Thursday, March 24, 2016

Mycoplasma mycoides Just Destroyed Evolution

“We’re Showing How Complex Life Is”

Call it Mycoplasma mycoides lite—researchers have established what is approximately a minimal organism by removing about half of the genes from the Mycoplasma mycoides genome. 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.”

Yes, humbling, if you are an evolutionist. This is because this result shows how astronomically impossible evolution is in its hypothetical early stages. Simply put, there is no way such an organism is going to randomly evolve.

The origin of life problem can be divided into two broad categories: ground-up and top-down. In the ground-up approach, evolutionists try to figure out how the first life could have arisen spontaneously from an inorganic world. In spite of the evolutionist’s claims to the contrary, the century-long ground-up research program has utterly failed.

That leaves the top-down approach. Here, evolutionists work with simple, unicellular life forms, carefully removing parts one at a time in their search for smaller, simpler life forms. If evolution is true, they should be able to reduce life to a very simple, basic form which could conceivably arise by chance somehow.

This approach has been failing as well, as in recent years all the signs pointed to a minimal life form consisting of at least a few hundred genes—far beyond evolution’s meager resources of random change.

Now, this latest research has upped the ante. It is just getting worse. A minimal organism consisting of 473 genes is many orders of magnitude beyond evolution’s capabilities. Simply put, the science contradicts the theory. What the science is telling us is that evolution is impossible, by any reasonable definition of that term.

Religion drives science, and it matters.

127 comments:

  1. You seem to have severely misread the article. You certainly missed this part which directly contradicts what you claimed in the OP.

    "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. For another, the minimum genome an organism needs depends on the environment in which it lives.

    And the new genome includes genes that are not absolutely essential to life, because they help the bacterial populations grow fast enough to be practical for lab work.

    The genome is "as small as we can get it and still have an organism that is ... useful," Hutchison said."


    Maybe read more slowly next time.

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    1. Sorry, we know all about that. There is a tradeoff between genome size and performance. You can get a few less genes, but you'll quickly end up with an organism that just sits there and is not viable in the real world (it may not even be viable at 473 genes). We are way, way beyond evolution's resources.

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    2. Cornelius: "We are way, way beyond evolution's resources."

      Given that I have yet to see you present anything but a misrepresentation of evolution, it's unclear how your assessment of its resources is relevant.

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    3. To give a very specific example of Cornelius misrepresentation, implicit in Venter's minimally viable organism is the need to exhibit high-fidelity replication. This is because, unless an organism can make a high-fidelity copy of itself, in addition to consuming a petroleum spill or synthesizing a drug, we would have to make them one at a time and replace them when they wore out. Nor could we test a specific set of genes for minimum viability because you'd end up with something else.

      Again..

      "Rather, the [earliest] history of [evolutionary theory] was a lengthly, highly inaccurate, non-purposeful period of construction that eventually produced those instructions out of elementary things where none existed. Those elementary things are simple chemicals, such as short strands of RNA, that can perform only low-fidelity replication and therefore do not exhibit the appearance of design."

      Venter's minimally viable organism doesn't fit that description. As such it's unclear how "Mycoplasma mycoides Just Destroyed Evolution."

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  2. Gee, thanks for the clarification ghostrider, 400 genes is infinitely less complex than 460. Do you understand the laws of probability? Do you know the limits of probability?

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    1. Do you understand that the earliest life on the planet wasn't made up of extant genes but their much simpler precursors? Do you realize these experiments are done to give insight as to what those earliest functions may have been, not try to get down to the smallest living cell with extant genes?

      Of course you don't.

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    2. much simpler precursors

      And what scientific evidence is there for those? Oh, that's right, there isn't any. Why not just follow the science instead of the dogma?

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    3. Joe Thornton's work on resurrecting ancient proteins for starters.

      Are you going to delete this answer too?

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    4. No, Thornton's work doesn't help. I'll take his recent January paper, for example:

      http://www.sciencedaily.com/releases/2016/01/160107140423.htm

      It relies on the preexistence of populations, cells, proteins, protein synthesis, etc. (There are other problems with it, by the way, which I will be blogging on.)

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    5. I look forward to your detailed technical rebuttal of the Thorton/Prehoda team's latest work. The paper is open access.

      Evolution of an ancient protein function involved in organized multicellularity in animals

      Of course the paper isn't about OOL which makes your objections about "preexistence of populations, cells, proteins, protein synthesis" all be irrelevant.

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    6. What peer reviewed scientific journal will this detailed technical rebuttal be published in? I assume you'll be submitting it to eLife, the publisher of the original paper. Is that correct?

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    7. Oh, of course. They just love papers that question evolution.

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    8. They love papers that back up their claims with supporting evidence. Of course if there is no such evidence it's not surprising the work won't be submitted to the publishing journal.

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    9. For sure, they're all about the science.

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    10. Cornelius, just out of curiosity, how many rebuttal papers (about evolution) have you tried to submit to peer-reviewed science journals only to have them rejected?

      Maybe you can post the one that you think has the most merit, along with the reviewers' comments, and we can discuss it.

      Just a thought.

