Q&A: Why Would an Infinite Creator Employ the Same Designs?

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BY FAZALE RANA – DECEMBER 21, 2016

Because I am a Christian, I see evidence for design in the biological realm. But for me, the converse is also true. Because I see design in the biological realm, I am a Christian. In fact, the elegant designs of biochemical systems convinced me as a graduate student that a Creator must exist and be responsible for life’s origin, paving the way for my conversion to Christianity.

Yet, many skeptics see the features of biological systems very differently than I do. They maintain that life’s origin, design, and diversity are best explained as the outworking of evolutionary processes. As evidence for this view, biologists point to the shared biological and biochemical features (homologies) possessed by organisms that naturally group or cluster together.

Homologous features may perform different functions and superficially appear different, yet they are fundamentally built around the same design. The quintessential example of a biological homology is the vertebrate forelimb—the human hand, the whale’s flipper, a dog’s paw, a bird’s wing, etc. Though these forelimbs are structurally distinct and perform different biological tasks, they are fundamentally built around the same design. The forelimb of every vertebrate consists of a long bone (humerus) in the arm, an elbow, two bones in the forearm (the radius and ulna), wrist bones (carpals), bones in the “hand” (metacarpals), and “fingers” (phalanges).

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Image: Homologous structures of the vertebrate forelimb. Image Credit: Wikipedia

Evolutionary biologists interpret homologous structures as evolutionarily derived from ancestral features possessed by the common ancestor of the group. With respect to the vertebrate forelimbs, biologists maintain that the forelimb of the first tetrapods had the same design as all vertebrate forelimbs. However, through the course of evolutionary history, natural selection altered the vertebrate forelimbs to perform a variety of functional roles.

However, as a creationist and a design proponent, I maintain that homologous structures have been designed around an archetypical plan that existed in the Creator’s mind. To put it another way, homologous structures reflect common design, not the outworking of common descent.

My view on shared biological features led my Facebook friend Phil, a skeptic, to ask the following questions:

“Just think about the diverse range of creatures an actual creator could have made. And yet we see creatures appearing like and acting like family cousins instead. What would compel an actual designer with unlimited power to design all creatures with the same template, as if the design was a restriction on the designer? Perhaps it was to make belief more difficult, to make only rebellious (non-credulous) hearts disbelieve?”

Interesting questions, to be certain. This question gets to the core reason why evolutionary biologists reject the arguments for intelligent design. For these many biologists, homologous structures only make sense from within an evolutionary framework.

The View of Biological Homologies before Darwin

Part of the response to my friend Phil’s question can be found in the theoretical work of Sir Richard Owen, a prominent biologist from the UK who predated Darwin. One of the world’s most important anatomists in his day, Owen played a key role in discovering, describing, and interpreting biological homologies. Owen understood homologies from a design perspective. Specifically, Owen saw these mutual features as manifestations of a common blueprint that existed in the Creator’s mind, and, in turn, were physically manifested in the created order.

Archetypes and God’s Creativity

Instead of seeing the concept of the archetype as restricting God’s creativity, Owen regarded the archetype as reflecting teleology of the highest order. In his presentation to the Royal Institution of Great Britain, Owen lectured: “The satisfaction felt by the rightly constituted mind must ever be great in recognizing the fitness of parts for their appropriate functions; but when this fitness is gained as in the great toe of the foot of man or the ostrich, by a structure which at the same time betokens harmonious concord with a common type, the prescient operations of the One Cause of all organization becomes strikingly manifested to our limited intelligence.”1

In other words, Owen marveled at the way the Creator generated so much functional diversity from a single template—for example, the pentadactyl architecture of the vertebrate forelimb.

In fact, the diversity of life on Earth today—even throughout life’s history—built from 30 or so body plans (corresponding to the known animal phyla) is nothing short of mind-boggling. So, apparently creating life on Earth around design templates has done little to limit the Creator. In fact, I would argue—as Owen did— it highlights God’s ingenuity.

Designed for Discovery

There are a few reasons why God would have created life’s diversity using a limited set of templates. But, perhaps the most important reason is discoverability.

