Introduction

The eukaryotic cell is one of the most complex systems, either alive or inanimate. The cell comprises several complex components, including the Nucleus, Mitochondria, and Lysosomes. Lysosomes play a role in the process of autophagy. It is part of the cell recycling system designed to eliminate unwanted waste, foreign debris, or damaged internal components. The umbrella term is called macroautophagy, which incorporates several different autophagy functions. This paper will examine the Autophagy system and determine which has better explanatory power for its existence, Evolution, or Intelligent Design (ID).

What is Autophagy?

Autophagy is defined as “the biological process that involves the enzymatic breakdown of a cell’s cytoplasm or cytoplasmic components (such as damaged or unneeded organelles or proteins) within the lysosomes of the same cell.”[1] Autophagy comes from the Greek meaning of “eating of self,” auto meaning self and phagein means to eat.[2] While the term is self-explanatory, the process is more akin to a garbage truck. A simple analogy to help clarify what is taking place is to consider a dump truck that picks up the garbage and delivers it to the recycling center. While this analogy might be simple, it illustrates the process of autophagy. Over time, the cell builds up misfolded proteins, damaged organelles, and intracellular pathogens that, if not removed, begin to cause problems within the cell. One of the primary purposes of autophagy is to provide the cell with internal nutrients during starvation conditions. This internal recycling process breaks down the material into usable energy for the cell. Glick, Barth, and Macleod write:

Autophagy is a self-degradative process that is important for balancing sources of energy at critical times in development and in response to nutrient stress. Autophagy also plays a housekeeping role in removing misfolded or aggregated proteins, clearing damaged organelles, such as mitochondria, endoplasmic reticulum, and peroxisomes, as well as eliminating intracellular pathogens. Thus, autophagy is generally thought of as a survival mechanism, although its deregulation has been linked to non-apoptotic cell death. Autophagy can be either non-selective or selective in the removal of specific organelles, ribosomes, and protein aggregates, although the mechanisms regulating aspects of selective autophagy are not fully worked out. In addition to elimination of intracellular aggregates and damaged organelles, autophagy promotes cellular senescence and cell surface antigen presentation, protects against genome instability, and prevents necrosis, giving it a key role in preventing diseases such as cancer, neurodegeneration, cardiomyopathy, diabetes, liver disease, autoimmune diseases, and infections.[3]

Programmed cell death is part of the autophagic system and ensures that degraded or dysfunctional cells die to prevent various diseases.

In 2016, Yoshinori Ohsumi was awarded the Nobel Peace Prize in Physiology/Medicine for his work in discovering the mechanisms of autophagy. In the early 1990s, Dr. Ohsumi began experimenting with baker’s yeast to identify and explain autophagy’s underlying mechanisms. Dr. Ohsumi’s Noble Peace Prize reads, “Ohsumi’s discoveries led to a new paradigm in our understanding of how the cell recycles its content. His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection. Mutations in autophagy genes can cause disease, and the autophagic process is involved in several conditions, including cancer and neurological disease.”[4] While autophagy had been discovered 50 years ago, Dr. Ohsumi’s work revealed how the mechanism of autophagy works. Like many systems in the mammalian body, autophagy is controlled by a complex chemical signals system that commands the macroautophagy process when and how to work. The illustration below shows the dump truck surrounding the garbage that needs transport. The next step is delivering the trash to the lysosome, which is recycled down to its constituent components and reused by the body. Once the garbage has been packaged up, it is called an autophagosome. The autophagic system is always active but is upregulated in times of stress when the body needs additional energy it does not have.[5]

How the Autophagy Process Works

Melendez and Neufeld describe the autophagy process as “divided into several distinct steps: signaling and induction; autophagosome nucleation; membrane expansion and vesicle completion; autophagosome targeting, docking and fusion with the lysosome; and, finally, degradation and export of materials to the cytoplasm.”[6] 

With the vesicle’s completion, the now-completed autophagosome is transported to the lysosome, where it is recycled. The lysosome is where the autophagosome is broken down due to the lysosome’s acidic conditions, ranging from ~ 4.5 to 5.0 in contrast with the cytosol with a ph of 7.2. With the breakdown of the garbage, the constituent material is released back into the cell for energy. The energy derived from the autophagy process is described by Melendez and Neufeld as, “in starved ATG mutant yeast cells, the intracellular level of free amino acids drops significantly, becoming limiting for protein synthesis (Onodera and Ohsumi, 2005).[8] Thus, nutrients derived from autophagy can be essential for both energetic and biosynthetic functions.”[9] The autophagic process is complex and elegant, but it only tells half the story. The other half is the chemical communication system required to trigger the autophagic process. Autophagy only begins once the chemical signal is sent to start the process.

