to the growing evidence of human exceptionalism. This scientific advance also has implications for the pro-life movement.

The Spanish research team was motivated to study brain changes in pregnant women because of the effects that sex hormones have on adolescent brains. During this time, sex hormones cause extensive reorganization of the brain. This process is a necessary part of the neural maturation process. The researchers posited that changes to the female brain should take place, because of the surge of sex hormones during pregnancy. While pregnant, women are exposed to 10 to 15 times the “normal” progesterone levels. During nine months of pregnancy, women are also subjected to more estrogen than the rest of their life when not pregnant.

To characterize the effect of pregnancy on brain structure, the research team employed a prospective study design. They imaged the brains of women who wanted to become pregnant for the first time. Then, they imaged the brains of the subjects once the women had given birth. Finally, they imaged the brains of the subjects two years after birth, if they didn’t become pregnant again. As controls, they imaged the brains of women who had never been pregnant and the brains of the fathers.

The Effects of Pregnancy on Women’s Brains

While the brain’s white matter is unaffected, the researchers found that pregnancy leads to a loss of grey matter that, minimally, lasts up to two years. They also discovered that the grey matter loss was not random or arbitrary. Instead, it occurred in highly specific areas of the brain. In fact, the grey matter loss was so consistent from subject to subject that the researchers could tell if a woman was pregnant or not from brain images alone.

As it turns out, the area of the brain that loses grey matter is the region involved in social cognition that harbors the theory-of-mind neural network. This network allows human beings to display a quality anthropologists call theory of mind. Along with symbolism, our theory-of-mind capacity makes us unique compared to other animals, providing scientific justification for the idea of human exceptionalism. As human beings, we recognize that other humans possess a mind like ours. Because of that recognition, we can anticipate what others are thinking and feeling. Our theory-of-mind capability makes possible complex social interactions characteristic of our species.

Even though the pregnant women lost grey matter, they showed no loss of memory or cognitive ability. The researchers believe that the loss of grey matter stems from synaptic pruning. This process occurs in adolescents and is a vital part of brain development and maturation. Through the loss of grey matter, neural networks form. The research team posits that synaptic pruning in pregnant women establishes a neural network that plays a role in the deep attachment mothers have with their children. This attachment helps mothers anticipate their babies’ needs. The deep social connection between mother and child is critical for human survival, because human infants are so vulnerable at birth and have a prolonged childhood.

In support of this proposal, the researchers found that when they showed the pregnant women pictures of their babies, the brain areas that lost grey matter became active. On the other hand, they saw no corresponding brain activity when the mothers were shown pictures of other babies.

The Case for Human Exceptionalism Mounts

This work highlights the elegant design of human pregnancy and child rearing—features that I take as evidence for a Creator’s handiwork. It is nothing short of brilliant to have the surge of sex hormones during pregnancy, priming the brain to ensure a close attachment between mother and child, at the time of birth and throughout the first few years of childhood.

More importantly, this work adds to the mounting scientific evidence for human exceptionalism. Not only do humans uniquely possess theory of mind, but our theory-of-mind neural network is more complex and sophisticated than previously thought. It is remarkable that this neural network can be adapted and fine-tuned to ensure an intimate mother-infant attachment while maintaining relationships in the midst of complex social surroundings, typical of human interactions.

As an interesting side note: Recent research indicates that for Neanderthals, the area of their brain devoted to maintaining social interactions was much smaller than the corresponding area in modern humans, highlighting our unique and exceptional nature even when compared to the hominids found in the fossil record.2

Pro-Life Implications

In my view, this work also has pro-life implications. I frequently hear pro-choice advocates argue that the fetus is a mass of tissue, just like a tumor. But, this study undermines this view. It is hard to think of a fetus as being just a lump of tissue, when such a sophisticated system is in place during pregnancy to form a neural network (that is, a subset of the theory-of-mind network) in the mother’s brain that generates the special capacity of the mother to bond with the fetus at birth.

It also raises concerns for the health of women who receive abortions. Though speculative, one has to wonder what effect prematurely terminating a pregnancy has on women whose brains have become fine-tuned to bond to the very infants that are destroyed by the abortion.

