Science News Flash: Has the Last Universal Common Ancestor Been Identified?

sciencenewsflashhasthelastuniversal

BY FAZALE RANA – JULY 28, 2016

Researchers from Germany made headlines by announcing that they are one step closer to identifying LUCA (the last universal common ancestor)—the single-celled organism that anchors the evolutionary tree of life.1

Because an organism’s genes reflect its environment, these researchers attempted to partially reconstruct LUCA’s genome. They reasoned that this reconstruction would tell them something about LUCA’s complexity and lifestyle.2 To accomplish this task, the researchers searched 6.1 million protein-coding genes found in archaeal and bacterial genomes for those with a special type of history (that is, they searched for universal, monophyletic genes).

They identified 355 types of genes that fit their criteria. A few of the genes appear to be involved with essential biochemical operations such as DNA replication, transcription, and translation. On the other hand, most of the 355 genes play highly specialized roles that reflect a thermophilic lifestyle. For example, they discovered an enzyme called reverse gyrase that is only found among microbes that live in high-temperature environments. They also discovered enzymes that are part of a metabolic route called the Wood-Ljungdahl pathway. This pathway uses molecular hydrogen as an electron donor, and carbon dioxide as an electron acceptor. The hydrogen had to come from a geological source. On this basis, the German scientists concluded that LUCA lived in a hydrothermal vent environment, providing a ready source for this life-giving gas.

The researchers also discovered that this microbe was able to: 1) fix nitrogen from the environment, incorporating this atom into it’s biomolecules; 2) lived in an anaerobic environment (devoid of oxygen); but 3) didn’t seem to have the ability to make amino acids. The investigators think that LUCA, though primitive, may have had more than 355 genes. If the investigators relax their search requirements a bit, they estimate that LUCA may have had nearly 575 genes.

The German research team argued that not only was LUCA a thermophile, but that the origin of life occurred at hydrothermal vents.

Have these researchers provided us with a key insight into LUCA’s identity? Have they identified the locale for the origin of life?

Not necessarily. Here are some points to consider:

In other words, there are good scientific reasons to question the high-temperature origin of life and the thermophilic identity of LUCA. And given the apparent complexity of LUCA, there is a strong basis to question evolutionary scenarios for life’s start.

In spite of the headlines, scientists have no true understanding of how chemical evolution could have produced the first life on Earth.

Resources
Too Hot to Handle” by Fazale Rana (Article)
Some Like It Hot—First Life Did Not” by Fazale Rana (Article)
Sea Vents Closed as Life-Origin Site” by Fazale Rana (Article)
Biochemists Ask, ‘How Low Can Life Go?’” by Fazale Rana (Article)
Origins of Life by Fazale Rana and Hugh Ross (Book)
Creating Life in the Lab by Fazale Rana (Book)

Endnotes

  1. Madeline C. Weiss et al., “The Physiology and Habitat of the Last Universal Common Ancestor,” Nature Microbiology 1 (July 2016): 16116, doi:10.1038/NMICROBIOL.2016.116; James O. McInerney, “Evolution: A Four Billion Year Old Metabolism,” Nature Microbiology 1 (July 2016): 16139, doi:10.1038/NMICROBIOL.2016.139.
  2. Scientists think that LUCA was a prokaryotic, single-celled microbe.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/28/science-news-flash-has-the-last-universal-common-ancestor-been-identified

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

likeafishoutofwater

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 2 (of 2)

historicalcontingencyandtheimprobability

BY FAZALE RANA – JULY 20, 2016

A few weeks ago, Kathy Emmons of WORD FM in Pittsburg interviewed me about the connection between human evolution and human trafficking. During the interview, she asked me if theological or scientific concerns drove my skepticism about human evolution. My answer is both.

I find it difficult to reconcile the idea of human evolution with passages in the Old and New Testaments that address human origins. But, I also think that there are significant scientific problems confronting the evolutionary paradigm. A recent study by scientists from the Universities of Oregon and Chicago highlights one of those scientific challenges.1

As described in a previous post, these researchers wanted to develop a better understanding of the role that chance historical events play in evolutionary processes. To do this, they reconstructed what they believe to be the evolutionary pathway that led to the emergence of the cortisol-specific glucocorticoid receptor protein, a key component of the vertebrate endocrine system. Based on their reconstruction, it appears that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol. They determined that two of the changes were permissive. That is, these changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur before any of the functional changes took place. Based on their analysis, it appears that the permissive changes were highly improbable, leading the researchers to conclude that historical contingency plays a central role in evolutionary transformations.