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    11. William Spearshake

      Maybe you can post the one that you think has the most merit, along with the reviewers' comments, and we can discuss it.


      I second this. Instead of the constant barrage of Baghdad Bob EVOLUTION IS DESTROYED!! assertions maybe we could see an actual entire scientific paper presenting the ID-Creationist case.

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    12. Cornelius: "It relies on the preexistence of populations, cells, proteins, protein synthesis, etc. (There are other problems with it, by the way, which I will be blogging on.)"

      I don't see how adding a designer to the mix improves the problem because it relies on the pre-existence of, well, a designer, which would be well adapted to the task of designing organisms. Or are you saying there can be a designer that isn't well adapted to designing things? How would that work, exactly? Can just anything design something?

      Cornelius: "And what scientific evidence is there for those? Oh, that's right, there isn't any. Why not just follow the science instead of the dogma?"

      First, see above. Do you have evidence of designers that are not themselves complex and well adapted for the purpose of designing things? If you're going to limit theories to what we have observations of (which is bad philosophy, by the way), every designer we've observed has had a complex, material brains. So, should one follow your own logic and philosophy regarding what is or is not scientific, a designer cannot be the solution to the problem.


      Second, no universal theory can be proven using a series of individual observations. Evolution, as a universal theory, is the best explanation for what we observe. Why?

      Some designer that "just was" complete with the knowledge of just the right genes would result in just the right proteins that would results in just the right features, already present, does't serve an explanatory purpose. That's because, one can more efficiently state that organisms "just appeared", complete with the knowledge of just the right genes would result in just the right proteins that would results in just the right features, already present. Neither case accounts for the origin of that knowledge.

      And, knowing how likely I'll be misrepresented, Neo-Darwinism isn't the latter. Neo-Darwinism is the theory that complexity arises from variation and selection. It genuinely didn't exist before. That's a universal explanation for the growth of knowledge, in brains, books and even genes. It's also the explanation for why we see specific order in which complexity appears.

      ID has no explanation for that order as, given an abstract designer with no defined limitations, It could have been in the most complex to the least complex, or all at once. Yet, that's not what we observe. Apparently, there can be no explanation for that order other than, "that just what the designer must have wanted"

      Of course, please correct me if I'm wrong. Do you have an explanation for that order?

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    13. I wrote: "Some designer that "just was" complete with the knowledge of just the right genes would result in just the right proteins that would results in just the right features, already present, does't serve an explanatory purpose. That's because, one can more efficiently state that organisms "just appeared", complete with the knowledge of just the right genes would result in just the right proteins that would results in just the right features, already present. Neither case accounts for the origin of that knowledge. "

      The funny thing is, I'm guessing Cornelius disagrees with this, yet apparently doesn't have any good criticism of it.

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  3. Let's see now. 473 genes having 531kb. In other words this minimal organism has over 500,000 base pairs. This means that the search space for this relatively simple lifeform is 2^500,000!

    Now imagine using RM+NS to arrive at this complexity. You would need a computer the size of trillions of universes running at trillions of cycles per second and you would not make a dent in it! This is the curse of dimensionality, the dreaded combinatorial explosion.

    Now, imagine evolving this gene via RM+NS to arrive at a whale or even a lowly insect with thousands of genes and you quickly realize that evolutionists are a bunch of stupid dirt worshippers and snake oil salesmen selling an unsuspecting public a stupid religion based on stupid superstition.

    When will the lie end?

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    1. This means that the search space for this relatively simple lifeform is 2^500,000

      Oh, but wait, that is just one possible solution of many. The search space is actually much smaller, more like 2^300,000. See, problem solved.

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    2. Yeah, I've seen this stupid response elsewhere. What else can one expect from dirt worshippers but stupidity and lies?

      Heck, it would not make any difference is the number of base pairs was just 1000 or even 500.

      But even if by some fairy magic, it were possible for dirt to be the natural mother life, it does not make the combinatorial explosion disappear and you end up dinosaurs and whales cavorting about. The search space continues to grow exponentially with every new base pair you add into the mix.

      We will need a new world order to dismantle this religion of crackpots and thieves. Somehow, the thieves managed to convince the governments of the world that their business was all about science and, as a result, they have stolen and continue to steal billions of dollars of the taxpayer's money with impunity. But not for long.

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    3. Very respectful reply there Louis.

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    4. Dirt worshippers are lying jackasses, members of a church of morons. You deserve no respect.

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    5. You don't know jackshit about Christianity other than what you learned from your YEC buddies. Go pack sand somewhere or something. You tree-dwelling, primitive jackass. LOL

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    6. There's Louis being respectful again. For some reason the blog owner doesn't mind Louis' constant potty mouth.

      Delete
    7. Cornelius: "Oh, but wait, that is just one possible solution of many. The search space is actually much smaller, more like 2^300,000. See, problem solved."

      Again, a designer doesn't solve this problem. It only pushes it up a level without improving it. You're still left with a designer that "just was", complete with that solution, and millions of others, already present. Nothing in ID explains the origin of that solution, or any others.

      Problem solved?

