Evolution is a Fact #38 - The Origin of Complex Cells

by cofty 71 Replies latest watchtower beliefs

  • cofty
    cofty

    In 1966 microbiologist Kwang Jeon was studying a population of amoebae in the lab when they began to die off unexpectedly. He noticed thousands of tiny dots in the cytoplasm of each individual which turned out to be a bacterial infection. Most of them weakened and died but surprisingly a small percentage recovered and seemed to be back to normal.

    Professor Jeon began to keep careful records expecting to discover that a few of his collection had an immunity to the bacteria. On examination however Jeon observed that each of the healthy amoebae that had survived the epidemic still contained more than 40,000 of the bacteria living inside them.

    To study what was going on Jeon tried using antibiotics to kill the infection but as the bacteria died their host also died. Jeon and his team also tried surgically removing the nucleus from infected cells and transplanting them into another cell. They found that again the cell would die if it was transplanted into one without the bacteria. It had taken about 18 months - 200 cell generations - for the amoebae to become dependent on their former attackers.


    Jeon eventually discovered that the bacteria had taken over the production of an enzyme that controls essential cellular functions such as cell growth and differentiation. In the following decades as genetic investigations became possible Jeon discovered that the bacteria and the host amoebae had actually exchanged some of their genes. By any possible definition this was more than a symbiotic relationship - the amoebae had become a different species with a radically altered genome. What Jeon and his team had observed was endosymbiosis in real time.

    Creationists often falsely complain that evolution cannot be observed. This example and Lenski's long term E coli experiment show otherwise.

    Kwang Jeon's work has implications for far more than just the evolution of one species of amoebae - it provides compelling evidence for the evolution of all complex cells.

    For approximately 3 billion years - from 4 to 1 billion years ago - all life consisted of a relatively simple type of cell known as a prokaryote. These are usually round or rod-like with a rigid cell wall. Inside the cell there is very little to see, Their genome is minimal with the DNA arranged in a loop. Everything is streamlined for fast duplication. Given sufficient resources a single bacterium weighing a trillionth of a gram could found a population with a weight equivalent to that of planet earth in two days.

    Every living thing you have ever seen from humans to oak trees are made up of more complex cells known as eukaryotes. These are significantly different from prokaryotes. By definition eukaryotes have a nucleus. This is the command centre of the cell where the DNA is kept behind a membrane. Unlike the single circular chromosome of prokaryotes the DNA of eukaryotes is arranged in a number of pairs of straight chromosomes. The genes come in chunks being divided by multiple stretches of random code. As a result many eukaryotes have massive genomes mostly made up of parasitic code. The record is held by the amoebae Amoeba dubia with 670 billion base pairs, 220 times as large as a human. On average eukaryotic cells are 10,000 to 100,000 times larger than prokaryotes although the two spectrums of size do overlap at the extremes.

    Just as our bodies contain numerous organs, eukaryotic cells contain a variety of organelles outside of the nucleus. On average a cell contains a few hundred mitochondria that produce ATP, the fuel that powers all of the body's activity.

    As early as the 1960s biologist Lynn Margulis proposed the hypothesis that mitochondria were originally free-living, oxygen-breathing bacteria that invaded anaerobic bacteria to their mutual benefit. For decades her ideas met robust opposition but the evidence continued to mount.

    • Mitochondria closely resemble bacteria in size and shape. In particular they resemble purple-aerobic bacteria.
    • They both use oxygen in the production of ATP, and they both do this by using the Kreb’s Cycle.
    • Eukaryotic cells are incapable of producing new mitochondria which replicate by fission just like bacteria not by mitosis like eukaryotes.
    • Mitochondria have a double membrane. The inner layer is very different from eukaryotes but has the same chemical composition as prokaryotes.
    • Some types of antibiotics that kill bacteria also inhibit function of mitochondria.
    • Margulis predicted that if her idea was correct then it would be found that mitochondria have their own DNA. This has also been proven correct. The DNA of mitochondria and chloroplasts is different from that of the eukaryotic cell in which they are found. Just like Kwang Jeon's amoebae gene transfer has occurred between mitochondria and the cell nucleus. More than 99% of genes have been given up by mitochondria with the exception a few genes that are essential to respiration so that power production in a cell can fluctuate to meet immediate demand.

