Analysis of Genomes Converges on the Case for a Creator

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By Fazale Rana – November 13, 2019

Are you a Marvel or a DC fan?

Do you like the Marvel superheroes better than those who occupy the DC universe? Or is it the other way around for you?

Even though you might prefer DC over Marvel (or Marvel over DC), over the years these two comic book rivals have often created superheroes with nearly identical powers. In fact, a number of Marvel and DC superheroes are so strikingly similar that their likeness to one another is obviously intentional.1

Here are just a few of the superheroes Marvel and DC have ripped off each other:

  • Superman (DC, created in 1938) and Hyperion (Marvel, created in 1969)
  • Batman (DC, created in 1939) and Moon Knight (Marvel, created in 1975)
  • Green Lantern (DC, created in 1940) and Nova (Marvel, created in 1976)
  • Catwoman (DC, created in 1940) and Black Cat (Marvel, created in 1979)
  • Atom (DC, created in 1961) and Ant-Man (Marvel, created in 1962)
  • Aquaman (DC, created in 1941) and Namor (Marvel, created in 1939)
  • Green Arrow (DC, created in 1941) and Hawkeye (Marvel, created in 1964)
  • Swamp Thing (DC, created in 1971) and Man Thing (Marvel, created in 1971)
  • Deathstroke (DC, created in 1980) and Deadpool (Marvel, created in 1991)

This same type of striking similarity is also found in biology. Life scientists have discovered countless examples of biological designs that are virtually exact replicas of one another. Yet, these identical (or nearly identical) designs occur in organisms that belong to distinct, unrelated groups (such as the camera eyes of vertebrates and octopi). Therefore, they must have an independent origin.

 

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Figure 1: The Camera Eyes of Vertebrates (left) and Cephalopods (right); 1: Retina; 2: Nerve Fibers; 3: Optic Nerve; 4: Blind Spot. Image credit: Wikipedia

From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again. As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books, Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.2 Scientists observe these repeated outcomes (known as convergence) at the ecological, organismal, biochemical, and genetic levels.

From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t genuinely explain. In fact, I see pervasive convergence as a failed scientific prediction—for the evolutionary paradigm. Recent work by a research team from Stanford University demonstrates my point.3

These researchers discovered that identical genetic changes occurred when: (1) bats and whales “evolved” echolocation, (2) killer whales and manatees “evolved” specialized skin in support of their aquatic lifestyles, and (3) pikas and alpacas “evolved” increased lung capacity required to live in high-altitude environments.

Why do I think this discovery is so problematic for the evolutionary paradigm? To understand my concern, we first need to consider the nature of the evolutionary process.

Biological Evolution Is Historically Contingent

Essentially, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature.

The concept of historical contingency embodies this idea and is the theme of Stephen Jay Gould’s book Wonderful Life.4 To help illustrate the concept, Gould uses the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Are Evolutionary Processes Historically Contingent?

Gould based the concept of historical contingency on his understanding of the evolutionary process. In the decades since Gould’s original description of historical contingency, several studies have affirmed his view.

For example, in a landmark study in 2002, two Canadian investigators simulated macroevolutionary processes using autonomously replicating computer programs, with the programs operating like digital organisms.5 These programs were placed into different “ecosystems” and, because they replicated autonomously, could evolve. By monitoring the long-term evolution of the digital organisms, the two researchers determined that evolutionary outcomes are historically contingent and unpredictable. Every time they placed the same digital organism in the same environment, it evolved along a unique trajectory.

In other words, given the historically contingent nature of the evolutionary mechanisms, we would expect convergence to be rare in the biological realm. Yet, biologists continue to uncover example after example of convergent features—some of which are quite astounding.

The Origin of Echolocation

One of the most remarkable examples of convergence is the independent origin of echolocation (sound waves emitted from an organism to an object and then back to the organism) in bats (chiropterans) and cetaceans (toothed whales). Research indicates that echolocation arose independently in two different groups of bats and also in the toothed whales.

 

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Figure 2: Echolocation in Bats. Image credit: Shutterstock

One reason why this example of convergence is so remarkable has to do with the way some evolutionary biologists account for the widespread occurrences of convergence in biological systems. Undaunted by the myriad examples of convergence, these scientists assert that independent evolutionary outcomes result when unrelated organisms encounter nearly identical selection forces (e.g., environmental, competitive, and predatory pressures). According to this idea, natural selection channels unrelated organisms down similar pathways toward the same endpoint.

