Resurrected Proteins and the Case for Biological Evolution

resurrectedproteinsandthecase

BY FAZALE RANA – OCTOBER 14, 2013

Recently, a team of researchers from Spain resurrected a 4-billion-year-old version of a protein that belongs to a class of proteins known as thioredoxins. The ability to resurrect ancient proteins using principles integral to the evolutionary paradigm is the type of advance that many scientists point to as evidence for biological evolution. In this article, I discuss how this work can be seamlessly accommodated within a creation/design paradigm.

Recently, a team of biochemists from Spain resurrected an ancient version of a protein, known as a thioredoxin. The successful restoration of this antiquated protein is the kind of advance that many scientists point to as evidence for the evolutionary paradigm.

Presumably, the protein they “brought back to life” would have been as it was 4 billion years ago.1 By studying the structure and function of the ancient thioredoxin, the research team was able to gain insight into the biology of some of the first life-forms on Earth. This is not the first time biochemists have pulled off this feat. Over the last several years, life scientists have announced the re-creation of a number of ancient proteins.2

The procedure for resurrecting ancient proteins makes use of evolutionary trees that are built using the amino acid sequences of extant proteins. From these trees, scientists infer the structure of the ancestral protein. They then go into the lab and make that protein—and more often than not, the molecule adopts a stable structure with discernible function. It is remarkable to think that scientists can use evolutionary trees to interpolate the probable structure of an ancestral protein to then make a biomolecule that displays function. I truly understand why people would point to this type of work as evidence for biological evolution.

So, how does someone who advocates for intelligent design/creationism make sense of scientists’ ability to resurrect ancient proteins?

For the sake of brevity, I will provide a quick response to this question. For a more detailed discussion of the production of ancient thioredoxins and how I view resurrected proteins from a design/creation model perspective listen to the August 12, 2013 episode of Science News Flash.

To appreciate a design/creation interpretation of this work, it is important to first understand how scientists determine the amino acid sequence for ancient proteins. Evolutionary biologists make an inference by comparing amino acid sequences of extant proteins. (In this most recent study, scientists compared around 200 thioredoxins from organisms representing all three domains of life.) Based on the patterns of similarities and differences in the sequences, they propose evolutionary relationships among the proteins.

The assumption is that the differences in the amino acid sequences of extant proteins stem from mutations to the genes encoding the proteins. Accordingly, these mutations would be passed on to subsequent generations. As the different lineages diverge, different types of mutations would accrue in the protein-coding genes in the distinct lineages. The branch points, or nodes, in the evolutionary tree, would then represent the ancestral protein shared by all proteins found in the lineages that split from that point. Researchers then infer the most likely amino acid sequence of the ancestral protein by working their way backwards from extant amino acid sequences of proteins which fall along the branches that stem from the node.

At this juncture, it is important to note that evolutionary biologists actively choose to interpret the similarities and differences in the amino acid sequences of extant proteins from an evolutionary perspective. I maintain that it is equally valid to interpret the sequence similarities and differences from a design/creation standpoint as well. With this approach, the archetype takes the place of the common ancestor. And the differences in the amino acid sequences represent variations around an archetypical design shared by all the proteins that are members of a particular family, such as the thioredoxins. In light of this concept, it is interesting the researchers discovered that the structure of ancient thioredoxins is highly conserved moving back through time, with only limited variation in the structure, which varied around a core design.

What about the process for determining the ancestral/archetypical sequence from an evolutionary tree? Doesn’t this fact run contrary to a design explanation?

Not necessarily. Consider the variety of automobiles that exist. These vehicles are all variants of an archetypical design. Even though automobiles are the products of intelligent agents, they can be organized into an “evolutionary tree” based on design similarities and differences. In this case, the nodes in the tree represent the core design of the automobiles that are found on the branches that arise from the node.

By analogy, one could also regard the extant members of a protein family as the work of a Designer. Just like automobiles, the protein variants can be organized into a tree-like diagram. In this case the nodes correspond to the common design elements of the proteins found on the branches.

In my view, when evolutionary biologists uncover what they believe to be the ancestral sequence of a protein family, they are really identifying

Endnotes

  1. Alvaro Ingles-Prieto et al., “Conservation of Protein Structure over Four Billion Years,” Structure21 (September 3, 2013): 1690–97.
  2. For example see Michael J. Harms and Joseph W. Thornton, “Analyzing Protein Structure and Function Using Ancestral Gene Reconstruction,” Current Opinion in Structural Biology 20 (June 2010): 360–66.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/todays-new-reason-to-believe/read/tnrtb/2013/10/15/resurrected-proteins-and-the-case-for-biological-evolution

Q&A: Why Would a Limitless Creator Face Trade-Offs in Biochemical Designs?

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BY FAZALE RANA – FEBRUARY 1, 2017

“Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”
—Francis Crick, What Mad Pursuit
In my experience, no one denies the complexity and sophistication of biochemical systems, regardless of their philosophical or religious views. To put it another way, there is no debate. Biochemical systems have the indisputable appearance of design. The question at the center of the creation/evolution controversy relates to the source of the design. Is it the handiwork of a Creator? Or, is it the product of unguided, evolutionary processes? Is the design authentic? Or is it only apparent?

As a creationist, I regard the elegant designs of biochemical systems as evidence for a Creator’s role in bringing life into existence. Yet, many in the scientific community would disagree, maintaining that the design emerges through evolutionary processes. In support of this position, these detractors point to so-called “bad” biochemical designs and argue that if an all-powerful, all-knowing, all-good Creator produced biochemical systems, these systems should display perfection. On the other hand, less-than-optimal designs are precisely what one would expect if life resulted from an evolutionary history.