Resources

Placenta Optimization Shows Creator’s Handiwork” by Fazale Rana (article)
Curvaceous Anatomy of the Female Spine Reveals Ingenious Obstetric Design” by Virgil Robertson (article)
Does the Childbirth Process Represent Clumsy Evolution or Good Engineering?” by Fazale Rana (article)
Neanderthal Brains Make Them Unlikely Social Networkers” by Fazale Rana (article)

Endnotes

  1. Elseline Hoekzema et al., “Pregnancy Leads to Long-Lasting Changes in Human Brain Structure,” Nature Neuroscience, published electronically December 19, 2016, doi:10.1038/nn.4458.
  2. Eiluned Pearce, Chris Stringer, and R. I. M. Dunbar, “New Insights into Differences in Brain Organization between Neanderthals and Anatomically Modern Humans,” Proceedings of the Royal Society B 280 (May 2013): doi:10.1098/rspb.2013.0168.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/01/25/the-female-brain-pregnant-with-design

Reactive Oxygen Species: Harbingers of Evolution or Signals of Design?

reactiveoxygenspeciesharbingers

BY FAZALE RANA – DECEMBER 14, 2016

“Few concepts have been embraced by popular science as enthusiastically as the idea that reactive oxygen species (ROS) are harmful and that their levels should be controlled by including antioxidants in the diet or as supplements.”1

–Ulrich Theopold

Antioxidants are the latest diet fad. Many people do whatever they can to include foods high in antioxidants in their diets. Some people even go a step further by taking antioxidant supplements. All these actions are meant to combat the harmful effects of reactive oxygen species (ROS). Produced in the mitochondria, these highly reactive chemical derivatives of molecular oxygen will destroy cellular components if left unchecked.

Yet things aren’t always what they seem. An increasing number of studies indicate that taking dietary supplements of antioxidants has questionable health benefits.2 In fact, taking certain antioxidant supplements may be harmful. For example, studies indicate that people who supplement their diets with vitamin E and beta-carotene have higher mortality rates compared to people who don’t take antioxidant supplements at all. Other studies demonstrate that instead of slowing cancer’s spread, antioxidants, in fact, accelerate the progression of certain cancers. Antioxidant consumption also impacts development, harming certain types of stem cells.

When it comes to antioxidants and ROS, the scientific community has made another surprising about-face. Biochemists no longer view ROS as harmful compounds, wreaking havoc on the cell’s components. Instead, they have learned that ROS play a key role in cell-signaling processes. As it turns out, consumption of excessive antioxidants interferes with ROS-based signaling pathways. And this interference explains why consuming inordinate levels of antioxidants aren’t part of a healthy lifestyle.

The surprising implications of this new insight regarding antioxidants and ROS extend beyond dietary considerations. This new understanding has bearing on the creation vs. evolution debate by providing a response to a common objection skeptics level against intelligent design arguments.

ROS Generation and the Case for Evolution

ROS are primarily produced in the mitochondria by the electron transport chain (ETC). The ETC harvests energy needed to carry out the various biochemical operations that take place within the cell. For the most part, the ETC is comprised of a series of protein complexes, conceptually organized into a linear array. The first complex of the ETC receives chemically energetic electrons (ultimately, derived from the breakdown of biochemical fuels) and passes them along to the next complex in the ETC. Eventually, these electrons are handed off from complex to complex, until they reach the terminal part of the ETC. When shuttled from one complex to the other, the electrons give up some of their energy. This released energy is captured, and ultimately used to produce compounds such as ATP, which serve as energy currency inside the cell.

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Image: Illustration of electron transport chain with oxidative phosphorylation.

One of the final steps carried out by the ETC is the conversion of molecular oxygen into water, with oxygen receiving the de-energized electrons. If the energy status of the cell is high, the movement of electrons through the ETC slows down, and, under some circumstances, becomes backed up. When this jam occurs, the electrons prematurely react with oxygen because they must go somewhere. (This usually happens between complex I and complex III). When this premature termination takes place, ROS (which include the superoxide ion, the hydroxyl free radical, and hydrogen peroxide) form instead of water.

At face value, it appears as if ROS form as an unintended side reaction. Traditionally, biochemists regard ROS as deadly compounds that oxidize membrane components, DNA, and proteins, causing untold damage to the cell.

