Tag: mitochondria

ATP Transport Challenges the Evolutionary Origin of Mitochondria

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By Fazale Rana – August 21, 2019

In high school, I spent most Sunday mornings with my family gathered around the TV watching weekly reruns of the old Abbott and Costello movies.

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Image: Bud Abbott and Lou Costello. Image credit: Wikipedia

One of my favorite routines has the two comedians trying to help a woman get her parallel-parked car out of a tight parking spot. As Costello takes his place behind the wheel, Abbott tells him to “Go ahead and back up.” And of course, confusion and hilarity follow as Costello repeatedly tries to clarify if he is to “go ahead” or “back up,” finally yelling, “Will you please make up your mind!”

As it turns out, biologists who are trying to account for the origin of mitochondria (through an evolutionary route) are just as confused about directions as Costello. Specifically, they are trying to determine which direction ATP transport occurred in the evolutionary precursors to mitochondria (referred to as pre-mitochondria).

In an attempt to address this question, a research team from the University of Virginia (UVA) has added to the frustration, raising new challenges for evolutionary explanations for the origin of mitochondria. Their work threatens to drive the scientific community off the evolutionary route into the ditch when it comes to explaining the origin of eukaryotic cells.1

To fully appreciate the problems this work creates for the endosymbiont hypothesis, a little background is in order. (For those familiar with the evidence for the endosymbiont hypothesis, you may want to skip ahead to The Role of Mitochondria.)

The Endosymbiont Hypothesis

Most biologists believe that the endosymbiont hypothesis serves as the best explanation for the origin of complex cells.

According to this idea, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe.

The “poster children” of the endosymbiont hypothesis are mitochondria. Presumably, the mitochondria started its evolutionary journey as an endosymbiont. Evolutionary biologists believe that once engulfed by the host cell, this microbe took up permanent residency, growing and dividing inside the host. Over time, the endosymbiont and the host became mutually interdependent, with the endosymbiont providing a metabolic benefit for the host cell (such as providing a source of ATP). In turn, the host cell provided nutrients to the endosymbiont. Presumably, the endosymbiont gradually evolved into an organelle through a process referred to as genome reduction. This reduction resulted when genes from the endosymbiont’s genome were transferred into the genome of the host organism, generating the mitonuclear genome.

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Image: Endosymbiont Hypothesis. Image credit: Wikipedia

Evidence for the Endosymbiont Hypothesis

Much of the evidence for the endosymbiotic origin of mitochondria centers around the similarity between mitochondria and bacteria. These organelles are about the same size and shape as typical bacteria and have a double membrane structure like gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

Biochemical evidence also exists for the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

The presence of the unique lipid, cardiolipin, in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. This important lipid component of bacterial inner membranes is absent in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider cardiolipin a signature lipid for mitochondria and a vestige of the organelle’s evolutionary history.

The Role of Mitochondria

Mitochondria serve cells in a number of ways, including:

  • Calcium storage
  • Calcium signaling
  • Signaling with reactive oxygen species
  • Regulation of cellular metabolism
  • Heat production
  • Apoptosis

Arguably one of the most important functions of mitochondria relates to their role in energy conversion. This organelle generates ATP molecules by processing the breakdown products of glycolysis through the tricarboxylic acid cycle and the electron transport chain.

Biochemists refer to ATP as a high-energy compound—it serves as an energy currency for the cell, and most cellular processes are powered by ATP. One way that ATP provides energy is through its conversion to ADP and an inorganic phosphate molecule. This breakdown reaction liberates energy that can be coupled to cellular activities that require energy.

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Image: The ATP/ADP Reaction Cycle. Image credit: Shutterstock

ATP Production and Transport

The enzyme complex ATP synthase, located in the mitochondrial inner membrane, generates ATP from ADP and inorganic phosphate, using a proton gradient generated by the flow of electrons through the electron transport chain. As ATP synthase generates ATP, it deposits this molecule in the innermost region of the mitochondria (called the matrix or the lumen).

In order for ATP to become available to power cellular processes, it has to be transported out of the lumen and across the mitochondrial inner membrane into the cytoplasm. Unfortunately, the inner mitochondrial membrane is impermeable to ATP (and ADP). In order to overcome this barrier, a protein embedded in the inner membrane called ATP/ADP translocase performs the transport operation. Conveniently, for every molecule of ATP transported out of the lumen, a molecule of ADP is transported from the cytoplasm into the lumen. In turn, this ADP is converted into ATP by ATP synthase.

Because of the importance of this process, copies of ATP/ADP translocase comprises 10% of the proteins in the inner membrane.

If this enzyme doesn’t function properly, it will result in mitochondrial myopathies.

The Problem ATP Transport Causes for The Endosymbiont Hypothesis

Two intertwined questions confronting the endosymbiont hypothesis relate to the evolutionary driving force behind symbiogenesis and the nature of pre-mitochondria.