      Sure, if you think that knowledge comes from authorities sources, then I guess you think that improves the problem. But that's a very specific philosophical position on knowledge. And a very parochial one at that.

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    8. ghostrider:

      There's Louis being respectful again. For some reason the blog owner doesn't mind Louis' constant potty mouth.

      Crybaby. You fool nobody with your crocodile tears, Mr. Dirt Worshipper. Stop proselytizing for the stupid Church of Flying Dirt Monster. Go back antievolution.org and stay there where you belong.

      LOL

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  4. Perhaps bio chemical control system made of a network of regulatory proteins that guide process of cell activities didn't evolve from a baggie of self replicating molecules :D

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    1. I think you have a paper there ...

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    2. Think. Again.

      Papers are better with DATA

      Delete
  5. Cornelius Hunter: The search space is actually much smaller, more like 2^300,000.

    You seem to be conflating evolution and abiogenesis. If the first life requires hundreds of genes in a precise configurations, then abiogenesis would not be possible. However, that doesn't mean that life hasn't evolved since the advent of life. Meanwhile, abiogenetic researchers believe that life began as much less integrated structures.

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    1. If the first life requires hundreds of genes in a precise configurations, then abiogenesis would not be possible.

      Well someone finally said it. Of course will never be held to this. They have already deployed the multiverse to get around any such nuisances. And ...

      Meanwhile, abiogenetic researchers believe that life began as much less integrated structures.

      There you go again. Those "researchers" are, of course, evolutionists who have an ax to grind and will never let science speak for itself. Why not just admit the truth?

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    2. Abiogeneis researchers are professional scientists who publish their results in peer reviewed scientific journals. Anyone who disputes their findings is free to write up their technical rebuttals and submit them to the same journals for publication. Yet this never happens. Seems like those who are rejecting the work only do so on religious grounds.

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    3. Cornelius Hunter: Those "researchers" are, of course, evolutionists who have an ax to grind and will never let science speak for itself.

      http://molbio.mgh.harvard.edu/szostakweb/

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    4. Jack Szostak also shared the Nobel Prize in 2009 for his work on telomerase.

      Maybe one of the astute readers out there can list the ID-creationists who have won the Nobel Prize for their work on creation science.

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    5. Jack Szostak also shared the Nobel Prize in 2009 for his work on telomerase.

      Oh, I forgot that. So OOL must be true.

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    6. Zachriel, the dirt worshipping psycho:

      However, that doesn't mean that life hasn't evolved since the advent of life.

      Moron. The search space increases exponentially with every new base pair. Learn some math, you superstitious imbecile. Go back to your cretinous church and leave other people alone.

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    7. Cornelius Hunter: Oh, I forgot that. So OOL must be true.

      No, but we should be able to dispense with the use of scare-quotes as in "Those 'researchers' are, of course, evolutionists who have an ax to grind and will never let science speak for itself."

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    8. Those tree-dwelling primitives are not researchers. They are lying dirt worshippers, just like you.

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    9. Cornelius: "There you go again. Those "researchers" are, of course, evolutionists who have an ax to grind and will never let science speak for itself. Why not just admit the truth?"

      Remind me, how does science "speak for it self?" Oh that's right. You never explained how that worked, in practice.

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    10. Cornelius, do you think dinosaurs are *the* explanation of fossils? Is this an example of science "speaking for it self"?

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  6. Could you please point me to a recent paper that suggests that the OOL process started with a DNA containing bacteria? As far as I know, the only people who claiming this hugely improbable scenario are IDists.

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    1. When evolutionists resort to less probable, more obscure, explanations because the science is contradicting them, it is not a good thing.

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    2. When you can produce the science that contradicts them, you can get back to me. Until then, you are just using the "incredulity" argument.

      OOL research has never suggested that the simplest of DNA based cells just proofed into existence. To make such a claim would just be crazy talk not supported by a speck of evidence. It's a good thing that no rational person would suggest that the OOL proceeded in this way. Well, nobody except creationists.

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    3. When you can produce the science that contradicts them, you can get back to me.

      This is the "shifting the burden" fallacy that Darwin used, and has been used ever since. From Origins:

      If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

      Claim evolution is true in spite of the science, then place the burden on the scientist to prove a universal negative. Assign to .

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    5. Dirt worshipper:

      When you can produce the science that contradicts them, you can get back to me. Until then, you are just using the "incredulity" argument.

      LOL. The dirt worshipper wants to see science. All you cretins have come up with a Himalayan-size mountain of superstition and bone-headed stupidity. Go back to school and learn some math, you small-cranium, cargo cult primitive.

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    6. This is the "shifting the burden" fallacy that Darwin used, and has been used ever since.

      And boy, have you learned it well.

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    7. This is the "shifting the burden" fallacy that Darwin used, and has been used ever since.

      And boy, have you learned it well.

      Delete
  7. WS:

    Somehow life arose spontaneously from non-life. That's the claim. That sounds like poofing to me.

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    1. All dirt worshippers are pooferists by nature. It's in their genes.

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  8. "Somehow life arose spontaneously from non-life."