The universal nature of biochemistry and the homologous and convergent biological systems allow scientists to generalize what they learn studying one organism to the entirety of the biological realm, in some instances. The universal and homologous designs in biology allow the scientific community to make use of organisms as model systems. For example: by studying DNA replication in bacteria, we have gained key insight that allows us to understand DNA replication in all life on the planet. Studying gene regulation in yeast helps us understand gene regulation in human beings. Studying the developmental pathways of the nematode C. elegans has yielded important knowledge that helps us understand growth and development in many multicellular organisms. Studying genetics in the fruit fly Drosophila has provided key understanding regarding inheritance.

If, as my friend Phil wants, the Creator used a near infinite array of biological designs when he created, it would be virtually impossible for us to know anything about the living realm. The process of discovery in biology would become cumbersome and laborious.

Because the living realm is intelligible, it is possible for human beings to take advantage of God’s provision for us, made available within the creation. As we study and develop an understanding of the living realm, we can deploy that knowledge to benefit humanity—in fact, all life on Earth—through agriculture, medicine, conservation efforts, and emerging biotechnologies.

Ultimately, I believe that God has designed the biological realm for discoverability because He wants us to see, understand, and appreciate his handiwork as a Creator, so through his creation we can know him.

“It is the glory of God to conceal a matter; to search out a matter is the glory of kings.”

Proverbs 25:2

Resources

Endnotes

  1. Richard Owen, On the Nature of Limbs: A Discourse, ed. Ron Amundson (Chicago: University of Chicago Press, 2007), 38.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/12/21/q-a-why-would-an-infinite-creator-employ-the-same-designs

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

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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

Science News Flash: An Old-Earth Perspective on Dinosaur Feathers Preserved in Amber

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BY FAZALE RANA – DECEMBER 9, 2016

Whenever we are in a foreign country, my wife loves to shop at local, out-of-the-way markets. She always finds some of the most interesting souvenirs.

It turns out the same is true for paleontologist Lida Xing who purchased several amber pieces from a market in Myitkyina in the country of Myanmar. The amber sold at the market comes from a nearby mine in the Hukawng Valley. While most buyers are looking for amber to make jewelry, Xing was looking for amber with inclusions of plant and animal remains. The amber from the mine dates to 99 million years. Because of the amber’s age, the well-preserved plant and animal remains entombed by this fossilized tree resin offer a unique glimpse at ancient life on Earth, providing details and insight that far exceed those available from highly compressed fossil remains that typically comprise the fossil record.

As fate would have it, one of the amber pieces Xing purchased contains a piece of a dinosaur tail (perhaps from a maniraptor) with attached feathers! This discovery is described in a paper that will appear in the December 19 issue of Current Biology.Yesterday the paper was published online ahead of the publication date and it has already generated headlines both in the popular news and on social media.

This is not the first time researchers have discovered feathers preserved in amber. But it isthe first time they have observed feathers associated with parts of a dinosaur, in this instance a section of the tail (near the middle or end) that includes eight vertebrae. The anatomical features clearly indicates that the preserved tail belongs to a large group of dinosaurs labeled the coelurosaurs.

It goes without saying that this find has already caused quite a bit of a stir because of its important implications for evolutionary and creation models for bird origins.

An Evolutionary Perspective of the Discovery

For many in the scientific community this discovery further affirms the evolutionary link between birds and dinosaurs, with feathered dinosaurs viewed as transitional intermediates. Along these lines, the researchers describe the dinosaur feathers preserved in amber as transitional, noting that the feather’s central shaft (rachis) is poorly defined. On this basis, the researchers argue that the rachis was a late-appearing feature in feathers, forming when the barbs of the feather fused together.

An Old-Earth Creationist Response

As an old-earth creationist, I’m skeptical about the evolutionary account that has birds evolving from theropods. In fact, this latest discovery only adds to my skepticism.

Paleontologists interpret feathered dinosaurs from the fossil record as transitional intermediates between theropods and birds—including the feathered dinosaur tail found in amber. Yet, each occurrence of feathered dinosaurs in the fossil record appear after the first true bird, Archaeopteryx.2 Based on the fossil record, this ancient bird appeared on Earth around 155 million years ago. Archaeopteryx’s feathers were identical to the feathers of modern birds. In fact, the same research team discovered bird feathers in 99-million-year-old amber from the same source that yielded the amber with the dinosaur feathers. The bird feathers, like those of Archaeopteryx, are identical to those found in modern birds.