Traditionally, evolutionary biologists have posited that the host cell was an anaerobe, while the endosymbiont was an aerobic microbe, producing ATP from lactic acid generated by the host cell. (Lactic acid is the breakdown product of glucose in the absence of oxygen).

But, as cell biologist Franklin Harold points out, this scenario has an inherent flaw. Namely, if the endosymbiont is producing ATP necessary for its survival from host cell nutrients, why would it relinquish some—or even all—of the ATP it produces to the host cell?

According to Harold, “The trouble is that unless the invaders share their bounty with the host, they will quickly outgrow him; they would be pathogens, not symbionts.”2

And, the only way they could share their bounty with the host cell is to transport ATP from the engulfed cell’s interior to the host cell’s cytoplasm. While mitochondria accomplish this task with the ATP/ADP translocase, there is no good reason to think that the engulfed cell would do this. Given the role ATP plays as the energy currency in the cell and the energy that is expended to make this molecule, there is no advantage for the engulfed cell to pump ATP from its interior to the exterior environment.

Harold sums up the problem this way: “Such a carrier would not have been present in the free-living symbiont but must have been acquired in the course of its enslavement; it cannot be called upon to explain the initial benefits of the association.”3

In other words, currently, there is no evolutionary explanation for why the ATP/ADP translocase in the mitochondrial inner membrane—a protein central to the role of mitochondria in eukaryotic cells—pumps ATP from the lumen to the cytoplasm.

Two Alternative Models

This problem has led evolutionary biologists to propose two alternative models to account for the evolutionary driving force behind symbiogenesis: 1) the hydrogen hypothesis; and 2) the oxygen scavenger hypothesis.

The hydrogen hypothesis argues that the host cell was a methanogenic member of archaea that consumed hydrogen gas and the symbiont was a hydrogen-generating alpha proteobacteria.

The oxygen-scavenging model suggests that the engulfed cell was aerobic, and because it used oxygen, it reduced the amount of oxygen in the cytoplasm of the host cell, thought to be an anaerobe.

Today, most evolutionary biologists prefer the hydrogen hypothesis—in part because the oxygen scavenger model, too, has a fatal flaw. As Harold points out, “This [oxygen scavenger model], too, is dubious, because respiration generates free radicals that are known to be a major source of damage to cellular membranes and genes.”4

Moving Forward, Or Moving Backward?

To help make headway, two researchers from UVA attempted to reconstruct the evolutionary precursor to mitochondria, dubbed pre-mitochondria.

Operating within the evolutionary framework, these two investigators reconstructed the putative genome of pre-mitochondria using genes in the mitochondrial genome and genes from the nuclear genomes of organisms they believe were transferred to the nucleus during the process of symbiogenesis. (Genes that clustered with alphaproteobacterial genes were deemed to be of mitochondrial origin.)

Based on their reconstruction, they conclude that the original engulfed cell actually used its ATP/ADP translocase to import ATP from the host cell cytoplasm into its interior, exchanging the ATP for an ADP. This is the type of ATP/ADP translocase found in obligate intracellular parasites alive today.

According to the authors, this means that:

“Pre-mitochondrion [was] an ‘energy scavenger’ and suggests an energy parasitism between the endosymbiont and its host at the origin of the mitochondria. . . . This is in sharp contrast with the current role of mitochondria as the cell’s energy producer and contradicts the traditional endosymbiotic theory that the symbiosis was driven by the symbiont supplying the host ATP.”5

The authors speculate that at some point during symbiogenesis the ATP/ADP translocase “went ahead and backed up,” reversing direction. But, this explanation is little more than a just-so story with no evidential support. Confounding their conjecture is their discovery that the ATP/ADP translocase found in mitochondria is evolutionarily unrelated to the ATP/ADP translocases found in obligate intracellular parasites.

The fact that the engulfed cell was an obligate intracellular parasite not only brings a halt to the traditional version of the endosymbiont hypothesis, it flattens the tires of both the oxygen scavenger model and hydrogen hypothesis. According to Wang and Wu (the UVA investigators):

“Our results suggest that mitochondria most likely originated from an obligate intracellular parasite and not from a free-living bacterium. This has important implications for our understanding of the origin of mitochondria. It implies that at the beginning of the endosymbiosis, the bacterial symbiont provided no benefits whatsoever to the host. Therefore we argue that the benefits proposed by various hypotheses (e.g, oxygen scavenger and hydrogen hypotheses) are irrelevant in explaining the establishment of the initial symbiosis.”6

If the results of the analysis by the UVA researchers stand, it leaves evolutionary biologists with no clear direction when it comes to determining the evolutionary driving force behind the early stages of symbiogenesis or the evolutionary route to mitochondria.

It seems that the more evolutionary biologists probe the question of mitochondrial origins, the more confusion and uncertainty results. In fact, there is not a coherent compelling evolutionary explanation for the origin of eukaryotic cells—one of the key events in life’s history. The study by the UVA investigators (along with other studies) casts aspersions on the most prominent evolutionary explanations for the origin of eukaryotes, justifying skepticism about the grand claim of the evolutionary paradigm: namely, that the origin, design, and history of life can be explained exclusively through evolutionary processes.