    If by "spontaneous" you mean through numerous incremental steps and chemical reactions, involving (at some stage) self replicating molecules, then yes. But only an IDist would claim that this was "poofed" into existence.

    Meanwhile, the competing claim is that some non-defined intelligence (who we all know is the Christian God) designed life as we know it, or at least the "kinds" of life we see today, and then "poofed" them into existence. Or is it the ID claim that they werent't "poofed" into existence? And if not, where is the research on the mechanisms that were used? Why is ID so adamant about refusing to propose mechanisms for realizing the designs and testing these hypotheses? What are they afraid they will find? Or not find? Or are they just concluding that God's ways are beyond our understanding, as they were taught since Sunday School, and therefore it would be a waste of time (or a sin) examining them?

    If ID wants to be a competing theory to evolution, it must come up with something other than "poof". This is not shifting the burden of proof, it is just asking for some "proof".

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    1. Dirt worshipping pooferist, accusing others of being pooferists:

      If ID wants to be a competing theory to evolution, it must come up with something other than "poof". This is not shifting the burden of proof, it is just asking for some "proof".

      Nobody needs to show you any proof, you jackass. You don't deserve squat. You are an imbecile who needs remedial math. You are an inconsequential, door-to-door missionary with stupid beady eyes, selling holy dirt.

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    2. WS:
      You are trying to make a straw man argument again. Intelligent design is an inference explanation just like evolution and origin of life. This finding is clearly supporting to the competing hypothesis for evolution and OOL research.

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    3. Bill: "You are trying to make a straw man argument again."

      You calling it a strawman argument doesn't make it one.

      "Intelligent design is an inference explanation just like evolution and origin of life."

      True. But not of equal validity. Not even close. One of them actively conducts research, develops hypotheses, tests the hypotheses and modifies the hypotheses based on the observation. The theory of evolution is constantly being tweaked to better fit the evidence. As science requires. It was significantly enhanced with the new synthesis, and continues to be modified with every new finding. What was the last (or most significant) modification to the theory of ID? Changing the name from Creationism to Scientific Creationism to Intelligent Design is just re-branding, not a modification based on evidence.

      There hasn't been one because ID refuses to develop any testable hypotheses about the mechanisms involved.

      "Poof" is not a testable hypothesis.

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    4. WS:

      If something happens that violates the laws of nature that we are familiar with, and we can't explain how it happened within the laws of nature, then that sounds a lot like poof to me.


      And how about this for a testable hypothesis? If organisms were designed then they should have characteristics of designed things. Do they have characteristics of designed things? Why yes, they do.

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    5. "If something happens that violates the laws of nature that we are familiar with, and we can't explain how it happened within the laws of nature, then that sounds a lot like poof to me."

      Did you ever think that maybe the laws of nature as we know them may need modification? But what laws of nature are you referring to that the evidence is violating?

      "
      And how about this for a testable hypothesis? If organisms were designed then they should have characteristics of designed things."


      The "appearance" of design is not testable. A crystal appears to be designed. They form naturally all the time, but I can also produce them in my kitchen. If you had the appearance of design and an explanation for the mechanisms for the manufacture, then that shoukd be testable. Do you have that?

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    6. natschuster

      If organisms were designed then they should have characteristics of designed things.


      What are the characteristics of designed things? AFAICT designed things can have any characteristics at all - simple, complex, many parts, one part, big, small, light, heavy - depending on what the designer wants.

      Name one characteristic present in all designed things.

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    7. Nat: "And how about this for a testable hypothesis? If organisms were designed then they should have characteristics of designed things. Do they have characteristics of designed things? Why yes, they do."

      Yes, Nat. Human beings are good explanations for human designed things. They have trade offs and exhibit complexity that appears in conjunction with corresponding limits in our knowledge.

      We did not observe ABS brakes on the first cars, not be cause we didn't want to stop better but because we had yet to create the knowledge of how to implement them. And when ABS did appear on cars it's because we created the knowledge. We can say the same about virtually everything else human beings have designed.

      Cars cannot be resigned every year because car manufacturers have limited resources. And they must price their cars so customers will buy them. They must be relatively safe, performant and efficient, but only to a limited degree or they will be too expensive. Of course, there are exceptions because there are customers that will pay millions of dollars for just one car. Tanks are significantly safer, but they cost significantly more to build and are significantly slower and less efficient, etc. So, the things we design are explained by our human limitations.

      However, ID's designer is abstract and has no defined limitations. As such it there is no limit on what it knew or when it knew it. It has no limitations on resources and needs no customers to pay for operations and research. So, it explains nothing beyond "That's just what the designer must have wanted." It could design all new cars every month, every day or even for each individual customer on the spot. And it upgrade them all instantly, rather than making customers come in for a recall. It would have known about the problem before it rolled of the assembly line.

      Sure, if you believe in a being that is completely self sufficient, perfectly complete, has no needs, gets what it wants by sheer will, and has some perfectly good plan that we cannot comprehend, I guess you might think that fits. But it doesn't explain anything beyond how to reconcile your theological beliefs with what we know about biology.