For many skeptics, the apparently random, unwanted generation of ROS which terrorize the cell undermines the case for intelligent design and serves as evidence for an evolutionary origin of biochemical systems. Why? Because the seemingly unintended production of chemically destructive ROS has all the markings of a flawed system—the type of system unguided evolutionary processes would produce, not the type of design befitting a Creator.

The Cellular Roles of ROS

Yet in recent years, biochemists have come to see ROS differently. Instead of the product of an unwanted side reaction, biochemists have come to discover that these compounds serve as second messengers, communicating the cell’s energy status to key metabolic processes, including those that regulate stem cell development.3 These mechanisms allow the cell to coordinate various metabolic processes for the available bioenergetics sources.

Because hydrogen peroxide has the chemical stability and capacity to dissolve through membranes, biochemists believe that it functions as the primary second messenger. Still, the other ROS do play a role in cell signaling.

ROS can serve as second messengers because they preferentially oxidize certain amino acids in proteins, with cysteine residues often targeted. The selective oxidation of amino acid residues modifies the activity of the protein targets. Targeted proteins include transcription factors (which control gene expression), and kinases and phosphatases (which regulate different stages of the cell cycle). These protein targets explain why ROS play a critical role in stem cell renewal, stem cell proliferation, and maturation.

Oxidative Damage by ROS Is a Trade-Off

ROS are ideal second messengers for communicating and coordinating the cell’s metabolic pathways with respect to the cell’s energy status, because their production is closely linked to the ETC. When the energy status of the cell is high, ROS production increases. And when the cell’s energy status dips, ROS production tails off. In my view, there is an exquisite molecular logic that undergirds the use of ROS as second messengers for communicating the cell’s energy balance.

Of course, the drawback to using ROS as second messengers is the oxidative damage these materials cause. But instead of viewing the damaging effects of these compounds as a flawed design, I maintain that it is better to think of it as a trade-off.

Towards that end, it is important to note that the cell has an extensive and elaborate system to buffer against the harmful effects of ROS. For example, superoxide dismutase converts superoxide into hydrogen peroxide. Two other enzymes, catalase and peroxiredoxin, transform hydrogen peroxide into water. In fact, one of the targets of ROS are transcription factors that trigger the production of proteins that are part of the cell’s antioxidant defenses and proteins that take part in pathways that clear damaged proteins from the cell. This ingenious design ensures that once ROS form and play a role as second messengers, the damaged proteins are quickly destroyed and any destruction they cause is mitigated.

It is truly remarkable how dramatically the scientific community’s views on ROS (and antioxidants) have changed in recent years. Instead of being the unwanted byproducts of metabolism that plagued the cell, ROS serve as a biochemical fuel gage, triggering processes such as quiescence and even autophagy (programmed cell death) when the energy balance is too low and the cell is experiencing starvation and cell differentiation (which impacts stem cell biology) when energy stores are sufficiently full.

Often, skeptics point to so-called bad designs as evidence for an evolutionary history for life. But, the changed perspective of ROS serves as a cautionary tale. Many times, what is perceived as a bad design turns out to be anything but as we learn more about the system, and these discoveries undermine the best arguments for evolution while adding to the mounting case for intelligent design.

Resources

The Cell’s Design by Fazale Rana (book)
30% Inefficiency by Design” by Fazale Rana (article)
The Human Appendix: What Is It Good For?” by Fazale Rana (article)
New Research Highlights Elegant Design in the Inverted Retina” by Fazale Rana (article)
Wisdom Teeth Reflect the Creator’s Foresight” by Fazale Rana (article)
Is the Whale Pelvis a Vestige of Evolution?” by Fazale Rana (article)