In light of this uncertainty, can the origin of mitochondria, and hence eukaryotic cells, be better explained by a creation model? I think so, but for many scientists this is a road less traveled.

Resources

Challenges to the Endosymbiont Hypothesis:

In Support of a Creation Model for the Origin of Eukaryotic Cells:

ATP Production and the Case for a Creator:

Endnotes
  1. Zhang Wang and Martin Wu, “Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite,” PLOS One 9, no. 10 (October 15, 2014): e110685, doi:10.1371/journal.pone.0110685.
  2. Franklin M. Harold, In Search of Cell History: The Evolution of Life’s Building Blocks (Chicago, IL: The University of Chicago Press, 2014), 131.
  3. Harold, In Search of Cell History, 131.
  4. Harold, In Search of Cell History, 132.
  5. Wang and Wu, “Phylogenomic Reconstruction.”
  6. Wang and Wu, “Phylogenomic Reconstruction.”

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

Why Mitochondria Make My List of Best Biological Designs

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BY FAZALE RANA – MAY 1, 2019

A few days ago, I ran across a BuzzFeed list that catalogs 24 of the most poorly designed things in our time. Some of the items that stood out from the list for me were:

  • serial-wired Christmas lights
  • economy airplane seats
  • clamshell packaging
  • juice cartons
  • motion sensor faucets
  • jewel CD packaging
  • umbrellas

What were people thinking when they designed these things? It’s difficult to argue with BuzzFeed’s list, though I bet you might add a few things of your own to their list of poor designs.

If biologists were to make a list of poorly designed things, many would probably include…everything in biology. Most life scientists are influenced by an evolutionary perspective. Thus, they view biological systems as inherently flawed vestiges cobbled together by a set of historically contingent mechanisms.

Yet as our understanding of biological systems improves, evidence shows that many “poorly designed” systems are actually exquisitely assembled. It also becomes evident that many biological designs reflect an impeccable logic that explains why these systems are the way they are. In other words, advances in biology reveal that it makes better sense to attribute biological systems to the work of a Mind, not to unguided evolution.

Based on recent insights by biochemist and origin-of-life researcher Nick Lane, I would add mitochondria to my list of well-designed biological systems. Lane argues that complex cells and, ultimately, multicellular organisms would be impossible if it weren’t for mitochondria.1(These organelles generate most of the ATP molecules used to power the operations of eukaryotic cells.) Toward this end, Lane has demonstrated that mitochondria’s properties are just-right for making complex eukaryotic cells possible. Without mitochondria, life would be limited to prokaryotic cells (bacteria and archaea).

To put it another way, Nick Lane has shown that prokaryotic cells could never evolve the complexity needed to form cells with complexity akin to the eukaryotic cells required for multicellular organisms. The reason has to do with bioenergetic constraints placed on prokaryotic cells. According to Lane, the advent of mitochondria allowed life to break free from these constraints, paving the way for complex life.

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Figure 1: A Mitochondrion. Image credit: Shutterstock

Through Lane’s discovery, mitochondria reveal exquisite design and logical architecture and operations. Yet this is not necessarily what I (or many others) would have expected if mitochondria were the result of evolution. Rather, we’d expect biological systems to appear haphazard and purposeless, just good enough for the organism to survive and nothing more.

To understand why I (and many evolutionary biologists) would hold this view about mitochondria and eukaryotic cells (assuming that they were the product of evolutionary processes), it is necessary to review the current evolutionary explanation for their origins.

The Endosymbiont Hypothesis

Most biologists believe that the endosymbiont hypothesis is the best explanation for the origin of complex eukaryotic cells. This hypothesis states that complex cells originated when single-celled microbes formed symbiotic relationships. “Host” microbes (most likely archaea) engulfed other archaea and/or bacteria, which then existed inside the host as endosymbionts.

The presumption, then, is that organelles, including mitochondria, were once endosymbionts. Evolutionary biologists believe that, once engulfed, the endosymbionts took up permanent residency within the host cell and even grew and divided inside the host. Over time, the endosymbionts and the host became mutually interdependent. For example, the endosymbionts provided a metabolic benefit for the host cell, such as serving as a source of ATP. In turn, the host cell provided nutrients to the endosymbionts. The endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism.

Based on this scenario, there is no real rationale for the existence of mitochondria (and eukaryotic cells). They are the way they are because they just wound up that way.

But Nick Lane’s insights suggest otherwise.

Lane’s analysis identifies a deep-seated rationale that accounts for the features of mitochondria (and eukaryotic cells) related to their contribution to cellular bioenergetics. To understand why mitochondria and eukaryotic cells are the way they are, we first need to understand why prokaryotic cells can never evolve into large complex cells, a necessary step for the advent of complex multicellular organisms.