    The first appearance of eukaryotic cells is dated to approximately 1.5 billion years ago following a period when earth's oxygen levels rose significantly. The energy production of complex cells set the scene for an amazing radiation of different complex life forms. Bacteria "breathe" through their membrane which puts a practical limit on their size. Hundreds of mitochondria all contributing energy within the same eukaryotic cell opens up new possibilities for evolution and natural selection to explore.

    Eukaryotic cells in plants have organelles called chloroplasts that convert energy from the sun into sugars. They too demonstrate all the same sort of evidence that they were once free-living cyanobacteria that merged with another prokaryotic cell through endosymbiosis. There is an interesting example of an intermediate stage of this process in the amoeba Paramecium bursaria that swims around pond water. It swallows photosynthetic green algae but doesn't digest them. When is swims into the light the algae produce sugar which both cells share on the go. It even shares food when they are in darker places where photosynthesis can't take place.

    Paramecium bursaria filled with Zoochlorella cells


    The hard work done by Margulis and others on endosymbiosis is an excellent example of how science works. A radical new hypothesis was rightly met with considerable skepticism. It was only after a long and difficult challenge over many decades when the evidence became irrefutable, that is was accepted as a valid scientific theory.

    There are lots more details that could be shared on this topic but hopefully this provides a hint of the amazing results of scientific research. Like all creationist arguments the challenge of how complex cells arose is simply a failure of imagination - an argument from personal incredulity.



    Index of Parts 1 -30

    #31 Ten Questions For Creationists ...
    The basic facts about reality covered so far pose an impossible challenge to creationism.

    #32 Sexual Selection
    How female mating preferences led to some of the most remarkable features of living things.

    #33 A Tale About Tails
    Human embryology reveals our primate history.

    #34 Hiccups and Tadpoles
    How hiccups are a relic of our amphibian ancestors.

    #35 Nature Red in Tooth and Claw
    Nature's ability to inflict pain and suffering in the battle for survival.

    #36 Mass Extinctions
    96% of life was wiped out in The Great Dying 250 million years ago.

    #37 Testicles
    The plumbing of the vas deferens gives evidence of our fish ancestry

  • Satan
    Satan

    Good job, Human apostate!

  • WhatshallIcallmyself
    WhatshallIcallmyself

    Excellent continuation to your series again Cofty.

    It's worth us all remembering just how many science hours have gone into learning the knowledge that these few paragraphs highlight. How many scientists have devoted their lives to researching these topics so we can understand our world just that little bit better? The efforts that go into understanding even the "simplest" things is testament to the character of these scientists who often earn relatively little when compared to other jobs requiring similar expertise and commitment. It is all too easy to forget all that when presented with a summary of knowledge, especially if you have had no experience or higher learning in those fields. So let's not forget!


  • LoveUniHateExams
    LoveUniHateExams

    Great OP, cofty - with lots of information.

    I'm still trying to take it all in.

  • LV101
    LV101

    Very interesting this amoebae - hope I can catch up/comprehend even though you do great job of 'splaining to we natives here.

    I recall learning decades ago in psych class (loved this) when an amoebae (brainless) runs into something noxious it immediately goes in an opposite direction.

  • cofty
    cofty

    Thank you. I should really give Vidqun a namecheck for raising this subject on another thread.

    He asserted that endosymbiosis "cannot be replicated in a lab". Well it turns out it can.

    There are a few other details that are really interesting about this subject. Maybe I will post that as #39

  • Vidqun
    Vidqun

    Perhaps now is a good time to clarify some of the terminology: Symbiogenesis cannot be replicated in a lab (and not endosymbiosis as previously stated). There is a difference. I cannot dispute the process of endosymbiosis which can be demonstrated. However the complete process of symbiogenesis (the evolutionary theory that explains the origin of eukaryotic cells from prokaryotic cells by symbiosis) cannot as yet be demonstrated.