The primary signal factors for autophagy are Atg4, S6K, Atg1, and Beclin 1. These four signaling factors are downstream of several pre-autophagic signals, with Akt being the initiating factor. Melendez and Neufeld write:

Autophagy proceeds constitutively at a low basal rate in most cells and can be induced to high levels in response to starvation, loss of growth factor signaling, and other stressors. The TOR signaling pathway plays a central role in many of these responses. The kinase activity of TOR is inhibited by Tsc1 and Tsc2, which form a complex, with GAP activity, against the small GTPase Rheb, a direct activator of TOR (Wullschleger et al., 2006).[11] The Tsc1/Tsc2 complex, in turn, is regulated by several upstream protein kinases, including Akt in response to insulin signaling and AMPK in response to AMP/ATP levels. Downstream of TOR, the protein kinases Atg1 and S6K have important roles in autophagy, but the relevant substrates of these kinases have not been determined (Kamada et al., 2000;[12] Scott et al., 2004).[13] In addition, both Atg1 and S6K inhibit TOR signaling through negative feedback loops (Lee et al., 2007;[14] Scott et al., 2007).[15] Signaling levels of reactive oxygen species (ROS) are generated in response to starvation and are required for activation of the autophagy-specific protease Atg4 (Scherz-Shouval et al., 2007)[16].[17]

The autophagic signaling system is both complex and responsive. By its nature, the system is finely balanced between actively clearing the cell of garbage and not recycling components that are still functioning correctly. If the autophagic system is not working correctly, the possibility of cancer increases. Jacomin, Gul, Sudhakar, Korcsmaros, and Nezis write:

While it is widely accepted that autophagy is involved in disease development and progression, its exact roles often appear to be controversial across similar studies, highlighting that its implication is most likely to be context-dependent. For instance, the cytoprotective function of autophagy is believed to have tumor-suppressive potential at the early stages of tumorigenesis, and that loss of autophagy can be associated with increased risk of cancer (Roy and Debnath, 2010)[18].[19]

The cell is a complex piece of biological machinery, and the autophagic system plays a critical role in maintaining homeostasis up to and including programmed cell death. Now the central question becomes, can the Neo-Darwinian process account for the complexity seen in the autophagic system?

The Rise of Autophagy: a Neo-Darwinian Account

The process of autophagy in eukaryotic cells, with all things in Neo-Darwinism, must start in the distant past with a common ancestor to all eukaryotic cells. Because autophagy uses cellular processes involved elsewhere, these processes cannot determine autophagy when studying common links to past cellular processes. An example would be a 1990 Ford truck with a turn signal light. That turn signal light cannot determine if the turned signal light indicates past turn signal lights because the said turn signal light is used in the dome lights, front turn indicator, or yellow running lights. Because the cellular precursor process is used elsewhere, they are non-specific to the autophagic system. Hughes and Rusten write, “Many of the genes involved in completing autophagy are clearly involved in other cellular processes and thus serve as poor indicators for the presence of autophagic capacity.”[20] Hughes and Rusten make the case because prokaryotes do not have the necessary internal components, specifically an internal membrane or lysosomes. Autophagy must have arisen later in the evolutionary process. The lysosome is the critical component in the autophagy system because it is the cell’s recycling center. With this information in hand, Hughes and Rusten state, “Since prokaryotes neither have internal membranes nor lysosomes, autophagy necessarily has originated at a later point of evolution.”[21] The interesting part of this statement is that autophagy necessarily originated later in evolution; later, we will return to this point. Because autophagy necessarily arose later, Hughes and Rusten ask if autophagy was present in the last common eukaryotic ancestor (LCEA).