Bioenergetics Constraints on Prokaryotic Cells

Lane has discovered that bioenergetics constraints keep bacterial and archaeal cells trapped at their current size and complexity. Key to discovering this constraint is a metric Lane devised called Available Energy per Gene (AEG). It turns out that AEG in eukaryotic cells can be as much as 200,000 times larger than the AEG in prokaryotic cells. This extra energy allows eukaryotic cells to engage in a wide range of metabolic processes that support cellular complexity. Prokaryotic cells simply can’t afford such processes.

An average eukaryotic cell has between 20,000 to 40,000 genes; a typical bacterial cell has about 5,000 genes. Each gene encodes the information the cell’s machinery needs to make a distinct protein. And proteins are the workhorse molecules of the cell. More genes mean a more diverse suite of proteins, which means greater biochemical complexity.

So, what is so special about eukaryotic cells? Why don’t prokaryotic cells have the same AEG? Why do eukaryotic cells have an expanded repertoire of genes and prokaryotic cells don’t?

In short, the answer is: mitochondria.

On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells. Eukaryotic cells’ larger size allows for their greater complexity. Lane estimates that for a prokaryotic cell to scale up to this volume, its radius would need to increase 25-fold and its surface area 625-fold.

Because the plasma membrane of bacteria is the site for ATP synthesis, increases in the surface area would allow the hypothetically enlarged bacteria to produce 625 times more ATP. But this increased ATP production doesn’t increase the AEG. Why is that?

The bacteria would have to produce 625 times more proteins to support the increased ATP production. Because the cell’s machinery must access the bacteria’s DNA to make these proteins, a single copy of the genome is insufficient to support all of the activity centered around the synthesis of that many proteins. In fact, Lane estimates that for bacteria to increase its ATP production 625-fold, it would require 625 copies of its genome. In other words, even though the bacteria increased in size, in effect, the AEG remains unchanged.

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Figure 2: ATP Production at the Cell Membrane Surface. Image credit: Shutterstock

Things become more complicated when factoring in cell volume. When the surface area (and concomitant ATP production) increase by a factor of 625, the volume of the cell expands 15,000 times. To satisfy the demands of a larger cell, even more copies of the genome would be required, perhaps as many as 15,000. But energy production tops off at a 625-fold increase. This mismatch means that the AEG drops by 25 percent per gene. For a genome consisting of 5,000 genes, this drop means that a bacterium the size of a eukaryotic cell would have about 125,000 times less AEG than a typical eukaryotic cell and 200,000 times less AEG when compared to eukaryotes with genome sizes approaching 40,000 genes.

Bioenergetic Freedom for Eukaryotic Cells

Thanks to mitochondria, eukaryotic cells are free from the bioenergetic constraints that ensnare prokaryotic cells. Mitochondria generate the same amount of ATP as a bacterial cell. However, their genome consists of only 13 proteins, thus the organelle’s ATP demand is low. The net effect is that the mitochondria’s AEG skyrockets. Furthermore, mitochondrial membranes come equipped with an ATP transport protein that can pump the vast excess of ATP from the organelle interior into the cytoplasm for the eukaryotic cell to use.

To summarize, mitochondria’s small genome plus its prodigious ATP output are the keys to eukaryotic cells’ large AEG.

Of course, this raises a question: Why do mitochondria have genomes at all? Well, as it turns out, mitochondria need genomes for several reasons (which I’ve detailed in previous articles).

Other features of mitochondria are also essential for ATP production. For example, cardiolipinin the organelle’s inner membrane plays a role in stabilizing and organizing specific proteinsneeded for cellular energy production.

From a creation perspective it seems that if a Creator was going to design a eukaryotic cell from scratch, he would have to create an organelle just like a mitochondrion to provide the energy needed to sustain the cell’s complexity with a high AEG. Far from being an evolutionary “kludge job,” mitochondria appear to be an elegantly designed feature of eukaryotic cells with a just-right set of properties that allow for the cellular complexity needed to sustain complex multicellular life. It is eerie to think that unguided evolutionary events just happened to traverse the just-right evolutionary path to yield such an organelle.

As a Christian, I see the rationale that undergirds the design of mitochondria as the signature of the Creator’s handiwork in biology. I also view the anthropic coincidence associated with the origin of eukaryotic cells as reason to believe that life’s history has purpose and meaning, pointing toward the advent of complex life and humanity.

So, now you know why mitochondria make my list.

Resources

Endnotes
  1. Nick Lane, “Bioenergetic Constraints on the Evolution of Complex Life,” Cold Spring Harbor Perspectives in Biology 6, no. 5 (May 2014): a015982, doi:10.1101/cshperspect.a015982.