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.”2

Historical Contingency

The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.3 According to this idea, 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.

Gould envisioned historical contingency as primarily resulting from external events (such as climate change or asteroid impacts). But this latest work indicates that the intrinsic complexity of proteins also contributes to historical contingency, because of the necessity and low probability of of permissive amino acid substitutions that support functional changes.

How Widespread Is Historical Contingency?

The question then becomes: How widely applicable is this result? The research team from the Universities of Oregon and Chicago expressed uncertainty regarding this point, but other studies indicate that historical contingency must play a prominent role in molecular evolution.

For example, the long-term evolution experiment conducted by Richard Lenski’s group at Michigan State University demonstrated that the emergence of citrate metabolism in E. coliunder aerobic conditions was historically contingent, predicated on a sequence of chance molecular events. (For more information, see the articles listed under “Resources.”)

Using simulations to monitor the evolution of a protein dubbed argT, researchers from the University of Pennsylvania showed that genetic mutations selected by the evolutionary process are dependent on previous mutations, and over time it becomes increasingly difficult to reverse mutational transformations.4 In other words, an amino acid substitution that occurs in a protein today and is accepted by the evolutionary process would most likely be deleterious if it occurred in the past (because of the central role permissive substitutions play in evolutionary history). Consequently, this mutational change would be selected against by the evolutionary process. One of the researchers involved in this study, Joshua Plotkin, stated,

“There is intrinsically a huge amount of contingency in evolution. Whatever mutations happen to come first set the stage for what other later mutations are permissible. Indeed, history channels evolution down a certain path. Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.”5

A Failed Prediction of the Evolutionary Paradigm

Because the evolutionary process is historically contingent, it seems unlikely that evolutionary processes would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes have been a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, that identical evolutionary outcomes are a characteristic feature of the biological realm.6 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

I regard the widespread occurrence of convergence to one of evolution’s failed predictions, and, as I told Kathy Emmons, a justifiable reason to be skeptical of the claim that evolutionary processes can fully explain the history, diversity, and design of life.

In an upcoming blog post, I will further explore the challenge convergence poses for the evolutionary paradigm.

Stay tuned… (or set your tape player to “record.”)

 

Resources

Endnotes

  1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–07, doi:10.1038/nature13410.
  2. Ibid., 207.
  3. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  4. Premal Shah, David McCandlish, and Joshua Plotkin, “Contingency and Entrenchment in Protein Evolution under Purifying Selection,” Proceedings of the National Academy of Sciences, USA 112 (June 2015): E3226–E3235, doi: 10.1073/pnas.1412933112.
  5. University of Pennsylvania, “Evolution Is Unpredictable and Irreversible, Biologists Show,” ScienceDaily,June 8, 2015, sciencedaily.com/releases/2015/06/150608213032.htm.
  6. 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).
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/20/historical-contingency-and-the-improbability-of-protein-evolution-part-2-(of-2)

Science News Flash: Stone Tool Use by Capuchin Monkeys Challenges Human Evolution

sciencenewsflashstonetoolusebycapuchin

BY FAZALE RANA – JULY 14, 2016

I love cashew nuts! Apparently, so do capuchin monkeys.

A team of scientists from Oxford University (in the UK) and the University of Sao Paulo (in Brazil) report that capuchin monkeys in the northeast forests of Brazil make sophisticated use of stone tools to extract cashew nuts from shells.1

These researchers claim that this find sheds light on the evolution of human behavior. However, I take a different view. I maintain that this discovery actually undermines the standard model for human evolution. At the same time, this work highlights human exceptionalism, which finds ready explanation in the biblical human origins account.2

Tools Engender New Scientific Possibilities

This discovery, reported in the journal Current Biology, has found its way into popular science outlets, spurring headlines such as “Scientists Unearthed a Trove of 700-Year-Old Stone Tools—Used by Monkeys.” And with good reason. It is the first archaeological evidence for the use of stone tools by nonhuman primates outside of Africa, suggesting a whole new arena of scientific investigation. Lydia Luncz, a member of the research team, stated, “We think we’re just at the beginning.”3