But this explanation is unsatisfactory because bats and whales live in different types of habitats (terrestrial and aquatic). Consequently, the genetic changes responsible for the independent emergence of echolocation in the chiropterans and cetaceans should be distinct. Presumably, the evolutionary pathways that converged on a complex biological system such as echolocation would have taken different routes that would be reflected in the genomes. In other words, even though the physical traits appear to be identical (or nearly identical), the genetic makeup of the organisms should reflect an independent evolutionary history.

But this expectation isn’t borne out by the data.

Genetic Convergence Parallels Trait Convergence

In recent years, evolutionary biologists have developed interest in understanding the genetic basis for convergence. Specifically, these scientists want to understand the genetic changes that lead to convergent anatomical and physiological features (how genotype leads to phenotype).

Toward this end, a Stanford research team developed an algorithm that allowed them to search through entire genome sequences of animals to identify similar genetic features that contribute to particular biological traits.6 In turn, they applied this method to three test cases related to the convergence of:

  • echolocation in bats and whales
  • scaly skin in killer whales
  • lung structure and capacity in pikas and alpacas

The investigators discovered that for echolocating animals, the same 25 convergent genetic changes took place in their genomes and were distributed among the same 18 genes. As it turns out, these genes play a role in the development of the cochlear ganglion, thought to be involved in echolocation. They also discovered that for aquatic mammals, there were 27 identical convergent genetic changes that occurred in same 15 genes that play a role in skin development. And finally, for high-altitude animals, they learned that the same 25 convergent genetic changes occurred in the same 16 genes that play a role in lung development.

In response to this finding, study author Gill Bejerano remarked, “These genes often control multiple functions in different tissues throughout the body, so it seems it would be very difficult to introduce even minor changes. But here we’ve found that not only do these very different species share specific genetic changes, but also that these changes occur in coding genes.”7

In other words, these results are not expected from an evolutionary standpoint. It is nothing short of amazing that genetic convergence would parallel phenotypic convergence.

On the other hand, these results make perfect sense from a creation model vantage point.

Convergence and the Case for Creation

Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a Divine Mind. In this scheme, the repeated origins of biological features equate to the repeated creations by an Intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

Like the superhero rip-offs in the Marvel and DC comics, the convergent features in biology appear to be intentional, reflecting a teleology that appears to be endemic in living systems.

Resources

Convergence of Echolocation

The Historical Contingency of the Evolutionary Process

Endnotes
  1. Jamie Gerber, “15 DC and Marvel Superheroes Who Are Strikingly Similar,” ScreenRant (November 12, 2016), screenrant.com/marvel-dc-superheroes-copies-rip-offs/.
  2. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  3. Amir Marcovitz et al., “A Functional Enrichment Test for Molecular Convergent Evolution Finds a Clear Protein-Coding Signal in Echolocating Bats and Whales,” Proceedings of the National Academy of Sciences, USA 116, no. 42 (October 15, 2019), 21094–21103, doi:10.1073/pnas.1818532116.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  5. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
  6. Marcovitz et al., “A Functional Enrichment Test.”
  7. Stanford Medicine, “Scientists Uncover Genetic Similarities among Species That Use Sound to Navigate,” ScienceDaily, October 4, 2019, sciencedaily.com/releases/2019/10/191004105643.htm.

Reprinted with permission by the author

Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/11/13/analysis-of-genomes-converges-on-the-case-for-a-creator

Like a Fish Out of Water: Why I’m Skeptical of the Evolutionary Paradigm

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BY FAZALE RANA – JULY 27, 2016

I am skeptical that evolutionary processes can fully account for life’s origin, history, and design—and that often makes me feel like a fish out of water.

“Mainstream” scientists view biological evolution as the organizing principle in biology. In fact, Russian geneticist Theodosius Dobzhansky famously wrote, “Nothing in biology makes sense except in the light of evolution.”1 So, when I question evolutionary explanations, I become an outsider. I am outside the fish bowl, looking in. Because I’m a biochemist, my critics accuse me of being either dishonest or incompetent. Why else would I question the “fact” of evolution in the face of the overwhelming evidence for common descent? They claim that theological—not scientific motivations fuel my skepticism.

I would partially agree with that assessment. I find it hard to square certain features of the evolutionary framework with some of Christianity’s most important biblical and theological ideas. But, I also think that there are some very real scientific problems associated with the evolutionary paradigm. The deficiencies are best exposed by failed predictions.

From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. Convergence stands as a failed prediction.