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/05/01/why-mitochondria-make-my-list-of-best-biological-designs

The Endosymbiont Hypothesis: Things Aren’t What They Seem to Be

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BY FAZALE RANA – AUGUST 29, 2018

Sometimes, things just aren’t what they seem to be. For example, when it comes to the world of biology:

  • Fireflies are not flies; they are beetles
  • Prairie dogs are not dogs; they are rodents
  • Horned toads are not toads; they are lizards
  • Douglas firs are not firs; they are pines
  • Silkworms are not worms; they are caterpillars
  • Peanuts are not nuts; they are legumes
  • Koala bears are not bears; they are marsupials
  • Guinea pigs are not from Guinea and they are not pigs; they are rodents from South America
  • Banana trees are not trees; they are herbs
  • Cucumbers are not vegetables; they are fruit
  • Mexican jumping beans are not beans; they are seeds with a larva inside

And . . . mitochondria are not alphaproteobacteria. In fact, evolutionary biologists don’t know what they are—at least, if recent work by researchers from Uppsala University in Sweden is to be taken seriously.1

As silly as this list may be, evolutionary biologists are not amused by this latest insight about the identity of mitochondria. Uncertainty about the evolutionary origin of mitochondria removes from the table one of the most compelling pieces of evidence for the endosymbiont hypothesis.

A cornerstone idea within the modern evolutionary framework, biology textbooks often present the endosymbiont hypothesis as a well-evidenced, well-established evolutionary explanation for the origin of complex cells (eukaryotic cells). Yet, confusion and uncertainty surround this idea, as this latest discovery attests. To put it another way: when it comes to the evolutionary explanation for the origin of complex cells in biology textbooks, things aren’t what they seem.

The Endosymbiont Hypothesis

Most evolutionary biologists believe that the endosymbiont hypothesis is the best explanation for one of the key transitions in life’s history—namely, the origin of complex cells from bacteria and archaea. Building on the ideas of Russian botanist Konstantin Mereschkowski, Lynn Margulis (1938–2011) advanced the endosymbiont hypothesis to explain the origin of eukaryotic cells in the 1960s.

Since that time, Margulis’s ideas on the origin of complex cells have become an integral part of the evolutionary paradigm. Many life scientists find the evidence for this hypothesis compelling; consequently, they view it as providing broad support for an evolutionary explanation for the history and design of life.

According to this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. (Ingested cells that take up permanent residence within other cells are referred to as endosymbionts.)

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The Evolution of Eukaryotic Cells According to the Endosymbiont Hypothesis

Image source: Wikipedia

Presumably, organelles such as mitochondria were once endosymbionts. Evolutionary biologists believe that once taken inside the host cell, the endosymbionts took up permanent residence, with the endosymbiont growing and dividing inside the host. Over time, endosymbionts and hosts became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. The endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from endosymbionts’ genomes were transferred into the genome of the host organism. Eventually, the host cell evolved machinery to produce proteins needed by the former endosymbiont and processes to transport those proteins into the organelle’s interior.

Evidence for the Endosymbiont Hypothesis

The morphological similarity between organelles and bacteria serve as one line of evidence for the endosymbiont hypothesis. For example, mitochondria are about the same size and shape as a typical bacterium and they have a double membrane structure like the gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

Biochemical evidence also seems to support the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. Additionally, biologists also take the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

The presence of the unique lipid cardiolipin in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. Cardiolipin is an important lipid component of bacterial inner membranes. Yet, it is not found in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider it a signature lipid for mitochondria and a vestige of this organelle’s evolutionary history.

But, as compelling as these observations may be, for many evolutionary biologists phylogenetic analysis provides the most convincing evidence for the endosymbiont hypothesis. Evolutionary trees built from the DNA sequences of mitochondria, bacteria, and archaea place these organelles among a group of microbes called alphaproteobacteria. And, for many (but not all) evolutionary trees, mitochondria cluster with the bacteria, Rickettsiales.For evolutionary biologists, these results mean that the endosymbionts that eventually became the first mitochondria were alphaproteobacteria. If mitochondria were notevolutionarily derived from alphaproteobacteria, why would the DNA sequences of these organelles group with these bacteria in evolutionary trees?

But . . . Mitochondria Are Not Alphaproteobacteria

Even though evolutionary biologists seem certain about the phylogenetic positioning of mitochondria among the alphaproteobacteria, there has been an ongoing dispute as to the precise positioning of mitochondria in evolutionary trees, specifically whether or not mitochondria group with Rickettsiales. Looking to bring an end to this dispute, the Uppsula University research team developed a more comprehensive data set to build their evolutionary trees, with the hope that they could more precisely locate mitochondria among alphaproteobacteria. The researchers point out that the alphaproteobacterial genomes used to construct evolutionary trees stem from microbes found in clinical and agricultural settings, which is a small sampling of the alphaproteobacteria found in nature. Researchers knew this was a limitation, but, up to this point, this was the only DNA sequence data available to them.

To avoid the bias that arises from this limited data set, the researchers screened databases of DNA sequences collected from the Pacific and Atlantic Oceans for undiscovered alphaproteobacteria. They uncovered twelve new groups of alphaproteobacteria. In turn, they included these new genome sequences along with DNA sequences from previously known alphaproteobacterial genomes to build a new set of evolutionary trees. To their surprise, their analysis indicates that mitochondria are not alphaproteobacteria.