Hughes and Rusten make the concession that some parasitic species lose the function of both ATG12 and ATG8, specifically citing G. Lamblia because it lacks organelles, mitochondria, peroxisomes, and lysosomes, which are all typically found in eukaryotes. Hughes and Rusten also highlight L. major, T. Cruzi, P. Falciparum, and C. Parvum as having spent some of their lifecycles in bodily fluids or a host. Because they live at least partially in an amino acid-rich environment, they do not have or need an autophagic system. The explanation is that the cells above lost their autophagy system over time. They no longer needed it because they never experienced nutrient deficiency. Hughes and Rusten state, “The core autophagy machinery was therefore present in the LCEA. Partial or complete loss of autophagic capacity most likely have occurred secondarily in parasitic species within both bikonts and unikonts. We postulate that macro and microautophagy will be present in most nonparasitic eukaryotes.”[22]

To summarize Hughes and Rusten’s argument, because autophagy must arise from LCEA, eukaryotes that do not display an autophagic system must have lost the system over time due to disuse. An alternative mentioned but not explored is that autophagy was part of a proto or first innate immune system. Hughes and Rusten close with “Caution should be shown when interpreting the original function of these machineries, since co-option of molecules for new functions is one of the main driving forces of evolution.”[23]

Problems with The Hughes and Rusten Explanation

The title of Hughes and Rusten’s paper, Origin and Evolution of Self-Consumption: Autophagy, presents the reader with the sense that a satisfactory explanation has been reached for the autophagy system’s existence. Unfortunately, this cannot be further from the truth. While they were able to construct a hypothesis for its origination, it relies upon an unstainable assumption that autophagy must lie within LCEA. Their premise is further compounded by their apparent adherence to naturalism, which is apparent in their statement that “autophagy necessarily has originated at a later point of evolution.”[24] Commitment to naturalism is unsurprising, if not disappointing. The seeds of their theories’ downfall are sown within their explanation.

Hughes and Rusten’s paper argues that autophagy must have been present in LCEA because autophagy is not present in prokaryotes. Autophagy absent in prokaryotes narrows down the tree of life but fails to explain how several eukaryotic cells lack an autophagy system. Degradation in the evolutionary process is common. It is more likely that information degradation is more likely the operative force in evolution that targeted beneficial mutations. In his book Darwin Devolves, Dr. Michael Behe makes the case the evolutionary process produces either neutral or detrimental mutations. Dr. Behe writes, “It seems, then, that the magnificent Ursus maritimus has adjusted to its harsh environment mainly by degrading genes that its ancestors already possessed. Despite its impressive abilities, it has adapted predominantly by devolving rather than evolving. What that portends for our conception of evolution is the principal topic of this book.”[25]

Despite Hughes and Rusten accidentally hitting on the degradation of information, it is not their primary argument. We can see this in their statement about autophagy being part of an early immune system. This statement would indicate that the autophagy system went from a state of simplicity to one of complexity. The idea of increasing complexity and information is also reflected in their statement that molecular co-option is a driving force in evolution. Again, this idea is one where information in a system increases, not decreases.

While creative, Hughes and Rusten’s argument does not live up to the title of their paper. All they have been able to do is show a hypothetical link between LCEA and all autophagy eukaryotes observed today. The first problem is that LCEA existed, which is mandatory in a naturalistic system, as an infusion of outside information is impossible. The second problem is they did not explain the origin of anything. They, via an a priori assumption, stated that LCEA existed, and from there, they built their case. Their case was weak. It undermined itself by first acknowledging the degradation of information yet speculating or assuming that targeted adaptation was the primary force in moving a proto-autophagy system to a fully working and complex system. While unspoken, the assumption is that chance and necessity drove autophagy from the simple to the complex despite growing evidence to the contrary. Change and necessity are implicit because they are the assumed prime mechanisms for all evolutionary change. Evolution is incapable of picking a target and adapting to meet that target.

Is Intelligent Design a Better Explanation for Autophagy?