It is hard to imagine how the “primitive” feathers associated with the dinosaur tail (again, dated at 99 million years in age) could be transitional if they appear over 50 million years after Archaeopteryx and co-occur with feathers from a bird belonging to enantiornithes.

This problem is not unique to the bird fossil record. There are several instances in which presumed transitional forms appear in the fossil record well after the first appearance of their “evolutionary descendants.” In fact, paleontologist have a name for this phenomenon: a temporal paradox.

For a more complete discussion of the problems I see with the proposed evolutionary link between birds and theropod dinosaurs, see “Birds in the Fossil Record” (listed in the resource section below).

A Young-Earth Creationist Perspective of the Discovery

One exciting aspect of this find is the possibility that soft-tissue remnants associated with the features may be preserved in the amber. The researchers discovered iron (in the ferrous form) associated with the carbonized feather remains. They speculate that this iron derives from hemoglobin originally found in the tail muscle tissue. On this basis, the research team speculates that soft-tissue remnants derived from keratin may be present in the amber-entombed specimen.

In recent years, young-earth creationists have made use of these types of finds to argue that it is impossible for such fossils to be millions of years old. They argue that soft tissues shouldn’t survive that long. These materials should readily degrade in a few thousand years. In their view, these finds challenge the reliability of radiometric dating methods used to determine the age of these fossils, and along with it, Earth’s antiquity. Instead, they argue that these breakthrough discoveries provide compelling scientific evidence for a young Earth and support the idea that the fossil record results from a recent global (worldwide) flood.

An Old-Earth Creationist Response

These types of claims prompted me to write Dinosaur Blood and the Age of the Earth. In this work (and elsewhere), I explain why the recovery of soft-tissue remnants associated with fossil finds is illegitimate evidence for a young Earth.

Given the structural robustness of keratin, and the preservative effect of ferrous iron, it is completely reasonable to think that keratin remnants associated with the feathers could survive long enough to be completely entombed by the amber and eventually persist for nearly 100 million years.

Though this find will be interpreted by the scientific community from an evolutionary vantage point and, more than likely, opted by young-earth creationists to challenge the antiquity of Earth and life on Earth, the dinosaur feathers entombed in amber can readily be accommodated from an old-earth creationist vantage point.

Resources

Creation vs. Evolution Controversy

Is There a Controversy about Evolution?” by Fazale Rana (article)
The Creation-Evolution Controversy in Jurassic World” by Fazale Rana (article)

Age-of-the-Earth Controversy

Dinosaur Blood and the Age of the Earth” by Fazale Rana (book).
Can Keratin in Feathers Survive for Millions of Years?” by Fazale Rana (article)

Endnotes

  1. Lida Xing et al., “A Feathered Dinosaur Tail with Primitive Plumage Trapped in Mid-Cretaceous Amber,” Current Biology 26 (December 19, 2016): 1–9, doi:10.1016/j.cub.2016.10.008.
  2. Some paleontologists claim that the temporal paradox for bird origins was solved based on the discovery of a feathered theropod that dates between 151 and 161 million years in age. (See Dongyu Hu et al., “A Pre-Archaeopteryx Troodontid Theropod from China with Long Feathers on the Metatarsus,” Nature 461 [October 1, 2009]: 640–43, doi:10.1038/nature08322.) However, at best, this find demonstrates the co-occurrence of feathered dinosaurs and the first true bird, when the error bars of the age-date measurements are taken into account.
  3. Lida Xing et al., “Mummified Precocial Bird Wings in Mid-Cretaceous Burmese Amber,” Nature Communications 7 (June 28, 2016): 12089, doi:10.1038/ncomms12089.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/12/09/science-news-flash-an-old-earth-perspective-on-dinosaur-feathers-preserved-in-amber

Pseudoenzymes Illustrate Science’s Philosophical Commitments

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BY FAZALE RANA – DECEMBER 7, 2016

A few months ago, I had a serious accident while shooting a compound bow in my backyard. The arrow jammed in the guide, and in my attempt to free the arrow, I caused the bow string to derail. When that happened, the string struck my left eye with such force that it fractured my orbit in five places and damaged my retina. I am now legally blind in my left eye. Thankfully, I still have some peripheral vision, but I lost all the central vision in my injured eye. (To mothers everywhere: Yes, I wasn’t careful and I shot my eye out. I should have listened.)