Endnotes

  1. Ulrich Theopold, “Developmental Biology: A Bad Boy Comes Good,” Nature 461 (September 2009): 486–87, doi:10.1038/461486a.
  2. Center for the Advancement of Health, “Antioxidant Users Don’t Live Longer, Analysis of Studies Concludes,” Science News (blog), ScienceDaily, April 16, 2008, https://www.sciencedaily.com/releases/2008/04/080415194233.htm; University of Gothenburg, “Antioxidants Cause Malignant Melanoma to Metastasize Faster,” Science News (blog), ScienceDaily, October 8, 2015, https://www.sciencedaily.com/releases/2015/10/151008131112.htm; Ed Yong, “Antioxidants Speed Up Lung Cancer,” Daily News (blog), The Scientist, January 29, 2014, https://www.the-scientist.com/?articles.view/articleNo/39022/title/Antioxidants-Speed-Up-Lung-Cancer/; University of Helsinki, “Large Doses of Antioxidants May Be Harmful to Neuronal Stem Cells,” Science News (blog), ScienceDaily, June 11, 2015, https://www.sciencedaily.com/releases/2015/06/150611091340.htm.
  3. Kira Holmström and Toren Finkel, “Cellular Mechanisms and Physiological Consequences of Redox-Dependent Signalling,” Nature Reviews Molecular Cell Biology 15 (June 2014): 411–21, doi:10.1038/nrm3801; Carolina Bigarella, Raymond Liang, and Saghi Ghaffari, “Stem Cells and the Impact of ROS Signaling,” Development 141 (November 2014): 4206–18, doi:10.1242/dev.107086.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/12/14/reactive-oxygen-species-harbingers-of-evolution-or-signals-of-design

DNA: Designed for Flexibility

dnadesignedforflexibility

BY FAZALE RANA – AUGUST 17, 2016

Over the years I’ve learned that flexibility is key to a happy and successful life. If you are too rigid, it can create problems for you and others and rob you of joy.

Recently, a team of collaborators from Duke University and several universities in the US discovered that DNA displays unexpected structural flexibility. As it turns out, this property appears to be key to life.1 In contrast, the researchers showed that RNA (DNA’s biochemical cousin) is extremely rigid, highlighting another one of DNA’s unique structural properties that make it ideal as the cell’s information storage system.

To appreciate DNA’s uniquely optimal properties, a review of this important biomolecule’s structure is in order.

DNA

DNA consists of two chain-like molecules (polynucleotides) that twist around each other to form the DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different sub-unit molecules called nucleotides. DNA is built from the nucleotides: adenosine, guanosine, cytidine, and thymine, famously abbreviated A, G, C, and T, respectively.

In turn, the nucleotide molecules that make up the strands of DNA are complex molecules, consisting of both a phosphate moiety, and a nucleobase (either adenine, guanine, cytosine, or thymine) joined to a 5-carbon sugar (deoxyribose). (In RNA, the five-carbon sugar ribose replaces deoxyribose.)

dna-designed-for-flexibility-1Image 1: Nucleotide Structure

The backbone of the DNA strand is formed when the cell’s machinery repeatedly links the phosphate group of one nucleotide to the deoxyribose unit of another nucleotide. The nucleobases extend as side chains from the backbone of the DNA molecule and serve as interaction points (like ladder rungs) when the two DNA strands align and twist to form the double helix.

dna-designed-for-flexibility-2Image 2: The DNA Backbone

When the two 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.

When the side chains pair, they form cross bridges between the two DNA strands. The length of the A-T and G–C cross bridges is nearly identical. Adenine and guanine are both composed of two rings and thymine (uracil) and cytosine are composed of one ring. Each cross bridge consists of three rings.

When A pairs with T, two hydrogen bonds mediate the interaction between these two nucleobases. Three hydrogen bonds accommodate the interaction between G and C. The specificity of the hydrogen bonding interactions accounts for the A-T and G-C base-pairing rules.

dna-designed-for-flexibility-3

Image 3: Watson-Crick Base Pairs

Watson-Crick and Hoogsteen Base Pairing

In DNA (and in RNA double helixes), the base pairing interactions occur at precise locations between the A and T nucleobases and the G and C nucleobases, respectively. Biochemists refer to these exacting interactions as Watson-Crick base pairing. However, in 1959—six years after Francis Crick and James Watson published their structure for DNA—a biochemist named Karst Hoogsteen discovered another way—albeit, rare—that the A and T nucleobases and the G and C nucleobases pair, called Hoogsteen base pairing.