As seen above, Neo-Darwinian explanations, as espoused by the Hughes and Rusten paper, run into the problem that the nature of progress from LCEA to current observations of autophagy is challenging to achieve. The evolution of the autophagy system is difficult because chance and necessity, by their nature, cannot steer the progress of evolutionary change to a specific target. The only force that is known to humanity capable of forethought and planning is intelligence. As seen above, the autophagy system has two main lines of complexity and one glaring problem. The first is found in the molecular mechanisms used to operate and execute the process of autophagy. The second is the complex signaling required to initiate and regulate autophagy. The glaring problem is what the natural process gave to the first proto-autophagy system. The last issue is beyond this paper’s scope because it will inherently involve abiogenesis, a topic for another paper.

The first problem is the molecular mechanisms, specifically creating the autophagosome and then transporting the autophagosome to the lysosome. The autophagosome must have been co-opted from a different process in a neo-Darwinian model. Ignoring the obvious question of what that different process was, the bigger problem is how this pro-system arose sequentially without killing the cell. The autophagy process is potent, and I guess that the environmental conditions required for it must be related to cell starvation. It would seem that the lysosome would recycle whatever contents enter it. What stopped this proto system from cannibalizing the entire cell? If the cell is dying of starvation and the pro-autophagy system is developing, what controlling mechanisms exist to prevent total cell death? Let’s look at this differently. There is a scenario called a gray goo scenario. The grey goo scenario postulates nano-machines designed to replicate themselves, go out of control, and turn the world’s biomass into more nano-machines, thus eliminating all life on Earth and leaving only more nano-machines. The autophagic system is no different; without proper controlling mechanisms, what stops the system from completely consuming the cell that is still functioning and has not reached programmed cell death? We will answer this later.

The second problem runs hand in glove with the first problem: how the chemical control system was developed to regulate autophagy. The process begins with a stress signal to Atk and ends with Atg1, Atg4, S6K, and Beclin 1. How does this process develop sequentially? At this juncture, we could postulate that the control system for autophagy is irreducibly complex and that the entire signaling and control system originated together. An irreducibly complex system is difficult to develop via chance and necessity because several control molecules come together in the right configuration to control the autophagy system. As Hughes and Rusten pointed out, an evolved system is not impossible because several of these control molecules exist elsewhere. A way to look at this is like an engineer who can make a computer by taking identical parts that do specific tasks and rearranging them to function in specific ways for the system he is designing. None of the elements work on their own, but in concert, they create a working system. The evolutionary process cannot do this as the design takes forethought and a targeted end goal, both of which intelligence can accomplish.

Conclusion

The autophagy system is extraordinarily complex and precisely controlled by necessity. If autophagy were uncontrolled, it would destroy the entire cell, which it is programmed to do in programmed cell death. As seen above, how can a system designed to eliminate the cell arise via simple incremental steps, both the process and the control mechanism, that prevents a grey goo scenario for all cells? If the autophagy system arose without the control system in place, then autophagy would always destroy the cell. Thus, the organism is eliminated, and it is not given any time to pass on its new mutations to the next generation of offspring. This author would go so far as to say that the autophagy system is irreducibly complex and must arise as a single system. An irreducibly complex system is possible within the evolutionary process but highly unlikely as several system components would have to wait for other parts, or all parts would evolve together. There is a better explanation, and it is nested within irreducible complexity. Intelligence is the best answer to autophagy. Intelligence with forethought, planning, and design can account for all the complex processes involved with autophagy. A designer who knows the end goal can create a controlled recycling system designed to clean out the cell of debris so the cell machinery can operate at peak efficiency without allowing the cell to eat itself before programmed cell death. Intelligent Design is the best explanation for autophagy. It can account for the complexity, design, and control exhibited within the system. Neo-Darwinism does not have enough time with the available probabilistic resources to accomplish the same task.

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[1] Merriam Webster, s.v., “Autophagy”, accessed November 6, 2020, from https://www.merriam-webster.com/dictionary/autophagy.

[2] Daniel Glick, Sandra Barth, Kay F. Macleod, “Autopahgy: Cellular and Molecular Mechanisms,” NMCBI HHS Public Access, November 23, 2010, accessed November 7, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990190/.

[3] Daniel Glick, Sandra Barth, Kay F. Macleod, “Autopahgy: Cellular and Molecular Mechanisms,” NMCBI HHS Public Access, November 23, 2010, accessed November 7, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990190/.

[4] Yoshinori Ohsumi, “Discoveries of Mechanisms for Autophagy,” Nobelforsamlingen, October 3, 2016, accessed November 7, 2020, from https://www.nobelprize.org/prizes/medicine/2016/press-release/.