Because of my injury, there is a blacked-out area in the center part of my field of vision which prevents me from focusing with my left eye. Sometimes, if something is on my left side, I can’t see it—even if it is in plain view.

Science’s Blind Spot

Over the years I have come to appreciate that, very often, the creation/intelligent design vs. evolution controversy has less to do with the evidence on hand, and more with how each side sees the evidence. As a case in point, when examining the features of biochemical systems, most creationists and intelligent design proponents readily see evidence of a Creator’s handiwork. Yet adherents to the evolutionary paradigm don’t see evidence for design at all. Instead, they see flawed designs. Why? Because they view biochemical systems as the outworking of an unguided evolutionary history. According to this view, evolution’s mechanisms have cobbled together biochemical systems by co-opting and repurposing existing systems to generate novel biochemical functions. As such, evolution produces kludge-job designs. Not the elegant, sophisticated systems expected if life stems from a Creator’s handiwork.

In part, the differing perspectives are shaped by philosophical commitments and the expectations that flow from them. To expound upon this point: the philosophical framework for contemporary science is methodological naturalism. Accordingly, scientific explanations for the universe and phenomena within the universe (such as the characteristics of biochemical systems) must have a mechanistic accounting—an explanation exclusively rooted in natural processes. Any explanation that appeals to the work of supernatural agency violates the tenets of methodological naturalism and is not even entertained as a possibility.

The consequences of methodological naturalism are far ranging for the creation/intelligent design vs. evolution controversy. The constraints of methodological naturalism exclude a priori any model that appeals to intelligent agency to explain, say, the design of biochemical systems. So although biochemical systems bear the appearance of design, the scientific community must explain the design as a product of evolutionary mechanisms. Why? Because they have no other option. If biochemical systems didn’t evolve, then they must have been created. But, the tenets of methodological naturalism forbid this explanation. Hence, biochemical systems must have evolved—by default.

If biochemical systems arise via evolutionary mechanisms, then they must be cobbled together. They must be poorly designed. Consequently, adherents of the evolutionary paradigm are conditioned to see biochemical systems as poorly designed—even if they aren’t—because of their commitment to methodological naturalism. Many can’t see the design that is in plain view for creationists and intelligent design adherents.

The recent discovery of pseudoenzymes helps illustrate this point.

Pseudoenzymes: Evidence for Evolution or Intelligent Design?

The existence of pseudoenzymes came to light about a decade ago when the human genome sequence was made available for researchers to study. It turns out that almost every enzyme family encoded by the human genome includes seemingly nonfunctioning members. (Enzymes are proteins that catalyze—or facilitate—chemical reactions in the cell.) Biochemists have dubbed these nonfunctioning enzymes pseudoenzymes. These proteins bear structural resemblances to other members of their enzyme families, yet they are unable to catalyze chemical reactions.

Because researchers have already detected pseudoenzymes within every known enzyme family, they expect that many more pseudoenzymes await discovery. In fact, analysis of thousands of genomes has identified pseudoenzymes throughout the biological realm. To put it another way: Pseudoenzymes seem to be pervasive in biochemical systems.

Evolutionary biologists view pseudoenzymes as a byproduct of life’s evolutionary history. Presumably, these noncatalytic enzymes arose when genes encoding their functional counterpart became duplicated. After this event, the duplicated genes experienced mutations that disabled the catalytic function of their protein products, generating pseudoenzymes.

For adherents of the evolutionary paradigm, the widespread occurrence of pseudoenzymes serves as a prima facie (based on first impression) challenge to intelligent design, and a compelling reason to think that biochemical systems are the product of an evolutionary history. In this framework, pseudoenzymes are vestiges of life’s evolutionary past; nonfunctional biochemical scars that impede cellular functions.

On the other hand, as a creationist and intelligent design proponent, I resist this conclusion. Why? Because I have a different set of presuppositions than most in the scientific community. I believe that life arose through a Creator’s direct intervention and that science has the tool kit to detect evidence of intelligent agency at work. Because of my precommitments, I would posit yet-to-be-discovered functions for pseudoenzymes and a rationale for why these enzymes bear structural similarity to catalytic counterparts within their enzyme family.

And this is exactly what biochemists have discovered—pseudoenzymes are, indeed, functional, and there are good reasons why these biomolecules resemble their catalytic analogs.