Are Bad Designs a Challenge to the Design Argument?

In my book The Cell’s Design, I offer a chapter-length rejoinder to this challenge, pointing out the following:

  • Often when life scientists interpret biochemical systems as poorly designed, their view is based on an incomplete understanding of the structure and function of these systems. Inevitably, as researchers develop new insight, these systems are revealed to be additional examples of the elegant designs, characteristic of biochemistry.

Junk DNA serves as the quintessential illustration of this point.

  • In some cases, biochemical systems labeled as flawed designs are suboptimal in reality. Their suboptimal nature is necessary for the overall system to optimally perform. Routinely, engineers intentionally suboptimize facets of the systems they design to achieve overall optimality. This practice is necessary for complex systems built to achieve multiple objectives. Inevitably, some of these objectives conflict with others. In other words, these systems face trade-offs. To manage the trade-offs, engineers must carefully suboptimize the performances of the systems’ components, again, so that the systems will result in overall optimal performances.

Some recently discovered examples of biochemical trade-offs include:

A Rejoinder

After recently posting the article I wrote on the trade-offs associated with glucose breakdown, my Facebook friend Riaz, a skeptic, offered this come back:

“There is no need for trade-offs if one has unlimited resources . . . not to mention being able to change [the] law[s] of physics and design/re-design the universe from scratch . . .”

Trade-Offs Are Inevitable

This is a reasonable question. Why would the Creator, described in the Bible, ever deal with trade-offs? But what if the God of the Bible did choose to produce a universe with fixed natural laws? If he did, trade-offs inevitably result. And, I contend, the elegance in which these trade-offs are managed in biochemical systems are nothing less than genius, befitting the God of the Bible.

A Follow-Up Question

What about Riaz’s second question? Why create a universe with unvarying natural laws, if that means suboptimal designs would necessarily result? If the Creator is infinite in power and extent, if the Creator is all-knowing and all-good, why would He confine himself so that He is forced to suboptimize even a single facet of His creation because of trade-offs?

Interesting questions, to be sure. From my perspective, there are at least three reasons why God created the universe with unvarying natural laws.

Constant Laws of Nature Reflect God’s Nature

A universe with constant natural laws reflects God’s character and nature as revealed in the Old and New Testaments. Scripture teaches that:

It is reasonable to think that the universe made by a God who does not waver would be governed by unvarying natural laws.

Along those lines, Psalm 50:6 tells us that the “heavens declare God’s righteousness.” From my vantage point, the righteousness revealed in the heavens would be most clearly manifested through the conformity of the heavenly bodies (and all of nature, for that matter) to constant laws.

An interesting interplay of these ideas is found in Jeremiah 33:25. Here, the Lord compares the certainty of the covenant He established with His people to the “established laws of heaven and earth.”1 To put it another way, if we ever wonder if God will keep his promises, all we need to do is look to the constancy of the laws of nature.

Constant Laws of Nature Are Necessary for Moral Accountability

This assertion may not seem obvious at first glance. But, careful consideration leads to the conclusion that apart from a universe with fixed laws governing nature, it is impossible to have moral laws. In his classic work Faith and Reason, the late philosopher Ron Nash writes:

“The existence of a lawlike and orderly creation is a necessary condition for a number of divine objectives. . . . it is also reasonable to believe that God placed these free moral agents in a universe exhibiting order. One can hardly act intentionally and responsibly in an unpredictable environment.”2

Ron Nash goes on to say:

“If the world were totally unpredictable, if we could never know from one moment to the next, what to expect from nature, both science and meaningful moral conduct would be impossible. While we often take the natural order for granted, this order and the predictability that accompanies it function as a necessary condition for free human action. . . . One reason people can be held accountable when they pull the trigger of a loaded gun is the predictability of what will follow such an action.”3

Constant Laws of Nature Permit Discoverability

Unchanging natural laws render the universe (and phenomena within its confines) intelligible. If the laws of nature changed from day-to-day—or at the Creator’s whim—it would be impossible to know anything about the world around us with any real confidence. In effect, science would be impossible. The orderliness of the universe leads to predictability, the most important condition for a rational investigation of the world.

Because the universe 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 laws of physics and chemistry, the composition of matter, and the nature of living systems, we can deploy that knowledge to benefit humanity—in fact, all life on Earth—through technology, agriculture, medicine, and conservation efforts. To put it in theological terms, the intelligibility of the universe allows us to unleash God’s providence for humanity as we come to understand the world around us.

Ultimately, I believe that God has designed the universe for discoverability because He wants us to see, understand, and appreciate His handiwork as a Creator, so through His creation we can know Him. Scripture teaches that we can glimpse God’s glory (Psalm 19:1), majesty (Psalm 8:1), and righteousness (Psalm 50:6) from nature. From the Old Testament, we learn that God’s eternal nature (Psalm 90:2) can be gleaned from the world around us. We can see God’s love, faithfulness, righteousness, and justice (Psalm 36:5–6) in creation. This powerful revelation of God’s character is only possible because the laws of nature are constant.

Scripture (Romans 1:20Job 12:7–9) also teaches that we can see evidence for God’s fingerprints as well—evidence for His existence. And toward that end, I maintain that we see God’s handiwork in the elegant way trade-offs are handled in biochemical systems.

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