      If our supposed immaterial soul can somehow interact with our material brains, then our material to non-material ratio is arbitrary. Having a brain would be unnecessary because our immaterial soul could just as well have interacted with our material nerves directly, rather than having a material intermediacy. And the same could be said about our eyes. If our soul can interact with our material brains, then it could just as well interact with material photons, etc. IOW, your own claims imply that human biology is arbitrary and inexplicable. "That's just what the designer must have wanted".

      It would come as no surprise that the work of a inexplicable mind in an explicable realm must be inexplicable, should we attempt to take it seriously. Otherwise, that inexplicable mind couldn't have done it. And you know it did because the inexplicable mind told you so, via some inexplicable means.

      Biology cannot be explained because, if it could, your inexplicable designer couldn't have done it. Therefore, explicably must be denied at all costs and we get blogs precisely like this one.

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    8. WS: The law of nature I was referring to the the law that says that small molecules don't spontaneously join together to from large molecules. And are you saying that we must modify the laws of nature we are familiar with to accomodate OOL theories? Isn't that cheating?

      And I guess I wasn't clear enough. I meant that we should in organisms characteristics that we know form making stuff that are characteristics of designed things only.

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    9. WS: The law of nature I was referring to the the law that says that small molecules don't spontaneously join together to from large molecules. And are you saying that we must modify the laws of nature we are familiar with to accomodate OOL theories? Isn't that cheating?

      And I guess I wasn't clear enough. I meant that we should in organisms characteristics that we know form making stuff that are characteristics of designed things only.

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    10. "Poofing" into existence is as good a term for the phenomenon as any. Poofing water into wine, loaves and fishes out of "nothingness", resurrecting a formerly inanimate pile of organic material (Lazarus). With ease and complete control over the outcome. Abject and total mastery of matter energy and time. Wow. I for one am impressed by those reports. And made the necessary adjustments and accommodations.

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    11. Creation is not falsifiable, or testable. We do not and will never have a toolbox by which to structure any experiment. Creation is NOT scientific and makes no claim to be. Creation is simply beyond the scrutiny of the created. On the other hand evolution is falsifiable, and easily dispatched. Strangely, spontaneous generation from dirt must have been an exceedingly rare event, because it has never been seen to occur since. How strange.

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    12. cv5:

      evolution is falsifiable

      It would be difficult to find an idea that has been contradicted more by the science. And yet it is proclaimed to be a fact. I wouldn't call that "falsifiable."

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    13. It would be difficult to find an idea that has been contradicted more by the science. And yet it is proclaimed to be a fact. I wouldn't call that "falsifiable."

      There's a difference between "not falsifiable" and "not falsified". Evolutionary theory is in the latter category.

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    14. Cv5:

      I, for one don't have a big problem with poofing. Evolutionists say poofing is cheating, yet are okay with life poofing into existence.

      And, if creationism is not falsifiable, why do evolutionists claim to falsify it?

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    15. Creation is not falsifiable, or testable. We do not and will never have a toolbox by which to structure any experiment. Creation is NOT scientific and makes no claim to be. Creation is simply beyond the scrutiny of the created. On the other hand evolution is falsifiable, and easily dispatched. Strangely, spontaneous generation from dirt must have been an exceedingly rare event, because it has never been seen to occur since. How strange.

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    16. The problem with evolutionist poofing is the long long odds. And yet....here we are. Accounting for the web of life and biosphere in total and compounding probabilities....fuggetaboutit.

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    17. Cv5:

      Evolutionist say that they have falsified creationism by claiming that God would never do things a certain way.

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    18. Second guessing a God they do not claim to know and expressly claim to disbelieve? Doesn't make much sense to me.

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    19. "Second guessing a God they do not claim to know and expressly claim to disbelieve?"

      Well said, however, many evolutionists *do* believe in that god. Remember, evolution comes from theists, not atheists. As for today's atheists, yes, I think you are right, their atheism provides no basis for their metaphysical claims about what a creator would do. As Alfred North Whitehead observed, the problem lies not in what people seek to defend, but in what they take for granted, and see no need to defend.

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    20. Cornelius: "As for today's atheists, yes, I think you are right, their atheism provides no basis for their metaphysical claims about what a creator would do."

      If you're referring to my comment, I'm wondering if you actually read it. My point was, since ID's designer is abstract and has no defined limitations, it's unclear why such a designer would design what we observe, as opposed to something dramatically different that what it could have designed. As such, it adds nothing to the explanation. That's not a metaphysical claim about what a designer would do. That's pointing out that ID adds nothing to the explanation.

      Of course, ID's designer has no defined limitations so one can insert their preferred supernatural designer. However, pointing out God could have chosen otherwise isn't any more of a claim of what a creator would do, either.

      On the other hand, the claim that a creator created what we observe is to claim that it *would* choose to create things in the order of least complex to most complex, which is entirely unnecessary, since it could have created them in the order of most complex to least complex or even all at once. Again, pointing that out is not a claim about what a creator would do, but would be capable of doing, should we attempt to take the claims of others about a creator seriously as an explanation for what we observe. You want to be taken seriously, right? Or is it just all dogma?

      It's ironic that being more open and less dogmatic about what a creator could have done is misrepresented here as being "metaphysical claims about what a creator would do."