Instead, it looks like mitochondria belong to a side branch that separated from the evolutionary tree before alphaproteobacteria emerged. Adding to their surprise, the research team was unable to identify any bacterial species alive today that would group with mitochondria.

To put it another way: the latest study indicates that evolutionary biologists have no candidate for the evolutionary ancestor of mitochondria.

Does the Endosymbiont Hypothesis Successfully Account for the Origin of Mitochondria?

Evolutionary biologists suggest that there’s compelling evidence for the endosymbiont hypothesis. But when researchers attempt to delineate the details of this presumed evolutionary transition, such as the identity of the original endosymbiont, it becomes readily apparent that biologists lack a genuine explanation for the origin of mitochondria and, in a broader context, the origin of eukaryotic cells.

As I have written previously, the problems with the endosymbiont hypothesis are not limited to the identity of the evolutionary ancestor of mitochondria. They are far more pervasive, confounding each evolutionary step that life scientists envision to be part of the emergence of complex cells. (For more examples, see the Resources section.)

When it comes to the endosymbiont hypothesis, things are not what they seem to be. If mitochondria are not alphaproteobacteria, and if evolutionary biologists have no candidate for their evolutionary ancestor, could it be possible that they are the handiwork of the Creator?

Resources

Endnotes

  1. Joran Martijn et al., “Deep Mitochondrial Origin Outside the Sampled Alphaproteobacteria,” Nature 557 (May 3, 2018): 101–5, doi:10.1038/s41586-018-0059-5.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/08/29/the-endosymbiont-hypothesis-things-aren-t-what-they-seem-to-be

Mitochondria’s Deviant Genetic Code: Evolution or Creation?

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BY FAZALE RANA – APRIL 18, 2018

When I was in high school, I had the well-deserved reputation of being a wise guy—though the people who knew me then might have preferred to call me a wise—, instead. Either way, for being a wise guy, I sure didn’t display much wisdom during my teenage years.

I would like to think that I am wiser today. But, the little wisdom I do possess didn’t come easy. To quote singer and songwriter, Helen Reddy, “It’s wisdom born of pain.”

Life’s hardships sure have a way of teaching you lessons. But, I also learned that there is a shortcut to gaining wisdom—if you are wise enough to recognize it. (See what I did there?) It is better to solicit the advice of wise people than to gain wisdom through life’s bitter experiences. And, perhaps there was no wiser person ever than Solomon. Thankfully, Solomon’s wisdom was captured in the book of Proverbs. Many of life’s difficulties can be sidestepped if we are willing to heed Solomon’s advice.

Solomon gained his wisdom through observation and careful reflection. But, his wisdom also came through divine inspiration, and according to Solomon, it was through wisdom that God created the world in which we live (Proverbs 8:22–31). And, it is out of this wisdom that the Holy Spirit inspired Solomon to offer the insights found in the Proverbs.

In Psalm 104, the Psalmist (presumably David) echoes the same idea as Solomon: God created our world through wisdom. The Psalmist writes:

How many are your works, Lord!

In wisdom you made them all;

Based on Proverbs 8 and Psalm 104, I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency but also display undeniable wisdom. In my view, that wisdom should be reflected in the elegance, cleverness, and ingenuity of the designs seen throughout nature. Designs that reflect an underlying purpose. And these features are exactly what we observe when we study the biological realm—as demonstrated by recent work on aquatic mammal body size conducted by investigators from Stanford University.1

Body Sizes of Aquatic Mammals

Though the majority of the world’s mammals live in terrestrial habitats, the most massive members of this group reside in Earth’s oceans. For evolutionary biologists, common wisdom has it that the larger size of aquatic mammals reflects fewer evolutionary constraints on their body size because they live in the ocean. After all, the ocean habitat is more expansive than those found on land, and aquatic animals don’t need to support their weight because they are buoyed by the ocean.

As it turns out, common wisdom is wrong in this case. Through the use of mathematical modeling (employing body mass data from about 3,800 living species of aquatic mammals and around 3,000 fossil species), the research team from Stanford learned that living in an aquatic setting imposes tight constraints on body size, much more so than when animals live on land. In fact, they discovered (all things being equal) that the optimal body mass for aquatic mammals is around 1,000 pounds. Interestingly, the body mass distributions for members of the order Sirenia (dugongs and manatees), and the clades Cetacea (whales and dolphins), and Pinnipeds (sea lions and seals) cluster near 1,000 pounds.