The Role and Rationale for Pseudoenzymes

In a recent primer written for the open access journal BMC Biology, two biochemists surveyed recent work on pseudoenzymes, concluding that this newly recognized class of biomolecules plays a key role in cellular signaling pathways.1

The authors reflect on the role the evolutionary paradigm played in delaying this insight. They state:

“Because of the prejudice that focused attention on the catalytic functions of enzymes in signalling pathways, for a long time pseudoenzymes were considered to be dead—and therefore evolutionary remnants or bystanders in cell signalling networks. Contrary to this view, however, pseudoenzymes have now emerged as crucial players operating with an impressive diversity of mechanisms that we are only beginning to understand.”2

In other words, the biases created by viewing pseudoenzymes as the byproduct of evolutionary processes hindered biochemists from identifying and characterizing the functional importance of pseudoenzymes.

But this flawed perspective of viewing pseudoenyzmes as junk is changing. To date, biochemists have identified at least four functional roles for pseudoenzymes:

  1. They serve as protein anchors, locating cell signaling enzymes to appropriate locations within the cell.
  2. They function as scaffolds bringing enzymes of the same signaling pathway into proximity with one another, allowing the enzymes to efficiently work in conjunction with one another.
  3. They modulate the function of cell signaling proteins by binding to them, exerting an allosteric-type effect.
  4. They compete with “catalytic” cell signaling enzymes by binding the substrate without transforming it, regulating substrate transformation.

In part, the functional significance of pseudoenzymes justifies viewing these biomolecules as the work of a Creator. But, if these biomolecules are designed, why would pseudoenzymes be so structurally like their catalytic cohorts? Evolutionary biologists maintain that these similarities reflect their evolutionary history. But, if there is reason for the structural similarities, it further justifies viewing pseudoenzymes as designed systems. As it turns out, a rationale does exist for the close similarity in structure between pseudoenzymes and other members of their enzyme family. As the authors of the survey note:

“Enzyme structures are predisposed to mediating interactions with protein or metabolite ligands and thus these folds are the ideal templates for nature to repurpose for entirely new functions.”3

In other words, for pseudoenzymes to influence cellular signaling pathways, they must bind substrates and interact with other proteins in the pathways with a high degree of specificity and with the identical specificity as their catalytic counterparts. Their close resemblance to their catalytic analogs allows these biomolecules to do just that.

In short, in fulfilling their vital role as regulators of cell signaling pathways, pseudoenzymes display elegance, sophistication, and ingenuity. As a creationist, this is the reason I view these systems as a Creator’s handiwork. Because the field of pseudoenzyme biochemistry is so young, I anticipate the evidence for design to dramatically expand as we learn more about these surprising biomolecules.

Yet, despite everything we have learned about pseudoenzymes, adherents to the evolutionary paradigm simply can’t see these biomolecules as anything other than the product of an evolutionary history.

Because of the blind spot created by their philosophical commitments, the design of these systems is occluded from their view—and that causes them to miss the mark.

Resources
The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)
Pseudoenzymes Make Real Case for Intelligent Design” by Fazale Rana (article)
Q&A: Is Christianity a Science Showstopper?” by Fazale Rana (article)
Does the Evolutionary Paradigm Stymie Scientific Advance?” by Fazale Rana (article)
Q&A: Is Evolution Falsifiable?” by Fazale Rana (article)

Endnotes

  1. Patrick Eyers and James Murphy, “The Evolving World of Pseudoenzymes: Proteins, Prejudice, and Zombies,” BMC Biology 14 (November 2016): 98, doi:10.1186/s12915-016-0322-x.
  2. Ibid.
  3. Ibid.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/12/07/pseudoenzymes-illustrate-science’s-philosophical-commitments

Ancient Muds Bog Down Evolutionary Explanation for Life’s Origin

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BY FAZALE RANA – NOVEMBER 30, 2016

When I was a kid, I played a lot of sandlot football. And nothing was more fun than playing football after a hard rain on a muddy field. It was a blast to slosh around in the mud. But if the field was too muddy, it was hard to run, making it difficult to advance the ball down the field.

Scientists like playing in the mud, too. And recently, a scientist from the University of Washington had a good time working with ancient mud from early Earth (dating to 3.8 billion years in age). As a result of her efforts, Eva Stüeken now argues that the nitrogen in some of the oldest muddy sediments on Earth was produced by microorganisms.