To get to cashew nuts, capuchins go through an elaborate process. These monkeys carefully select large flat sandstones and quartzite to use as an anvil and hammer, respectively. They transport these stones to the base of the cashew trees. There, they place the cashew nut on the flat anvil (which is about four times the size of the hammer) and carefully strike the shell with the hammer (which is about four times the size of an average stone) breaking it open so they can get to the nut inside. Once they are done with the tools, the capuchins leave them at the base of cashew trees. A walk through the forest reveals a number of cashew nut processing centers, established by these industrious creatures.

To determine how long capuchins have engaged in this behavior, the research team excavated beneath several cashew trees located in the Brazilian forest. They discovered stone tools at least 2 feet beneath the surface that date back to about 700 years old. The excavated tools had a dark organic residue on them. Analysis of the residue indicates that it is the leftover remnants of cashew nuts, confirming the use of these stones as tools. Based on the excavations, it appears that about 100 generations of capuchins have employed stone tools to extract cashews from shells. It is reasonable to think that this behavior extends even further back in time.

This discovery follows on the heels of earlier work by the same team. In a previous study, these scientists observed Burmese long-tailed macaques in Thailand using stone tools to crack open shellfish, crabs, and nuts. Excavations at macaque sites on the island of Piak Nam Yai have identified stone tools that are about 65 years in age, going back two generations.

The use of stone tools among nonhuman primates is not limited to capuchins and macaques. Researchers have also uncovered evidence for chimpanzee stone tool use in Africa that dates back to over 4,000 years ago.

It seems as if hominids aren’t the only primates to leave behind an archaeological record.

Tools Throw Evolution into Question

The use of stone tools by capuchins, macaques, and chimpanzees has important implications for the creation-evolution debate. The tools used by these nonhuman primates is reminiscent of tools used by hominids. The similar behavior of hominids, Great Apes, and Old and New World monkeys renders the activities of hominids much less remarkable. I wrote elsewhere about the implications of tool use by chimpanzees (see here). The point I raised applies to the use of stone tools by capuchins and macaques:

“Chimpanzee behavior is closer to what we infer about hominid behavior from the fossil record, particularly Homo habilis and Homo erectus. These creatures, too, made tools and engaged in hunting and scavenging activity. The temptation is to see hominid behavior as transitional, representing a path to modern human behavior. Yet the newly recognized behavior of chimpanzees distances the hominids from modern humans. Just because the habilines and erectines made tools and engaged in other remarkable behaviors doesn’t mean that they were ‘becoming human.’ Instead, their behavior appears to be increasingly animal-like, particularly when compared to chimp activities.”4

And, I would add, hominid behavior becomes even more animal-like when compared to the behavior of capuchins and macaques.

Resources
Who Was Adam? (book)
Chimpanzee’s Behavior Supports RTB’s Model for Humanity’s Origin” (article)
Chimpanzees’ Sleeping Habits Closer to Hominid Behavior Than to Humans’” (article)

Endnotes
  1. Michael Haslam et al., “Pre-Columbian Monkey Tools,” Current Biology 26 (July 2016): pR521–R522, doi:10.1016/j.cub.2016.05.046.
  2. RTB’s biblical creation model for human origins views the hominids as creatures, created by God’s divine fiat, possessing intelligence and emotional capacity. These animals were able to employ crude tools and even adopt some level of “culture,” much like baboons, gorillas, and chimpanzees. But they were not spiritual beings made in God’s image. That position—and all of the intellectual, relational, and symbolic capabilities that come with it—remains reserved for modern humans alone.
  3. Darryl Fears, “Scientists Unearthed a Trove of 700-Year-Old Stone Tools—Used by Monkeys,” The Washington Post, July 11, 2016, https://www.washingtonpost.com/news/animalia/wp/2016/07/11/in-brazil-scientists-unearth-a-trove-of-ancient-stone-tools-used-by-monkeys/.
  4. Fazale Rana, “Chimpanzees’ Sleeping Habits Closer to Hominid Behavior Than to Humans,’” Today’s New Reason to Believe (blog), Reasons to Believe, June 9, 2014, https://www.reasons.org/articles/chimpanzees-sleeping-habits-closer-to-hominid-behavior-than-to-humans.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/14/science-news-flash-stone-tool-use-by-capuchin-monkeys-challenges-human-evolution