Scientists have learned that the optimal body mass of aquatic mammals displays an underlying biological rationale and logic. It reflects a trade-off between two opposing demands: heat retention and caloric intake. Because the water temperatures of the oceans are below mammals’ body temperatures, heat retention becomes a real problem. Mammals with smaller bodies can’t consume enough food to compensate for heat loss to the oceans, and they don’t have the mass to retain body heat. The way around this problem is to increase their body mass. Larger bodies do a much better job at retaining heat than do smaller bodies. But, the increase in body mass can’t go unchecked. Maintaining a large body requires calories. At some point, metabolic demands outpace the capacity for aquatic mammals to feed, so body mass has to be capped (near 1,000 pounds).

The researchers noted a few exceptions to this newly discovered “rule.” Baleen whales have a body mass that is much greater than 1,000 pounds. But, as the researchers noted, these creatures employ a unique feeding mechanism that allows them to consume calories needed to support their massive body sizes. Filter feeding is a more efficient way to consume calories than hunting prey. The other exception is creatures such as otters. The researchers believe that their small size reflects a lifestyle that exploits both aquatic and terrestrial habitats.

Argument for God’s Existence from Wisdom

The discovery that the body mass of aquatic mammals has been optimized is one more example of the many elegant designs found in biological systems—designs worthy to be called the Creator’s handiwork. However, from my perspective, this optimization also reflects the Creator’s sagacity as he designed mammals for the purpose of living in the earth’s oceans.

But, instead of relying on intuition alone to make a case for a Creator, I want to present a formal argument for God’s existence based on the wisdom of biology’s designs. To make this argument, I follow after philosopher Richard Swinburne’s case for God’s existence based on beauty. Swinburne argues, “If God creates a universe, as a good workman he will create a beautiful universe. On the other hand, if the universe came into existence without being created by God, there is no reason to suppose that it would be a beautiful universe.”2 In other words, the beauty in the world around us signifies the Divine.

In like manner, if God created the universe, including the biological realm, we should expect to see wisdom permeating the designs in nature. On the other hand, if the universe came into being without God’s involvement, then there is no reason to think that the designs in nature would display a cleverness and ingenuity that affords a purpose—a sagacity, if you will. In fact, evolutionary biologists are quick to assert that most biological designs are flawed in some way. They argue that there is no purpose that undergirds biological systems. Why? Because evolutionary processes do not produce biological systems from scratch, but from preexisting systems that are co-opted through a process dubbed exaptation (by the late evolutionary biologist Stephen Jay Gould), and then modified by natural selection to produce new designs.3 According to biologist Ken Miller:

“Evolution . . . does not produce perfection. The fact that every intermediate stage in the development of an organ must confer a selective advantage means that the simplest and most elegant design for an organ cannot always be produced by evolution. In fact, the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification.”4

And yet we see designs in biology that are not just optimized, but characterized by elegance, cleverness, and ingenuity—wisdom.

Truly, God is a wise guy.

Resources

Endnotes

  1. William Gearty, Craig R. McClain, and Jonathan L. Payne, “Energetic Tradeoffs Control the Size Distribution of Aquatic Mammals,” Proceedings of the National Academy of Sciences USA (March 2018): doi:10.1073/pnas.1712629115.
  2. Richard Swinburne, The Existence of God, 2nd ed. (New York: Oxford University Press, 2004), 190–91.
  3. Stephen Jay Gould and Elizabeth S. Vrba, “Exaptation: A Missing Term in the Science of Form,” Paleobiology8 (January 1, 1982): 4–15, doi:10.1017/S0094837300004310.
  4. Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994): 24–32.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/04/11/mitochondria-s-deviant-genetic-code-evolution-or-creation

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

reactiveoxygenspeciesharbingers

BY FAZALE RANA – DECEMBER 14, 2016

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

–Ulrich Theopold

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

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

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

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

ROS Generation and the Case for Evolution

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

reactive-oxygen-species-1
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

Can a Creation Model Explain the Origin of Mitochondria?

canacreationmodelexplaintheorigin

BY FAZALE RANA – NOVEMBER 23, 2016

Some called her a scientific heretic. Others were a bit more kind, describing her as a maverick.

Lynn Margulis (1938–2011) earned her reputation in the late 1960s when she proposed the endosymbiont hypothesis for the origin of eukaryotic cells. Because her ideas about evolution didn’t conform to Darwinian principles, evolutionary biologists summarily dismissed her idea out of hand and then went on to ignore her work for a couple of decades. She was ultimately vindicated, however, as the endosymbiont hypothesis gradually gained acceptance.

Today, Margulis’s proposal has become a cornerstone idea of the evolutionary paradigm and is taught in introductory high school and college biology courses. This classroom exposure explains why I am often asked about the endosymbiont hypothesis when I speak on university campuses. Many first-year biology students and professional life scientists alike find the evidence for this idea compelling, and consequently view it as providing broad support for an evolutionary explanation for the history and design of life.

Yet, new work by biochemists from Cambridge University make it possible to account for the origin of eukaryotic cells from a creation model perspective, providing a response to the endosymbiont hypothesis.1

The Endosymbiont Hypothesis

According to this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. (Ingested cells that take up permanent residence within other cells are referred to as endosymbionts.)