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    21. Cornelius: "It would be difficult to find an idea that has been contradicted more by the science. And yet it is proclaimed to be a fact. I wouldn't call that "falsifiable.""

      Of course, the idea you're referring to is the history of life on earth, rather than evolution, the universal theory. You do realize they are not the same thing, right?

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    22. Scott:

      "If you're referring to my comment, I'm wondering if you actually read it."

      No, I was referring to a great many comments, made by many atheists over the years, making metaphysical claims. Here is an example from the LA Times:

      http://darwins-god.blogspot.com/2009/05/sermon-from-pz-myers.html

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    23. So, first, you're referinng to something that wasn't mentioned at all on this post?

      Second, if God being good has virtually no consequences for what he would or would not do, then what does it mean to say God is good? How can we criticize the claims of others?

      Do I need to believe that Superman exists to criticize a claim that someone who was injured by lead projectiles while in the process of stoping a bank robbery was Superman? No, I don't. I'm merely taking the claims of others seriously for the purpose of criticism. Since Supeman is supposedly impervious to normal projectiles, the claim contradicts itself. No personal belief is required.

      What you seem to be implying is that God cannot be explained. Therefore, no consequences can deduced to give meaning to the statement "shaping history for the benefit of human beings".

      Otherwise, what prevents us from doing just exactly that?

      Delete
  9. Not much new here :

    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.

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  10. (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.

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  11. William
    Sorry to post down here: the reply button was stuck. When you say that ID refuses to propose a testable mechanism I say you are making a straw man because you are not arguing against the evidence for design you are saying you won't engage the discussion until ID has a testable mechanism which it may never have. If evolution can show a directly testable mechanism that validates how diversity arose then it is game over. Until then the debate is over indirect evidence not mechanisms. I agree with you that there has been more testing on the evolutionary biology side but we still short of testable hypothesis that validates a mechanism for diversity. I am honestly interested to see how an argument would go focused on the design vs nature inference.

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    1. Bill: "Sorry to post down here: the reply button was stuck."

      Not a problem, I run into that as well. I like Apple but it is not always compatible.

      "I say you are making a straw man because you are not arguing against the evidence for design you are saying you won't engage the discussion until ID has a testable mechanism which it may never have."

      Let's turn this upside down. If you found a crystal and knew absolutely nothing about the chemistry of crystallization. It has all of the earmarks of design. Based on that, should you jump to the conclusion that it is designed? That is what you are asking me to do. You are asking me to accept that a flagellum (eye, whatever) simply because it has the "appearance" of design.

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  12. William
    "Let's turn this upside down. If you found a crystal and knew absolutely nothing about the chemistry of crystallization. It has all of the earmarks of design. Based on that, should you jump to the conclusion that it is designed? That is what you are asking me to do. You are asking me to accept that a flagellum (eye, whatever) simply because it has the "appearance" of design."
    Nice volley thanks.
    I am asking us to consider this as positive evidence for design and then weigh it against the evidence for nature or negative evidence for design. I don't know where this comes out but I have yet to see a good debate here where each side is not constantly moving the goal posts. It would actually be interesting to debate it and then change sides.

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    Replies
    1. Thanks Bill. All I am trying to say is that the burden of proof seems to all be on the evolution side. I don't really have a problem with this because we are the only ones that seem to be doing any work on this. But if ID wants to make the claim that they have a competing explanation, don't you think that they should have a similar burden of proof?

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  13. WilliamThanks Bill.
    "All I am trying to say is that the burden of proof seems to all be on the evolution side."
    I don't think either side is in position to prove anything. Since there is no direct testable mechanism then there is evidence based on inference. I am proposing lets have a friendly brainstorm and see what we think afterwords. I am on the fence if ID is a value added to science. Thats why I would like to discuss it. I agree when creationists argue from the position that you can't test your mechanism they in this case are creating a straw man. Thats why a discussion with stable goal posts might lead to some interesting ideas.

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    Replies
    1. Bill, thank you for a respectful discussion.

      " I don't think either side is in position to prove anything. Since there is no direct testable mechanism then there is evidence based on inference."

      I am not sure how you can argue that evolution does not have direct testable mechanisms. Random mutations are a mechanism and testable. Natural selection is a mechanism and testable. Genetic drift is a mechanism and testable. Transposition, shifts, inversions, etc. Are all mechanisms and testable.

      ID on the other hand, "poof".

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    2. William
      For evolution to have a testable mechanism for the overall theory it would have to establish how specie A turned in to specie B. You can show how the genes vary through the mechanisms you mentioned but evolving a complex new protein function or new alternative splicing codes takes specified sequences. i.e. How does genetic drift etc move specie A to specie B. The emergence of novel sequences is a mystery at this point. On the ID side I can devise a test for a specified sequence i.e. does the measured sequence match a known sequence but I still don't have a mechanism that made the change from specie A to specie B. Without a known cause of the effect we are claiming we really don't have a theory. We have an argument based on inference.

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    3. I'm afraid that I have to disagree. Allopathic speciation proposes that reproductive isolation will result in the different populations going along different variation and selection paths. This has been demonstrated (tested) in bacterial cultures. It predicts that island populations will differ from island-to island, and from island to mainland.

