March 27, 2023 | Jerry Bergman

Cell Organelles that Defy Evolution: The Lysosome

New research proves that the lysosome system
is much more complex than previously believed



by Jerry Bergman, PhD

The understanding of the cell design in Darwin’s day was, in stark contrast to our knowledge today, a simple structure; just a bag of fluids, enzymes, and chemicals.[1] The cell is now known to be far more complex than was believed just a few years ago. This trend has been true of every cell organelle. The major organelles in the cytoplasm (see Figure 1) include the: (1) nucleolus, (2) nucleus, (3) ribosome, (4) vesicle, (5) rough endoplasmic reticulum, (6) Golgi apparatus, (7) cytoskeleton, (8) smooth endoplasmic reticulum, (9) mitochondria, (10) vacuole, (11) cytosol, (12) centriole, (13) and lysosome.  The lysosome, for decades considered the simplest organelle, is now realized to be much more complicated as a result of research done by the University of Bonn in Germany.

Figure 1. The basic organelles of a cell. From Wikimedia Commons.

The Importance of Lysosomes

The Bonn research team focused on the main degradative organelles of mammalian cells, called lysosomes. Lysosomes break up (lyse) other organelles into their building blocks, thus acting as the recycling facility of the cell. They are also the central part of the cell’s waste disposal-recycling system. Under the microscope they look simple, like tiny bubbles surrounded by a fat-like membrane. Lysosomes form by budding off of another organelle, the  Golgi apparatus. The hydrolytic enzymes within the lysosomes are formed in the endoplasmic reticulum (ER). The enzymes are tagged with the mannose-6-phosphate molecule, transported to the Golgi apparatus in vesicles, then transferred into the lysosomes.

Lysosomes contain over 60 different digestive enzymes. These enzymes break down defective cell components into their individual parts, such as carbohydrates, lipids, proteins, and nucleic acids.[2] These parts are then available for use in other parts of the cell or other cells.[3] The lysosome’s pH is weakly acidic (around pH 5) because their hydrolytic enzymes require an acidic pH (< 7) instead of the neutral pH (= 7) existing in the rest of the cell. Consequently, they are designed to produce and maintain this acidic pH, as is also true of the stomach.

Lysosomes are only used in animal and human cells, and each human cell contains close to 300 of them. The many different enzyme types in lysosomes include proteases, amylases, nucleases, lipases, and acid phosphatases, among many others. Although lysosomes are comparatively simple structures, the 60 different digestive enzymes are complex molecules that must be coded in the cell’s DNA, then transcribed, translated, folded,  and transported to the lysosome to carry out their digestive functions. These functions include destroying improperly functioning organelles, a process called autophagy.

Lysosomes in Action

White blood cells called phagocytes ingest invading bacteria. The bacterium is enclosed by a vesicle that the lysosomes fuse with. Lysosomes then use hydrolytic enzymes to destroy pathogens via water-based dissolution. For example, in phagocytosis (Figure 2), a section of the plasma macrophage membrane invaginates and engulfs a pathogen. The vesicle then fuses with a lysosome prior to the lysosome’s hydrolytic enzymes, destroying the pathogen.

Figure 2. A simplified illustration of phagocytosis. From Wikimedia Commons.

One of many examples of our increased understanding of the cell’s complexity includes the function of the enzymes used in lysosomes. Of these enzymes, the University of Washington said they depend

on how those proteins are physically folded. Researchers around the world are examining the countless complex structures of proteins and their functions …. Protein folding has been compared in complexity to the folding of delicate origami. While the folding process is already complicated, …  imagine trying to unfold the origami in a wind tunnel while countless other hands are also pulling at the paper. And yet, that’s comparable in complexity to what the hundreds of thousands of cells and proteins are doing in your body right now.[4]

Lysosomes are also involved in a range of other processes, including the transport of molecules across the lysosomal membrane, nutrient sensing, and the interaction of lysosomes with other organelles to achieve metabolite exchanges.[5] Lysosomes are thus critical to the cell’s function. No eukaryotic cell can survive without lysosomes, and this produces a major problem for the evolution of a prokaryotic cell into a eukaryotic cell.

The Bonn Research Findings

The Bonn research found that the disassembling and recycling of defective cell components, or those no longer required, differs from cell type to cell type. They also found evidence for 100 new potential lysosomal proteins.[6] This research adds significantly to our knowledge of the level of cell complexity:

Lysosomes, the main degradative organelles of mammalian cells, play a key role in the regulation of metabolism. It is becoming more and more apparent that they are highly active, diverse, and involved in a large variety of processes. The essential role of lysosomes is exemplified by the detrimental consequences of their malfunction, which can result in lysosomal storage disorders, neurodegenerative diseases, and cancer.[7]

Lysosome research has also provided evidence for specific differences in lysosomes, depending on the cell type, documenting “that levels of distinct lysosomal proteins are highly variable within one cell type, while expression of others is highly conserved across several cell lines.”[8]

Progress in understanding the complexity and design of eukaryotic organelles has forced the realization that evolution from prokaryote to eukaryote is far less plausible than was once believed. As a result, the common explanation of the origin of the eukaryote cell, endosymbiosis, has become even less plausible.[9]  The set of required organelles for this cell type must exist as a set and must function as a set. The system is thus irreducibly complex.

A prokaryotic cell compared to a eukaryotic cell. Notice how comparatively simple the prokaryote’s cell is compared to the eukaryote’s cell. From Wikimedia Commons.


Lysosomes are irreducibly complex organelles used in all animal cells. The Bonn research has revealed that they are much more complex than previously believed. The differences found to exist in each cell type now need to be researched, as also do the functions and specific characteristics of the 100 new potential lysosomal proteins. Thus, the Bonn team’s findings have opened the door to a new research area that will significantly increase our understanding of the complexity of this formerly “simple” organelle.


[1] Therapeutics 1. Section 2:3. U.S. Army Medical Department, Sam Houston, TX, 2023.

[2] Maxfield, Frederick R., et al. Lysosomes: Biology, Diseases, and Therapeutics. John Wiley & Sons, Hoboken, NJ, 2016.

[3] Xu, H., and D. Ren. Lysosomal physiology. Annual Review of Physiology 77:57–80, 2015.

[4] Neary, Walter. Proteins are vastly more complicated than previously realized. University of Washington News., 1 May 2001.

[5] Ballabio, Andrea, and Juan S. Bonifacino. Lysosomes as dynamic regulators of cell and organismal homeostasis. Nature Review of  Molecular Cell Biology 21(2):101–118, 25 November 2019.

[6] University of Bonn. Cellular waste removal differs according to cell type. Study identifies different types of so-called lysosomes. Science Daily., 16 March 2023.

[7] Akter, Fatema, et al.  Multi–Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins. Molecular & Cellular Proteomics 22(3):100509, 14 February 2023.

[8] Akter, et al., 2023.

[9] Bergman, Jerry. Research has overturned endosymbiosis: The unbridgeable gap between prokaryotes and eukaryotes remains. Journal of Creation 35(1):38-47, 2021.

Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,800 college libraries in 27 countries. So far over 80,000 copies of the 60 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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  • astroimagery says:

    Can someone please fathom how the first cells formed as they are already highly complex and needed several mechanisms to function. They needed an energy source and other essentail parts to exist.

    My work as in astrophotography (see also convinces me that the universe is far more amazing than we thought.

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