Accordingly, organelles, such as mitochondria, were once endosymbionts. Once taken inside the host cell, the endosymbionts presumably took up permanent residency within the host, with the endosymbionts growing and dividing inside the host. Over time, the endosymbionts and the host became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. The endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism. Eventually, the host cell evolved both the machinery to produce the proteins needed by the former endosymbiont and the processes needed to transport those proteins into the organelle’s interior.

Evidence for the Endosymbiont Hypothesis

The main line of evidence for the endosymbiont hypothesis is the similarity between organelles and bacteria. For example, mitochondria—which are believed to be descended from a group of α-proteobacteria—are about the same size and shape as a typical bacterium and have a double membrane structure like gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

There is also biochemical evidence for the endosymbiont hypothesis. Evolutionary biologists view the existence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. Additionally, the biochemical similarities between mitochondrial and bacterial genomes are taken as further evidence for the evolutionary origin of these organelles.

The presence of the unique lipid called cardiolipin in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. Cardiolipin is an important lipid component of bacterial inner membranes, yet it is not found in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider it a signature lipid for mitochondria and a vestige of this organelle’s evolutionary history.

A Creation Model Perspective on Mitochondria

So, as a creationist, how do I make sense of the evidence for the endosymbiont hypothesis?

Instead of focusing my efforts on refuting the endosymbiont hypothesis, here, I take a different approach. I maintain that it is reasonable to view eukaryotic cells as the work of a Creator, with the shared similarities between mitochondria and bacteria reflecting common design rather than common descent.

However, to legitimately interpret mitochondrial origins from a creation model perspective, there must be a reason for the biochemical similarities between mitochondria and bacteria. Previously, I wrote about discoveries that provide a rationale for why mitochondria have their own genomes. (See “Resources.”) Thanks to recent research advances, an explanation now exists for why the mitochondrial inner membranes harbor cardiolipin.

Cardiolipin’s Function

Previous studies identified close associations between cardiolipin and a number of proteins found in the mitochondrial inner membrane. These proteins play a role in harvesting energy for the cell to use. Compared to other lipid components found in the inner membrane, cardiolipin appears to preferentially associate with these proteins. Evidence indicates that cardiolipin helps to stabilize the structures of these proteins and serves to organize the proteins into larger functional complexes within the membrane.2 In fact, several studies have implicated defects in cardiolipin metabolism in the onset of a number of neuromuscular disorders.

The work of the Cambridge University investigators adds to this insight. These researchers were using computer simulations to model the interactions between cardiolipin and a protein complex called F1-F0 ATPase. Embedded within the inner membrane of mitochondria, this complex is a biomolecular rotary motor that produces the compound ATP—an energy storage material the cell’s machinery uses to power its operations.

Like other proteins found in the inner membrane, cardiolipin forms a close association with F1-F0 ATPase. However, instead of permanently binding to the surface of the protein complex, cardiolipin dynamically interacts with this membrane-embedded protein complex. The researchers think that this dynamic association and the unusual chemical structure of cardiolipin (which gives it the flexibility to interact with a protein surface) are critical for its role within the mitochondrial inner membrane. As it turns out, cardiolipin not only stabilizes the F1-F0 ATPase complex (as it does for other inner membrane proteins), but it also lubricates the protein’s rotor, allowing it to turn in the viscous cell membrane environment. Also, its unique structure helps move protons through the F1-F0 ATPase motor, providing the electrical power to operate this biochemical motor.

The bottom line: There is an exquisite biochemical rationale for why cardiolipin is found in mitochondrial inner membranes (and bacterial membranes). In light of this new insight, it is reasonable to view the shared similarities between these organelles and bacteria as reflecting common design—the product of the Creator’s handiwork. Like most biological systems, this organelle appears to be designed for a purpose.

Resources
“Why Do Mitochondria Have DNA?” by Fazale Rana (article)
“Mitochondrial Genomes: Evidence for Evolution or Creation?” by Fazale Rana (article)
“Complex Protein Biogenesis Hints at Intelligent Design” by Fazale Rana (article)
“Archetype or Ancestor? Sir Richard Owen and the Case for Design” by Fazale Rana (article)
“Nanodevices Make Megascopic Statement” by Fazale Rana (article)

Endnotes

  1. Anna Duncan, Alan Robinson, and John Walker, “Cardiolipin Binds Selectively but Transiently to Conserved Lysine Residues in the Rotor of Metazoan ATP Synthases,” Proceedings of the National Academy of Sciences USA 113 (August 2016): 8687–92, doi:10.1073/pnas.1608396113.
  2. Giuseppe Paradies et al., “Functional Role of Cardiolipin in Mitochondrial Bioenergetics,” Biochimica et Biophysica Acta—Bioenergetics 1837 (April 2014): 408–17, doi:10.1016/j.bbabio.2013.10.006.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/11/23/can-a-creation-model-explain-the-origin-of-mitochondria