Convergence

One of evolution’s failed predictions relates to the phenomenon known as convergence. This concept describes instances in which unrelated organisms possess nearly identical anatomical and physiological characteristics. Presumably, evolutionary pathways independently produced these identical (or near identical) features. Yet convergence doesn’t make much sense from an evolutionary perspective. Indeed, if evolution is responsible for the diversity of life, one would expect convergence to be extremely rare. As a I wrote in a previous blog post, the mechanism that drives the evolutionary process consists of an extended sequence of unpredictable, chance events. Given this mechanism, it seems improbable that disparate evolutionary pathways would ever lead to the same biological feature. To put it another way, examples of convergence should be rare.

The concept of historical contingency embodies the notion that evolution should be nonrepeatable, and is the theme of Stephen Jay Gould’s book Wonderful Life.2 To help clarify the concept of historical contingency, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Yet, biological convergence is widespread.3 Recently, researchers from the University of New South Wales (in Australia) added to the examples of convergence at an organismal level. From an evolutionary perspective, they showed that amphibious behavior in fish evolved 33 separate times among extant groups! In fact, in one family, fish adopted a terrestrial life style between 3 to 7 times.

This result was unexpected. One of the researchers involved with the study stated, “Because of the challenges fish face in being able to breathe and move and reproduce on land, it had been thought this was a rare occurrence.”4

Recently, another team of investigators from the University of Kansas identified another example of biochemical convergence. They showed that venom evolved, separately and independently, 18 times in fish that live in freshwater and marine environments. This result is all the more surprising because—as William Leo Smith, one of the study’s authors points out— “fish venoms are often super complicated, big molecules.”5

Does the Widespread Occurrence of Convergence Falsify Evolution?

From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. It stands as a failed prediction. Yet many evolutionary biologists don’t see it that way. For example, the scientists from the University of New South Wales responded to their unexpected find this way: “Now we have shown this initial transition to land is quite common, it seems these challenges can be readily overcome.”6 However, their interpretation entails circular reasoning. Biologists thought that fish moving to land would be difficult given the immense challenges associated with this transition. But, when it was found to be a frequent occurrence, then they conclude it must be easy. But they have no reason to think it must be easy other than the widespread occurrence of this transition. I would contend that this circular reasoning reflects a deep-seated, a priori commitment to the evolutionary paradigm, in which evolution is accepted as fact, and no evidence can ever count against it.

Convergence and the Case for Intelligent Design

Though the idea of convergence fits awkwardly within the evolutionary framework, it makes perfect sense if a Creator is responsible for life. Instead of convergent features emerging through repeated evolutionary outcomes, they could be understood as reflecting the work of a Divine mind. The repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

Resources
The Cell’s Design (book)

Endnotes
  1. Theodosius Dobzhansky, “Nothing in Biology Makes Sense Except in the Light of Evolution,” American Biology Teacher 35 (March 1971): 125–29.
  2. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  3. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  4. University of New South Wales, “Fish Out of Water Are More Common Than Thought,” ScienceDaily, June 22, 2016, https://www.sciencedaily.com/releases/2016/06/160622102129.htm.
  5. University of Kansas, “Researchers Tally Huge Number of Venomous Fishes, Tout Potential for Medical Therapies,” ScienceDaily, July 5, 2016, https://www.sciencedaily.com/releases/2016/07/160705160206.htm.
  6. “Fish Out of Water,” ScienceDaily.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/27/like-a-fish-out-of-water-why-i’m-skeptical-of-the-evolutionary-paradigm

Historical Contingency and the Improbability of Protein Evolution, Part 1 (of 2)

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BY FAZALE RANA – JULY 13, 2016

Can evolutionary processes produce biological innovation?

Critics of the evolutionary paradigm—including me—would say, “No.” However, the reasons for my skepticism differ from many of evolution’s chief detractors. One argument against the evolutionary paradigm that causes me discomfort has to do with the “improbability” of the evolutionary process. For example, one common version of this argument relates to the evolutionary emergence of proteins, with critics asserting that the evolution of novel proteins from preexisting proteins would have been so improbable that it defies an evolutionary explanation. To justify this position, these critics often point to studies such as the one published by scientists from the Universities of Oregon and Chicago that seemingly buttresses their point.But does it?

The Evolutionary Origin of a Protein Receptor

This research team hoped to gain insight into the role that chance historical events play in evolutionary processes. Working within the framework of the evolutionary paradigm, they determined what they believe to be the amino acid sequence and structure of the ancestral protein that evolved into the cellular receptor protein that binds the hormone cortisol. They claim to have resurrected an ancient protein they believe existed 450 million years ago, before the cortisol-specific glucocorticoid receptor evolved its specificity for this particular hormone.2

Today, the cortisol-specific glucocorticoid receptor assumes a key role in the endocrine system by regulating development and the stress response. The activity of this protein is mediated by cortisol binding. However, the researchers believe that in the past the ancestral protein was biochemically promiscuous, binding a number of hormones, and only later evolved its specificity for cortisol through amino acid changes mediated by the putative evolutionary process. Based on a reconstruction of the evolutionary pathway, they conclude that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol.