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

historicalcontingencypart1

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)

Science News Flash: Reinterpretation of Sea Worm Fossil Challenges Evolution

sciencenewsflashreinterpretationofseaworm

BY FAZALE RANA – JULY 8, 2016

In a recent article published by the BBC, researchers from the University of Toronto announced the reinterpretation of an enigmatic fossil, Oesia disjuncta, now classifying this creature as a hemichordate.1 They also now think that tube-like structures, originally thought to be a type of seaweed, were made by Oesia.

This reinterpretation was based on the recovery of new fossil specimens from Marble Canyon in the Canadian Rockies. Oesia disjuncta is part of a fossil assemblage known as the Cambrian explosion, so researchers estimate the creature’s age to be around 510 million years old. (The Cambrian explosion refers to a dramatic event in life’s history in which 50 to 80 percent of all known animal phyla appear in a geological instant.)

According to lead researcher in the study, Karma Nanglu:

Hemichordates are central to our understanding of how deuterostomes evolved.2

I would partially agree with Nanglu: Hemichordate fossils are central to our understanding of life’s history; but instead of shedding light on evolutionary history, I would maintain that the appearance of this phylum during the Cambrian explosion creates problems for the evolutionary paradigm. (To learn why I hold this view see my article “Cambrian Flash.”) At the same time, this find adds to the evidence for the scientific credibility of the Genesis 1 creation account. (For details see my article “The ‘Great Unconformity’ and the Cambrian Explosion Conform to the Genesis 1 Creation Account.”)

For more on the Cambrian explosion, check out the following resources.

Endnotes

  1. Karma Nanglu et al., “Cambrian Suspension-Feeding Tubicolous Hemichordates,” BMC Biology 14 (July 2016): 56, doi: 10.1186/s12915-016-0271-4.
  2. “Sea Worm Fossil Gives Clues to ‘Common Ancestor,’” Science & Environment (blog), BBC News, July 7, 2016, https://www.bbc.com/news/science-environment-36724562.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/08/science-news-flash-reinterpretation-of-sea-worm-fossil-challenges-evolution

Adam and Eve: A Primordial Pair or a Population?

adamandeveaprimordialpair

BY FAZALE RANA – JULY 6, 2016

Today, one of the central science-faith issues facing evangelical Christianity centers around the historicity of Adam and Eve. Did Adam and Eve actually exist? Or are they merely mythical, functioning as theological constructs meant to represent every man and every woman? And if they did exist, were they the primordial pair that gave rise to all humanity? Or were they representatives, part of a population?

My ministry activities during the month of June reminded me of the importance of these questions. I participated in the Dabar Conference, which centered on “Reading Genesis in an Age of Science,” so naturally, there was much discussion about the identity of Adam and Eve. I also taught a weeklong intensive course for Southern Evangelical Seminary on the biblical and scientific perspectives on human origins. As part of the course, we explored the scientific case for Adam and Eve’s historicity and the importance of this idea for the Christian faith. And finally, at the end of the month, I taught at the RZIM Summer Institute, where we examined the relationship between the biblical account of human origins and the key tenets of Christian ethics.

Adam and Eve’s existence and relationship to humanity are not merely academic concerns. Instead, these questions influence key doctrines of the Christian faith such as: inerrancy, the image of God, the Fall, original sin, marriage, and the atonement. Because of the importance of a historical Adam and Eve to the Christian faith, it is important to be able to demonstrate the scientific credibility of the biblical view of human origins.

A Scientific Case for a Historical Adam and Eve

Part of the scientific support for the traditional biblical view comes from work in molecular anthropology. One of the most important advances in human origins research has been the use of DNA sequence data to gain insight into the origin and early history of humanity.

Of particular interest are the results of mitochondrial DNA and Y-chromosomal studies that trace humanity’s origin to single ancestral sequences referred to as “mitochondrial Eve” and “Y-chromosomal Adam.” These ancestral sequences correspond to single female and male individuals. I interpret mitochondrial Eve and Y-chromosomal Adam as pointers to the biblical Adam and Eve.