Hoogsteen base pairing results when the nucleobase attached to the sugar rotates by 180°. Because of the dynamics of the DNA molecule, this nucleobase rotation occurs occasionally, converting a Watson-Crick base pair into a Hoogsteen base pair. However, the same dynamics will eventually revert the Hoogsteen base pair to a Watson-Crick pairing. Hoogsteen base pairs aren’t preferred because they cause a distortion in the DNA double helix. For a “naked” piece of DNA in a test tube, at any point in time, about 1 percent of the base pairs are of the Hoogsteen variety.

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Image 4: Watson-Crick and Hoogsteen Base Pairs
Image Credit: Wikimedia Commons

While rare in naked DNA, biochemists have recently discovered that the Hoogsteen configuration occurs frequently when: 1) proteins bind to DNA; 2) DNA is methylated; and 3) DNA is damaged. Biochemists now think that Hoogsteen base pairing is important to maintain the stability of the DNA double helix, ensuring the integrity of the information stored in the DNA molecule.

According to Hashim Al-Hashimi, “There is an amazing complexity built into these simple beautiful structures, whole new layers or dimensions that we have been blinded to because we didn’t have the tools to see them, until now.”2

It looks like the capacity to form Hoogsteen base pairs is a unique property of DNA. Al-Hashimi and his team failed to detect any evidence for Hoogsteen base pairs in double helixes made up of two strands of RNA. When they chemically attached a methyl group to the nucleobases of RNA to block the formation of Watson-Crick base pairs and force Hoogsteen base pairing, they discovered that the RNA double helix fell apart. Unlike the DNA double—which is flexible—the RNA double helix is rigid and cannot tolerate a distortion to its structure. Instead, the RNA strands can only dissociate.

It turns out that the flexibility of DNA and the rigidity of RNA is explained by the absence of a hydroxyl group in the 2’ position of the deoxyribose sugar of DNA and the presence of the 2’ hydroxyl group on ribose sugar of RNA, respectively. The 2’ position is the only structural difference between the two sugars. The presence or absence of the 2’ hydroxyl group makes all the difference. The deoxyribose ring can more freely adopt alternate conformations (called puckering) than the ribose ring, leading to differences in double helix flexibility.

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Image 5: Difference between Deoxyribose and Ribose

This difference makes DNA ideally suited as an information storage molecule. Because of its ability to form Hoogsteen base pairs, the DNA double helix remains intact, even when the molecule becomes chemically damaged. It also makes it possible for the cell’s machinery to control the expression of the genetic information harbored in DNA through protein binding and DNA methylation.

It is intriguing that DNA’s closet biochemical analogue lacks this property.

It appears that DNA has been optimized for data storage and retrieval. This property is critical for DNA’s capacity to store genetic information. DNA harbors the information needed for the cell’s machinery to make proteins. It also houses the genetic information passed on to subsequent generations. If DNA isn’t stable, then the information it harbors will become distorted or lost. This will have disastrous consequences for the cell’s day-to-day operations and make long-term survival of life impossible.

As I discuss in The Cell’s Design, flexibility is not the only feature of DNA that has been optimized. Other chemical and biochemical features appear to be carefully chosen to ensure its stability; again, a necessary property for a molecule that harbors the genetic information.

Optimized biochemical systems comprise evidence for biochemical intelligent design. Optimization of an engineered system doesn’t just happen—it results from engineers carefully developing their designs. It requires forethought, planning, and careful attention to detail. In the same way, the optimized features of DNA logically point to the work of a Divine engineer.

Resources
DNA Soaks Up Sun’s Rays” by Fazale Rana (Article)
The Cell’s Design by Fazale Rana (Book)
The Cell’s Design: The Proper Arrangement of Elements” by Fazale Rana (Podcast)

Endnotes

  1. Huiqing Zhou et al., “m1A and m1G Disrupt A-RNA Structure through the Intrinsic Instability of Hoogsteen Base Pairs,” Nature Structure and Molecular Biology, published electronically August 1, 2016, doi:10.1038/nsmb.3270.
  2. Duke University, “DNA’s Dynamic Nature Makes It Well-Suited to Serve as the Blueprint of Life,” Science News (blog), ScienceDaily, August 1, 2016, www.sciencedaily.com/releases/2016/08/160801113823.htm.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/08/17/dna-designed-for-flexibility