Mycoplasma mycoides Just Destroyed Evolution

_{Cornelius Hunter

March 24, 2016

Cell biology, Intelligent Design, Origin Of Life}

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Call it Mycoplasma mycoides lite—researchers have established what is approximately a minimal organism by removing about have of the genes from theMycoplasma mycoidesgenome. The result is a set of 473 genes which, collectively, appear to be required for any kind of reasonable performance. That is an enormous level of complexity. Furthermore, about one third of that minimal gene set is of unknown function. As J. Craig Venter put it, “We’re showing how complex life is, even in the simplest of organisms. These findings are very humbling.” Read more

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In fact, there’s no single set of genes that all living things need in order to exist. When scientists first began searching for such a thing 20 years ago, they hoped that simply comparing the genome sequences from a bunch of different species would reveal an essential core shared by all species. But as the number of genome sequences blossomed, that essential core disappeared. In 2010, David Ussery, a biologist at Oak Ridge National Laboratory in Tennessee, and his collaborators compared 1,000 genomes. They found that not a single gene is shared across all of life. “There are different ways to have a core set of instructions,” Szostak said.
It's honestly beginning to look like "Mycoplasma mycoides Just Destroyed" ID's odds related "evidence" that assumed otherwise. I expect the number of DNA coded genes required for something "living" to be zero. The reason is: DNA coding is a long term memory that shorter term RNA memory reads and writes much like an assembly instruction book. And like us the RNA that puts the instructions into action may improvise. There is more than one way to put the product together. On its own DNA does nothing. It's a relatively inert crystal. It's what brings that to life/action that's important. That's where the "RNA World" that still exists is at. Putting the DNA from an embryonic cell into another results in the development of something in between.GaryGaulin_{March 29, 2016
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Venter is careful to avoid calling syn3.0 a universal minimal cell. If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes.
https://www.quantamagazine.org/20160324-in-newly-created-life-form-a-major-mystery/GaryGaulin_{March 29, 2016
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I just wan to point out taht appearance of design is not evidence of design. A little about by who, as well as how, where and when design is required, Not to forget the all-important question of how implementation is performed, before that has been established, ID remains religious faith more than estabished fact. There's a lot more research required to be done, is anyone in the ID movement presently busy doing that instead of making unsubstantiated claims?Cabal_{March 28, 2016
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tjguy, I think you read my comment the exact opposite of the way it was intended. :) Darwinian explanations fail at the single cell level. Yes, the simplest cell screams design.Mung_{March 27, 2016
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Mung @ 5
This post from Dr. Hunter fits right in with one of my pet peeves about ID. Forget about debating human-chimp ancestry and missing fossil intermediates. Just look at a single cell. The simplest cell screams design.
Mung, do you disagree with the idea that the simplest cell screams design? Just curious. I don't see why, if the cell screams design, that you would think this is a bad thing to point out. I think using every avenue of attack is fair game and indeed a good strategy.tjguy_{March 27, 2016
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Forgive me, Me_Think. Stating facts only muddy the waters if they are irrelevant to the topic under discussion. You obviously think that the number of genes in a banana is somehow relevant to the number of genes in a minimal organism. I don't see it. So why don't you explain yourself instead of answering a question with a question? Besides, given the fact that there are a minimum number of genes necessary for basic life to function, I'm wondering why the banana is yellow. Hmmm....RexTugwell_{March 26, 2016
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RexTugwell @ 7
What does your question have to do with the current topic? Or are you simply trying to muddy the water?