Many evolutionary biologists reject the notion that mitochondrial Eve and Y-chromosomal Adam were the original biblical couple. Instead, they argue that human beings originated as a population. Accordingly, there were many “Eves” and “Adams.” In other words, we descend from the two who were lucky enough for their genetic material to persist to the present. The genetic lines of the other first humans were lost over time.

Perhaps most challenging to the view that mitochondrial Eve and Y-chromosomal Adam are the biblical Adam and Eve are the population size estimates determined from human genetic diversity data. These methods all indicate that the initial human population size was never less than several thousand individuals. It is largely based on these results that evolutionary biologists argue that mitochondrial Eve and Y-chromosomal Adam weren’t the primordial pair.

5 Reasons Why Humanity Didn’t Begin as a Population

Evolutionary biologists argue for this mainstream idea (that there were many first humans, not just two), but I’m reluctant to accept these claims for a number of reasons.1

  1. The idea that humanity arose as a population is a theory-laden concept that is a necessary entailment of the evolutionary paradigm. Biologists view evolution as a population-level phenomenon. Populations evolve, individuals don’t. As a consequence, there can’t be a primordial pair—if one views human origins from an evolutionary framework. To put it another way, humans must have emerged from a population by definition.
  2. The methods used to determine population sizes rely on simplified and idealized mathematical models that are highly sensitive to input parameters. Because of that the population numbers need to be viewed as rough estimates, at best.
  3. These models do a poor job in taking into account the effects of population structure, migrations, and gene flow all of which can lead to misleading population size calculations.2
  4. Population size methods have not been validated. That is, there are not any studies that demonstrate that these methods produce accurate results for population size estimates, when applied to known situations. Studies in conservation biology suggest that these models don’t accurately predict genetic variability when the original population size is known. As a case in point, in three separate studies involving Mouflon sheep, Przewalski’s horses, and gray whales, genetic diversity (measured generations after the initial population) was much greater than expected based on the models.
  5. Other studies in conservation biology raise questions about the validity of the mathematical relationships that undergird the population size methods. In fact, these concerns prompted one research team to question if these problems invalidate population size estimates in humans. These researchers state, “Recently, however, Bazin et al. (2006) have argued that mtDNA variation is a poor indicator of population size in animals. . . . This raises the question of whether mtDNA is in fact a reliable predictor of human population size.”3

Did Humanity Begin as a Pair?

Because of the central importance of Adam and Eve’s historicity to the Christian faith, I am reluctant to embrace the idea that humanity began as a population, not a pair. But, I’m as equally reluctant to accept this scientific claim—mainstream or not—knowing that the population size measurements are based on simplified, idealized methods that struggle to take into account population dynamics that can influence population size estimates and haven’t been validated. Questions about the validity of the mathematical relationships that form the basis of these methods compound these problems. To put it another way: Even if I accepted the notion of common descent, I still wouldn’t be convinced that humans arose as a population because of the scientific questions that surround the population size estimates.

In my view, science has yet to falsify the notion that humanity descended from a primordial pair.

Resources

Endnotes
  1. Some of my concerns with population size estimates are also detailed in the article, Fazale Rana, “Were They Real? The Scientific Case for Adam and Eve,” Today’s New Reason to Believe (blog), Reasons to Believe, October 1, 2010, https://www.reasons.org/articles/were-they-real-the-scientific-case-for-adam-and-eve.
  2. For example, see Olivier Mazet et al., “On the Importance of Being Structured: Instantaneous Coalescence Rates and Human Evolution—Lessons for Ancestral Population Size Inference?” Heredity 116 (April 2016): 362–71, doi:10.1038/hdy.2015.104; Thomas Broquet et al., “Genetic Bottlenecks Driven by Population Disconnection,” Conservation Biology 24 (December 2010): 1596–1605, doi:10.1111/j.1523-1739.2010.01556.x.
  3. Quentin Atkinson, Russell Gray, and Alexei Drummond, “mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory,” Molecular Biology and Evolution 25 (February 2008): 468–74, doi:10.1093/molbev/msm277.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/06/adam-and-eve-a-primordial-pair-or-a-population