The researchers classified the changes into two categories: 1) functional; and 2) permissive. They deemed five of the changes as functional, meaning that these changes contributed to the receptor’s cortisol-binding specificity. They dubbed the other two changes as permissive. These changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur for the functional changes to take effect. In other words, if the functional changes took place independently of the permissive changes, the resulting hormone receptor would not bind cortisol. The researchers determined that the permissive changes help to stabilize the receptor protein’s structure so that it can tolerate the five functional changes.

Because cortisol binding depends upon the permissive mutations, the researchers reasoned that historical contingency must have played some role in the evolution of the cortisol-specific receptor protein. The permissive mutations must have appeared first, because if they didn’t, the functional changes would not have been selected (again) since they aren’t functional apart from the permissive changes.

The Improbability of Protein Evolution

The question then becomes, “How prominent is contingency in the evolutionary history of the cortisol-specific receptor protein?” To address this point, the investigators synthesized the ancestral receptor protein with the five functional amino acid changes (AP+5). Then, they subjected the AP+5 protein to random amino acid changes to try and determine the number of possible alternate permissive changes that could stabilize the receptor protein in the same way as the historical permissive changes.

They screened about 12,500 random variants of the AP+5 protein. These variants yielded an estimated 1,025 unique single amino acid replacements, 1,802 unique double amino acid replacements, and 825 unique higher order combinations of amino acid substitutions. That is, they examined about 3,650 variants of the AP+5 protein. (The other 8,850 variants were duplicates of the 3,650 variants.) They also engineered 10 additional AP+5 variants using rational design principles. To their surprise, none of the 3,660 variants (3,650 in the screened library, plus the additional 10 engineered double mutants) yielded a functional cortisol-specific receptor that would not disrupt the function of the ancestral protein. (Four of the AP+5 variants displayed cortisol-specific binding, but these four changes destroyed the function of the ancestral protein. From an evolutionary perspective, these alternate permissive substitutions would have been selected against because of their disruptive influence.)

This result indicates that it is highly improbable that the permissive amino acid changes necessary to support the evolution of a cortisol-specific receptor protein could ever occur (with an upper bound of 0.03 percent). The researchers conclude:

“The total frequency is probably far lower…The universe of possible variants containing two or more replacements is very large, so alternative permissive sets may exist; however, these genotypes would require multiple independent substitutions, and the joint probability of such events would be very low because they cannot be acquired deterministically by selection for the derived function.”3

Their probability assessment doesn’t even include the likelihood of the five functional changes occurring after the two permissive changes took place, meaning that the probabilities for the evolution of the cortisol-specific receptor protein from a promiscuous ancestral receptor are even more unlikely.

The Contingency of the Evolutionary Process

As a skeptic of the evolutionary paradigm, it is tempting to point to this study as evidence that evolutionary transformations are so improbable that these processes cannot account for biological innovation. But this would be an unfair conclusion that misrepresents the way evolutionary biologists interpret these results. Instead, these scientists argue that these results tell them something about the evolutionary process: Namely, that historical contingency plays a central role in evolutionary transformations.

The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.4 According to this idea, the mechanism that drives the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

According to the researchers:

“If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR—or the vertebrate endocrine system more generally—would be substantially different.”5

A Flawed Argument

In other words, while evolutionary transformations are highly improbable, their unlikelihood cannot be used as a legitimate basis for skepticism about the evolutionary paradigm. To use them in this way would be to make a straw man argument against biological evolution. This probability argument assumes that evolutionary end points are fixed, but evolutionary biologists don’t see them that way at all—because of the historically contingent nature of the process.

Still, there are some legitimate reasons to be skeptical about the capacity of evolutionary mechanisms to account for the design and diversity of life. And one of those reasons is exposed by this study and the historically contingent nature of the evolutionary process.

I will elaborate in my next blog post.

Resources

Endnotes
  1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–7.
  2. For a Christian perspective on resurrected ancient proteins, see my article, Fazale Rana, “Resurrected Proteins and the Case for Biological Evolution,” Today’s New Reason to Believe (blog), Reasons to Believe, October 14, 2013, https://www.reasons.org/articles/resurrected-proteins-and-the-case-for-biological-evolution.
  3. Harms and Thornton, “Historical Contingency,” 204.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  5. Harms and Thornton, “Historical Contingency,” 207.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/13/historical-contingency-and-the-improbability-of-protein-evolution-part-1-(of-2)