Interesting comment. Why would stating facts 'muddy the water' ?Me_Think_{March 25, 2016
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The hardware and software of the cell, evidence of design http://reasonandscience.heavenforum.org/t2221-the-hardware-and-software-of-the-cell-evidence-of-design Paul Davies: the fifth miracle page 62 Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 1 We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take-on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics. Software and hardware are irreducible complex and interdependent. There is no reason for information processing machinery to exist without the software, and vice versa. Systems of interconnected software and hardware are irreducibly complex. 2 All cellular functions are irreducibly complex 3 http://reasonandscience.heavenforum.org/t2179-the-cell-is-a-interdependent-irreducible-complex-system chemist Wilhelm Huck, professor at Radboud University Nijmegen 5 A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity," Paul Davies, the fifth miracle page 53: Pluck the DNA from a living cell and it would be stranded, unable to carry out its familiar role. Only within the context of a highly specific molecular milieu will a given molecule play its role in life. To function properly, DNA must be part of a large team, with each molecule executing its assigned task alongside the others in a cooperative manner. Acknowledging the interdependability of the component molecules within a living organism immediately presents us with a stark philosophical puzzle. If everything needs everything else, how did the community of molecules ever arise in the first place? Since most large molecules needed for life are produced only by living organisms, and are not found outside the cell, how did they come to exist originally, without the help of a meddling scientist? Could we seriously expect a Miller-Urey type of soup to make them all at once, given the hit-and-miss nature of its chemistry? Being part of a large team,cooperative manner,interdependability,everything needs everything else, are just other words for irreducibility and interdependence. For a nonliving system, questions about irreducible complexity are even more challenging for a totally natural non-design scenario, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce. For an origin of life we can think about the minimal complexity that would be required for reproduction and other basic life-functions. Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap or in my imaginary LMNOP system. And current science has no plausible theories to explain how the minimal complexity required for life (and the beginning of biological natural selection) could have been produced by natural process before the beginning of biological natural selection.Elshamah_{March 25, 2016
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Elshamah @ 8
indeed, life can be viewed as resulting substantially from the chemical activity of proteins.
And indeed, information can be viewed as resulting substantially from the chemical activity of ink on paper.awstar_{March 25, 2016
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http://reasonandscience.heavenforum.org/t2110-what-might-be-a-protocells-minimal-requirement-of-parts#3797 Proteins are essential building blocks of living cells; indeed, life can be viewed as resulting substantially from the chemical activity of proteins. Because of their importance, it is hardly surprising that ancestors for most proteins observed today were already present at the time of the 'last common ancestor', a primordial organism from which all life on Earth is descended. How did the first proteins arise? How can we bring a taxonomic order to the diversity of forms that evolved from them? These two questions are at the center of our scientific efforts, on which we bring to bear methods in bioinformatics, protein biochemistry and structural biology. Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features. (i) A virtually complete DNA replication machinery, composed of one nucleoid DNA binding protein, SSB, DNA helicase, primase, gyrase, polymerase III, and ligase. No initiation and recruiting proteins seem to be essential, and the DNA gyrase is the only topoisomerase included, which should perform both replication and chromosome segregation functions. (ii) A very rudimentary system for DNA repair, including only one endonuclease, one exonuclease, and a uracyl-DNA glycosylase. (iii) A virtually complete transcriptional machinery, including the three subunits of the RNA polymerase, a factor, an RNA helicase, and four transcriptional factors (with elongation, antitermination, and transcription-translation coupling functions). Regulation of transcription does not appear to be essential in bacteria with reduced genomes, and therefore the minimal gene set does not contain any transcriptional regulators. (iv) A nearly complete translational system. It contains the 20 aminoacyl-tRNA synthases, a methionyl-tRNA formyltransferase, five enzymes involved in tRNA maturation and modification, 50 ribosomal proteins (31 proteins for the large ribosomal subunit and 19 proteins for the small one), six proteins necessary for ribosome function and maturation (four of which are GTP binding proteins whose specific function is not well known), 12 translation factors, and 2 RNases involved in RNA degradation. (v) Protein-processing, -folding, secretion, and degradation functions are performed by at least three proteins for posttranslational modification, two