    What should also be kept in mind, is the process of adaptation at work, which is confirmed by Dr. K. W. Jeon.

    It is suggested that the presence of a potent P2 in the X-bacterial gene is an adaptation for the endosymbiotic bacteria to survive within a potentially hostile intracellular environment. 1

    The following discusses the organisms or possible organisms involved in Dr. Jeon’s experiment. Important to note that these organisms remain individual and identifiable as specific species.

    The X-bacteria which initiated organismic association with the D strain of Amoeba proteus in 1966 as parasites have changed to obligate endosymbionts on which the host depends for survival. Owing to the difficulty in cultivating the bacteria in vitro, the identity of X-bacteria has not been determined. The life cycle of X-bacteria is similar to that of Legionella spp. in soil amoebae. 2

    Not sure why this oversight has occurred, but what is described here is the typical (or atypical) immune response of the Amoeba organism, which is not unusual at all. Our immune system has similar response mechanisms to counter invading bacteria and viruses.

    This indicates that phylogenetically and ecologically diverse bacteria which thrive inside amoebae exploit common mechanisms for interaction with their hosts, and it provides further evidence for the role of amoebae as training grounds for bacterial pathogens of humans. 3

    Again, one should not accept as fact that these organisms are a new species. The warning is sounded by two renowned biologists:

    On the basis of the structural and physiological changes brought about by the endosymbionts of xD amoebae as described above, one could consider the the symbiont-bearing xD strain a new species of Amoeba. However, until evidence for genetic differences between D and xD amoebae is obtained, it would be more prudent to treat xD amoebae as belonging to a variant strain. 4

    There are huge barriers to overcome in the proposed process of symbiogenesis. I believe the barriers are insurmountable:


    Barriers to endosymbiogenesis

    The transformation of an independent endosmbiont into an organelle faces tremendous barriers. The hurdles include the transfer of much of the endosymbiont’s genetic material to the host’s nucleus, the acquisition of the proper regulatory and targeting sequences to ensure that the transferred gene not only is expressed but possesses the correct targeting information to redirect it into the plastid. This, of course, leads us to the significant challenge of acquiring the appropriate protein import apparatus to ensure that the targeted proteins are properly imported and sorted within the organelle. There is also the issue of integrating and regulating metabolic pathways. 5

    We will see that the archaeal translation machinery is neither bacterial, nor eukaryotic, but customized to the archaea. Indeed some parts of the archaeal translation machinery and those of bacteria or eukarya have similar sequence and/or structures since all life forms share the same task of decoding information carried by mRNA and translating the message into the amino acid sequences of proteins. However, the archaeal translation machinery can’t be exchanged with those of bacteria or eukarya, including ribosomes, tRNAs, and translation factors. Thus, there exists an evolutionarily unbridgeable gap between archaea and eukarya and bacteria in translation, just as in DNA replication and transcription.

    The above comparisons of a few molecules involved in the information processing in the three domains of life reveals several interesting phenomena: 1) Molecular machines are employed as modules, that is, a process is either bacterial-like or eukaryote-like. 2) Each machine is a molecular mosaic of modules that is fine-tuned to meet the unique need of an organism. 3) The machines for DNA replication, transcription, and translation in bacteria, archaea, and eukarya are unique and specific for each domain of life, and thus, can’t be exchanged. 4) Functional annotations of genes based on sequence homology comparisons can be misleading because they only take into account isolated parts of proteins, not the entire gene. 5) Organism-specific protein extensions, such as the CTD of eukaryotic Rpb1, can be the determinant factor of life vs. death for the specific organism.