Her interpretation of the nitrogen in ancient muds adds to the mounting evidence for an early and rapid origin of life, making it more difficult for the scientific community to advance an evolutionary explanation for life’s start.1

In earlier studies, geochemists measured about 430 parts per million (ppm) nitrogen in biotiteminerals recovered from 3.8-billion-year-old sediments of the Isua Formation of Greenland. Typically, the highest levels of nitrogen co-occur with graphite granules. (Some geochemists regard the graphite granules as a biomarker.) Because nitrogen is an integral component of biomolecules such as DNA and proteins, the occurrence of this element in the biotite can be taken as a biosignature.

Unfortunately, it is not that straightforward. Some geochemists claim that the nitrogen in the ancient mud comes from abiotic sources. For example, lightning and volcanism can fix atmospheric nitrogen, conceivably accounting for its presence in the biotite grains.

To test this idea, University of Washington earth scientist Eva Stüeken modeled the amount of abiotic nitrogen that would be expected in ancient muds if it came exclusively from abiotic processes. She determined that abiotic pathways were insufficient to explain nitrogen levels, meaning that some of the nitrogen must be biogenic.

Early Life on Earth

The presence of nitrogen in ancient muds adds to the mounting geochemical and fossil evidence that points to the presence of life on early Earth. (See the Resources section below to learn about other evidences for early life on Earth.) It looks like life appeared on Earth as soon as our planet could sustain it. In fact, a case can be made that life could not have originated and persisted on Earth prior to 3.8 billion years ago. This constraint means that life must have originated within a geological instant.

Both the geochemical and fossil evidence indicate that Earth’s first life was microbial in nature. Though morphologically simple, the geochemical data indicates this life was biochemically diverse and complex. There are good reasons to think that the first life-forms could engage in a wide range of metabolic activities including: photosynthesis, methanogenesis, methanotrophism, and sulfur disproportionation. While far from conclusive, the biogenic nitrogen in the ancient muds suggests that Earth’s first life also had the capacity to fix nitrogen.

Evidence for Evolution or Creation?

As discussed in Origins of Life, the sudden, early appearance of metabolically sophisticated life on Earth is difficult to accommodate within an evolutionary framework. Traditionally, origin-of-life researchers have maintained that the origin-of-life process would have required hundreds of millions of years—maybe even a billion years. To put it another way, when viewed from an evolutionary standpoint, no one would have expected that life’s origin would have happened so rapidly.

This latest insight about the ancient muds creates an additional problem for evolutionary models. It argues against the existence of a prebiotic soup on early Earth. This idea is a cornerstone for most origin-of-life models. Accordingly, life emerged on early Earth out of a prebiotic soup—a complex chemical mixture—as the molecules in the soup became more complex and, eventually, self-organized into the first cellular entities.

If a prebiotic soup existed on Earth, it should leave behind a geochemical signature in the oldest rocks on Earth. Geochemists have uncovered chemical residues in the oldest rock formations on Earth—including the nitrogen in the ancient muds—but inevitably, these residues turn out to be biogenic in origin, not abiotic. In other words, there is no geochemical evidence for a prebiotic soup. This idea is all covered with the mud.

On the other hand, the sudden appearance of biochemically complex life on early Earth bears the signature of the Creator’s handiwork. They are also key predictions for the RTB model for life’s origin.

Resources

Origins of Life: Biblical and Evolutionary Models Face Off by Fazale Rana and Hugh Ross (book)
Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator by Fazale Rana (book)
Science News Flash: 3.7-Billion-Year-Old Fossils Perplex Origin-of-Life Researchers” by Fazale Rana (article)
Early Life was More Complex than We Thought” by Fazale Rana (article)
When Did Life First Appear on Earth?” by Fazale Rana (article)
Origin-of-Life Predictions Face Off: Evolution vs. Biblical Creation” by Fazale Rana (article)
Fossils Indicate Early Life Was Metabolically Complex and Diverse” by Fazale Rana (podcast)
Life May Have Begun 300 Million Years Earlier Than We Thought” by Fazale Rana (podcast)

Endnotes

  1. Eva Stüeken, “Nitrogen in Ancient Mud: A Biosignature?” Astrobiology 16 (September 2016): 730–35, doi:10.1089/ast.2016.1478.