molecular chaperone systems (GroEL/S and DnaK/DnaJ/GrpE), six components of the translocase machinery (including the signal recognition particle, its receptor, the three essential components of the translocase channel, and a signal peptidase), one endopeptidase, and two proteases. (vi) Cell division can be driven by FtsZ only, considering that, in a protected environment, the cell wall might not be necessary for cellular structure. (vii) A basic substrate transport machinery cannot be clearly defined, based on our current knowledge. Although it appears that several cation and ABC transporters are always present in all analyzed bacteria, we have included in the minimal set only a PTS for glucose transport and a phosphate transporter. Further analysis should be performed to define a more complete set of transporters. (viii) The energetic metabolism is based on ATP synthesis by glycolytic substrate-level phosphorylation. (ix) The nonoxidative branch of the pentose pathway contains three enzymes (ribulose-phosphate epimerase, ribosephosphate isomerase, and transketolase), allowing the synthesis of pentoses (PRPP) from trioses or hexoses. (x) No biosynthetic pathways for amino acids, since we suppose that they can be provided by the environment. (xi) Lipid biosynthesis is reduced to the biosynthesis of phosphatidylethanolamine from the glycolytic intermediate dihydroxyacetone phosphate and activated fatty acids provided by the environment. (xii) Nucleotide biosynthesis proceeds through the salvage pathways, from PRPP and the free bases adenine, guanine, and uracil, which are obtained from the environment. (xiii) Most cofactor precursors (i.e., vitamins) are provided by the environment. Our proposed minimal cell performs only the steps for the syntheses of the strictly necessary coenzymes tetrahydrofolate, NAD, flavin aderine dinucleotide, thiamine diphosphate, pyridoxal phosphate, and CoA.Elshamah_{March 25, 2016
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Me_Think @ 1 What does your question have to do with the current topic? Or are you simply trying to muddy the water?RexTugwell_{March 25, 2016
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If the first step in the OOL was this simplified cell then it would be impossible. No scientist denies this.Indiana Effigy_{March 25, 2016
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This post from Dr. Hunter fits right in with one of my pet peeves about ID. Forget about debating human-chimp ancestry and missing fossil intermediates. Just look at a single cell. The simplest cell screams design.Mung_{March 25, 2016
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@Cornelius Hunter: "The origin of life problem can be divided into two broad categories:..." The origin of life problem is nothing compared to the origin of higher life forms. Often brought up in the origins debate is that abiogenesis and evolution are two completely different things due to the mutability of organism or its ability to reproduce. But, the ability to reproduce and thus producing gene duplications and mutations is nothing but the possibility to add some new molecular structure to the existing living system. But exactly the same possibility exist in some lifeless chemical system also - some new molecular structure can be added to the existing lifeless chemical system. Natural selection of this chemical system is then differential survival(existence in time) and the ability to add new molecular structures. Those structures that are not stable enough will cease to exist while the others will be selected. Variation exists within all populations of chemical systems. This occurs partly because changes arise through chemical reactions in the structure of an individual system, and these changes can be stable enough to exist in time. Through the existance in time structures of systems interact with their environments to cause variations. The environment of a chemical system includes other chemical systems, atoms, molecules, compounds, as well as various physical objects. Individual chemical systems with certain variants of the structure may survive and exist longer than systems with other, less successful or less stable, variants. Therefore, the population of chemical systems evolves... So how does the ability to "add new structure"(ability to reproduce) differentiate between evolution and abiogenesis if exactly the same ability exist in countless lifeless chemical systems in nature also? Evolutionists invented this distinction because it has never been observed that lifeless molecular component parts can gain the ability to maintain and to replicate themselves and because chances for that are practically zero. But if this "adding" process is not able to turn molecular component parts into the ability to maintain and to replicate themselves by what means would this "adding" process be able to turn collection of cells or collection of tissues into organs or organ systems with the ability to maintain and to replicate themselves? If there is a problem with the origin of life then the origin of higher life forms is a much bigger problem.forexhr_{March 25, 2016
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a few more related notes:
Ocean microbes display remarkable genetic diversity - April 24, 2014 Excerpt: Prochlorococcus, is a photosynthetic bacteria,, forming the base of the marine food chain,, scientists in MIT's Department of Civil and Environmental Engineering (CEE) recently performed a cell-by-cell genomic analysis on a wild population of Prochlorococcus living in a milliliter—less than a quarter teaspoon—of ocean water, and found hundreds of distinct genetic subpopulations.,,, "The sheer enormity of diversity that must be in the octillion Prochlorococcus cells living in the seas is daunting to consider," Chisholm says. "It creates a robust and stable population in the face of environmental instability.",,, "The interesting question is, 'Why does such a diverse set of subpopulations exist?'" Kashtan says. "The huge population size of Prochlorococcus suggests that this remarkable diversity and the way it is organized is not random, but is a masterpiece product of (ahem) natural selection." http://phys.org/news/2014-04-ocean-microbes-remarkable-genetic-diversity.html
Meet Mycoplasma, a parasitic bare-bones bacterium, with approx 500 genes
First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009 Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. "At all three levels, we found M. pneumoniae was more complex than we expected," http://www.sciencedaily.com/releases/2009/11/091126173027.htm There’s No Such Thing as a ‘Simple’ Organism - November 2009 Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function. http://www.wired.com/wiredscience/2009/11/basics-of-life/ Simplest Microbes More Complex than Thought - Dec. 2009 Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes." http://www.creationsafaris.com/crev200912.htm#20091229a To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ Twitter discussion criticizing the cell model.. - 2012 Umm – claims of first full computer simulation of an organism seem, well, way way overhyped… one of the worst NY Times science articles I have seen in a while… I do not think they made a complete model … Another commenter, Steffen Christensen, voiced his agreement: Aye: a model is NOT a complete simulation…There are what, 1000s of molecule types in a typical cell, and their model tracks less than 30?!? They might’ve done a better job of it. You know, modeled spatial interactions, 1000s of moieties, etc… As it is, I just feel… disappointed. http://phylogenomics.blogspot.jp/2012/07/for-those-interested-storification-of.html Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf
bornagain77_{March 25, 2016
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Microbe with stripped-down DNA may hint at secrets of life - Mar 24, 2016 Excerpt: The newly created bacterium has a smaller genetic code than does any natural free-living counterpart, with 531,000 DNA building blocks containing 473 genes. (Humans have more than 3 billion building blocks and more than 20,000 genes). But even this stripped-down organism is full of mystery. Scientists say they have little to no idea what a third of its genes actually do. "We're showing how complex life is, even in the simplest of organisms," researcher J. Craig Venter told reporters. "These findings are very humbling.",,, The genome is not some one-and-only minimal set of genes needed for life itself. For one thing, if the researchers had pared DNA from a different bacterium they would probably have ended up with a different set of genes.,,, The genome is "as small as we can get it and still have an organism that is ... useful," Hutchison said.,,, http://hosted.ap.org/dynamic/stories/U/US_SCI_SKINNY_GENES
as to:
The genome is not some one-and-only minimal set of genes needed for life itself. For one thing, if the researchers had pared DNA from a different bacterium they would probably have ended up with a different set of genes.,,,
In the following video, Dr. Paul Nelson gives the main reason why you will get a different set of genes:
,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.” Paul Nelson – quoted from 103:48 minute mark of the following video Whatever Happened To Darwin's Tree Of Life? – Paul Nelson – video https://youtu.be/9UTrZX47e00?t=3820
You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:
Estimating the size of the bacterial pan-genome Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,, http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf
And completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm
Thus that is the main reason why you will get a different set of Genes for different bacteria. This is not the first time Venter has ruffled Darwinian feathers. In the following video, Dawkins just about had a cow when Venter told him there was not really a Darwinian 'tree of life':
Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! - video Quote: "I think the tree of life is an artifact of some early scientific studies that aren't really holding up.,, So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. " - Dr. Craig Venter, American Biologist involved in sequencing the human genome http://www.youtube.com/watch?v=MXrYhINutuI Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 19 variants of the genetic code). Simple counting question: does "one or two" equal 19? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html Universal Genetic Code? No! - January 18, 2016 Excerpt: “To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA… “,,, This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal. This, of course, is often cited as evidence for evolution.,,, In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book. http://blog.drwile.com/?p=14280
bornagain77_{March 25, 2016
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I am wondering how banana genome with its 37,000 genes and Apple genome with 57,000 genes (both more than human genomes) ever evolved.Me_Think_{March 25, 2016
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