    We will see that the archaeal translation machinery is neither bacterial, nor eukaryotic, but customized to the archaea. Indeed some parts of the archaeal translation machinery and those of bacteria or eukarya have similar sequence and/or structures since all life forms share the same task of decoding information carried by mRNA and translating the message into the amino acid sequences of proteins. However, the archaeal translation machinery can’t be exchanged with those of bacteria or eukarya, including ribosomes, tRNAs, and translation factors. Thus, there exists an evolutionarily unbridgeable gap between archaea and eukarya and bacteria in translation, just as in DNA replication and transcription.

    The above comparisons of a few molecules involved in the information processing in the three domains of life reveals several interesting phenomena: 1) Molecular machines are employed as modules, that is, a process is either bacterial-like or eukaryote-like. 2) Each machine is a molecular mosaic of modules that is fine-tuned to meet the unique need of an organism. 3) The machines for DNA replication, transcription, and translation in bacteria, archaea, and eukarya are unique and specific for each domain of life, and thus, can’t be exchanged. 4) Functional annotations of genes based on sequence homology comparisons can be misleading because they only take into account isolated parts of proteins, not the entire gene. 5) Organism-specific protein extensions, such as the CTD of eukaryotic Rpb1, can be the determinant factor of life vs. death for the specific organism. 6

    At variance with the earlier belief that mitochondrial genomes are represented by circular DNA molecules, a large number of organisms have been found to carry linear mitochondrial DNA. Studies of linear mitochondrial genomes might provide a novel view on the evolutionary history of organelle genomes and contribute to delineating mechanisms of maintenance and functioning of telomeres. Because linear mitochondrial DNA is present in a number of human pathogens, its replication mechanisms might become a target for drugs that would not interfere with replication of human circular mitochondrial DNA. 7

    1. Abstract: “A novel strong promoter of the groEx operon of symbiotic bacteria in Amoeba proteus.” Abstract: Dr K.W. Jeon, Department of Zoology, University of Tennessee, Knoxville, TN 37996-0810, USA.

    2. Abstract: “Phylogenetic characterization of Legionella-like endosymbiotic X-bacteria in Amoeba proteus: a proposal for ‘Candidatus Legionella jeonii’ sp. nov.”

    3. Abstract: “The Genome of the Amoeba Symbiont “Candidatus Amoebophilus asiaticus” Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria.”

    4. Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis, by Lynn Margulis and René Fester, p. 125.

    5. Molecular Phylogeny of Microorganisms, by Aharon Oren and R. Thane Papke, p. 198.

    6. “Information Processing Differences Between Archaea and Eukarya—Implications for Homologs and the Myth of Eukaryogenesis,” by C. L. Tan and J. P. Tomkins.

    7. Linear mitochondrial genomes: 30 years down the line. Josef Nosek, L’Ubomir Tomaska, Hiroshi Fukuhara, and Ladislav Kovac.

  • cofty
    cofty

    Vidqun - For the fifth time you have used copy-paste without indicting your source.

    On two occasions when I found your sources it turned out you had totally twisted the meaning of the reference.

    So please provide a link to the source of your post.

  • cofty
    cofty

    You have even plagiarised the same text twice in the same post!

    If you must steal the work of others at least try to learn how to copy-paste properly.

  • Vidqun
    Vidqun

    Here’s a few calculations by scientists and researchers. I am not good with Maths so I cannot verify them. I have to take their word for it:

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”

    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Evolution vs. Functional Proteins (“Mount Improbable”) – Doug Axe and Stephen Meyer – Video

    https://www.youtube.com/watch?v=7rgainpMXa8

    Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance.

    http://www.evolutionnews.org/2.....35561.html


    On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story

    Jonathan M. – January 10, 2012

    Excerpt: While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to — at the very least — give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist — and justifiably gives one cause for skepticism.

    http://www.evolutionnews.org/2.....54891.html

    Bacteria Too Complex To Be Primitive Eukaryote Ancestors – July 2010
    Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified…. There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote.

    http://www.creationsafaris.com.....#20100712b

    Bacterial Protein Acetylation: The Dawning of a New Age – July 2012


    Excerpt: Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely.

    http://darwins-god.blogspot.co.....wning.html

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