      If you are asking for a step-by-step explanation down to the molecular level, you will never get it. I assume that this is not what you are asking.

      With regard to evolving new protein functions, we have seen this both in the wild and in the lab. And we know the specific mutations that were needed.

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    4. Bill Cole

      For evolution to have a testable mechanism for the overall theory it would have to establish how specie A turned in to specie B.


      This has been done.

      Molecular evolution tracks macroevolutionary transitions in Cetacea


      Of course it doesn't detail every last mutation as ID-Creationists stupidly demand but it's more than enough compelling evidence to the scientific community.

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    5. Of course it doesn't detail every last mutation as ID-Creationists stupidly demand but it's more than enough compelling evidence to the scientific community.

      So here we have a dirt worshipping crybaby complaining for being called a stupid moron while calling critics of his dirt worshipping religion, "ID-Creationists who stupidly demand".

      You just love to shed those crocodile tears, don't you, dirt worshipper? Go back to your stupid Church of the Flying Dirt Monster and leave those creationists alone, you hypocritical jackass.

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    6. William
      "If you are asking for a step-by-step explanation down to the molecular level, you will never get it. I assume that this is not what you are asking."

      Unfortunately the molecular data is in conflict with the observed data. Gene timing alternative splicing and the formation of sequences. Since there is contradiction of the stated mechanisms of modern evolutionary theory we currently only have an inference that it can be formed in nature. The genome is a sequence and we have no idea how specific sequences are formed in nature except by humans. How would you try to prove how the genome of specie A is modified to create the genome of specie B without a detailed biochemical reconciliation. Without that work I don't see anyway to determine the cause. Since making this detailed case is currently out of reach, the strongest case you can make is an inference based of observations. So which side has the strongest case supporting its inference, design or an undiscovered law of nature?

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    7. Bill Cole

      How would you try to prove how the genome of specie A is modified to create the genome of specie B without a detailed biochemical reconciliation. Without that work I don't see anyway to determine the cause.


      Once again Bill Cole ignores the evidence presented and keeps singing his sad little Creationist song "I don't see no evidence!". Pathetic.

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    8. Bill: "The genome is a sequence and we have no idea how specific sequences are formed in nature except by humans."

      That's simply false, Bill. Neo-Darinsims is the idea that biological complexity emerges from variation and selection. The sequence is an emergent property. Organisms are template replicators as described by Von Neumann.

      Now, you might subscribe to the idea that theories are derived from observations, but that would be mistaken. There are multiple examples to the contrary. For example, we never actually observed atoms doing anything before atomic theory was developed. Rather, atoms were an unseen, conjectured explanation about how a part of the world works. And that explanation has survived criticism in the form of observations from experimental tests designed to find errors in that theory.

      So, there is plenty of empirical evidence. It just takes the form of criticism post theory development, rather than positive proof or evidence used to create the theory in the first place.

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    9. ScottBill: "The genome is a sequence and we have no idea how specific sequences are formed in nature except by humans."

      That's simply false,

      You claim this is false but you don't show why.

      That's simply false, Bill. Neo-Darinsims is the idea that biological complexity emerges from variation and selection.

      Can you cite an example of a complex functional sequence forming from the process you describe?

      If not then you claim that my statement is false turns out to be false:-)

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    10. Biill, you said we had "no idea" how sequences form beyond human beings. Again that's false. I provided such an idea that is widely accepted in the field of biology because it has withstood over 150 years of criticism.

      Now, what you seem to be asking for is positive proof that sequences appeared in the distant past in a different environment with different competing factors and which cannot be reproduced because not all life is recorded in the fossil record. Unless we had a time machine, no number of empirical tests could ever satisfy that demand.

      Simple organisms that are not viable today could be viable in the past due to the lack of competition from more complex and better adapted life. No one thinks the minimum organism we can build out of existing parts today is equivalent to be most primotive replicator in the past. That is because this minimal organism is capable of high-fidelity replication, which is not thought to be a feature of the most primotive replicators.

      For example, to be useful in the lab, organisms needs to exhibit high-fidelity replication. But that's not necessarily a requirement in the past. The earliest history of evolutionary theory consisted of a protracted period of non-purposeful, low-fidelity replication, which would or net us from build organisms that can produce new drugs, eat chemical spills or even test genetic variations.

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    11. Scott
      "Biill, you said we had "no idea" how sequences form beyond human beings. Again that's false. I provided such an idea that is widely accepted in the field of biology because it has withstood over 150 years of criticism."
      I think this point is melting down under criticism at this point based on discussions I have had and observed on this blog and others. I have yet to hear a good explanation how you can find function mutating through sequences, the largest mathematical spaces in the universe. If you are willing to try to debate this subject with evidence I will keep an open mind.

      "For example, to be useful in the lab, organisms needs to exhibit high-fidelity replication. But that's not necessarily a requirement in the past."

      Why would the past be any different? The theory requires simple to complex to make sense. The only evidence that is surfacing is that minimum life is complex so the origin event is quite a mystery.