[5] Ibid.,

[6] Alicia Melendez, Thomas P. Neufeld, “The Cell Biology of Autophagy in Metazoans: A Developing Story,” The Company of Biologists, 2008, accessed November 7, 2020, from https://dev.biologists.org/content/135/14/2347.

[8] J. Onodera, Yoshinori Ohsumi, “TGF Beta-related pathways: Roles in Caenorhabditis Elegans Development” Trends in Genetics Vol. 16, Issue 1 (January 2000), 27-33.

[9] Alicia Melendez, Thomas P. Neufeld, “The Cell Biology of Autophagy in Metazoans: A Developing Story,” The Company of Biologists, 2008, accessed November 7, 2020, from https://dev.biologists.org/content/135/14/2347.

[11] S. Wullschleger, R. Loewith, M.N. Hall, “TOR Signaling in Growth and Metabolism,” Cell, Vol. 124, Issue 3 (February 10, 2006), 471-484.

[12] Yoshiaki, Kamada, Tomoko Funakoshi, Takahiro Shintani, Kazuya Nagano, Marikeo Ohsumi, Yoshinori Ohsumi, “Tor-Mediated Induction or Autopahgy via an Apg1 Protein Kinase Complex,” Journal of Cell Biology, Vol. 150, Issue 6 (September 18, 2000), 1507-1513.

[13] RC. Scott, O. Schuldiner, TP. Neufeld, “Role and Regulation of Starvation-induced Autophagy in the Drosophila Fat Body,” Developmental Cell, Vol. 7, Issue 2 (August 2004), 167-178.

[14] Sung Bae Lee, Sunhong Kim, Jiwoon Lee, Jeehye Park, Gina Lee, Yongsung Kim, Kinman Kim, Jongkyeong Chung, “Atg1, an Autophagy regulator, Inhibits Cell Growth by Negatively Regulating S6 Kinase,” EMBO Reports, Vol. 8, Issue 4 (April 2007), 360-365.

[15] Ryan C. Scott, Gabor Junhasz, Thomas P. Neufeld, “Direct Induction of Autophagy by Atg1 Inhibits Cell Growth and Unduces Apoptotic Cell Death,” Current Biology, Vol. 17, Issue 1 (January 9, 2007), 1-11.

[16] Ruth Schez-Shouval, Elena Shvets, Ephraim Fass, Hagai Shorer, Lidor Gil, Zvulun Elazar, “Reactive Oxygen Species are Essential for Autophagy and Specifically Regulate the Activity of Atg4, EMBO Journal, Vol. 26, Issue 7 (April 4, 2007), 1749-1760.

[17] Alicia Melendez, Thomas P. Neufeld, “The Cell Biology of Autophagy in Metazoans: A Developing Story,” The Company of Biologists, 2008, accessed November 7, 2020, from https://dev.biologists.org/content/135/14/2347.

[18] Roy Srirupa, Jayanta Debnath, “Autophagy and Tumorigenesis,” Seminars in Immunopathology, Vol. 32, Issue 4 (December), 383-396.

[19] Anne-Claire Jacomin, Lejla Gul, Padhmanand Sudhakar, Tamas Korcsmaros, Loannis P. Nezis, “What We Learned from Big Data Autophagy Research,” Frontiers in Cell and Developmental Biology, August 17, 2018, accessed November 7, 2020, from https://www.frontiersin.org/articles/10.3389/fcell.2018.00092/full.

[20] Timothy Hughes, Tor Erik Rusten, “Origin and Evolution of Self-Consumption: Autophagy,” NCBI, accessed November 7, 2020, from https://www.ncbi.nlm.nih.gov/books/NBK6274/.

[21] Ibid.,

[22] Ibid.,

[23] Ibid.,

[24] Timothy Hughes, Tor Erik Rusten, “Origin and Evolution of Self-Consumption: Autophagy,” NCBI, accessed November 7, 2020, from https://www.ncbi.nlm.nih.gov/books/NBK6274/.

[25] Michael J. Behe, Darwin Devolves: The New Science about DNA that Challenges Evolution (New York: NY, Harper Collins, 2019), Kindle Edition, 17.