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    12. Bill Cole

      I have yet to hear a good explanation how you can find function mutating through sequences, the largest mathematical spaces in the universe


      Why do you continue to repeat this dishonest claim? You've had it explained to you many times evolution doesn't have to search through the entire search space of all possible genetic combinations. It merely searches the space immediately next to an already existing functional configuration. Selection / drift then keeps the modifications that work the same or better in the current environment. That process has been ongoing since the first biotic self replicators formed over 3.5 billion years ago, slowly building up the forms we see today.

      Please stop repeating your tired old creationist canard.

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    13. ghost
      "Why do you continue to repeat this dishonest claim? You've had it explained to you many times evolution doesn't have to search through the entire search space of all possible genetic combinations."

      Then how would a entirely new typer of protein evolve? Ie a nuclear protein that has to fit together with shape and charge with a dozen other transcriptional proteins? What is your proposed mechanism of how this happens?

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    14. Then how would a entirely new typer of protein evolve?

      Through the same mechanisms. Evolution works by modifying existing structures.

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    15. GR
      "Through the same mechanisms. Evolution works by modifying existing structures."

      A very solid just so story. Travel to the end of the universe and back. No problem evolution can do it :-)

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    16. Bill Cole

      "Through the same mechanisms. Evolution works by modifying existing structures."

      A very solid just so story.


      You can see evidence for it in any freshman level biology book or even with a simple Google search. But as a Creationist I understand you aren't interested in educating yourself.

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    17. GR
      "You can see evidence for it in any freshman level biology book or even with a simple Google search."
      Really? I can find experimental evidence of nuclear proteins being formed by RMNS.
      An even better just so story. What a wonderful imagination you have:-) In the prior post you named chemistry as the evolutionary mechanism for forming the flagellar motor . Again, very imaginative.

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    18. Bill Cole

      In the prior post you named chemistry as the evolutionary mechanism for forming the flagellar motor . Again, very imaginative.


      Darn Bill, you nailed us scientists again. Here's the real way the flagellum was created

      Delete
  14. This comment has been removed by the author.

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  15. If he minimal cell was created 15 years ago the conclusions would be that scientist do not know what 90% of the genes do. Right now there are only about 30% left. In the next 10 years i predict that there will be 10% or less of genes with unknown function. The whole point of the minimal genome paper was to find out what we do we know and what we still need to investigate. How is that destroying the theory of evolution? Looks like someone is really confused here.

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    1. Because the *minimal* organism is light years beyond what spontaneous evolution can create.

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    2. Of course that this model minimal cell is still very complex organism but look at this huge progress that was made in the last 60-70 years. First we learned about DNA, then we learned how to read it and now we are getting better at "writing" DNA. The progress will be just exponential now since we can design build and test new microbes. My point was that just because we do not understand something now that is not a reason to believe that we will never understand it.

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    3. My point was that just because we do not understand something now that is not a reason to believe that we will never understand it.

      Don't forget that goes against the most basic Creationist tenet:

      "Any new scientific discovery no matter how small that changes and improves our understanding automatically invalidates all the rest of the scientific evidence for evolution."

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    4. Karas:

      My point was that just because we do not understand something now that is not a reason to believe that we will never understand it.

      There is something that we understand perfectly, however. We understand that there are over 500,000 base pairs in this minimal organism. We understand that the search space for a stochastic search mechanism like RM+NS is 2^500,000!

      You could have a massively parallel supercomputer the size of trillions of universes running at trillions of cycles per second and it would not make a dent in this search space.

      Now, imagine evolving this organism via RM+NS to obtain frogs, chickens and whales. That's when you realize that all Darwinists are dirt worshippers who belong to the Church of the Flying Dirt Monster.

      ahahaha...AHAHAHA...ahahaha...

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    5. Bogumil:

      My point was that just because we do not understand something now that is not a reason to believe that we will never understand it.

      Agreed. What we are talking about is the current state of science. Evolutionists are always saying "Don't worry, we'll figure it out in the future," but the science has always, and continues, to contradict the idea that the species arose spontaneously.

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    6. Cornelius: "Evolutionists are always saying "Don't worry, we'll figure it out in the future," but the science has always, and continues, to contradict the idea that the species arose spontaneously."

      Except, neo-Darwinism isn't the theory that any species arose "spontaneously." That's the straw man you keep peddling.

      For example, organisms contains instructions of which transformations of matter to perform to result in a copy of itself. That process occurs in a highly accurate way, which includes error detection, etc. The ability to perform high-fidelity replication is the appearance of design. However, none of that is though to have appeared spontaneously.

      Rather, the easiest history of evolution was a lengthly, highly inaccurate, non-purposeful period of construction that eventually produced those instructions out of elementary things where none existed. Those elementary things are simple chemicals, such as short strands of RNA, that can perform only low-fidelity replication and therefore do not exhibit the appearance of design.

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    7. Scott:

      For example, organisms contains instructions of which transformations of matter to perform to result in a copy of itself. That process occurs in a highly accurate way, which includes error detection, etc. The ability to perform high-fidelity replication is the appearance of design. However, none of that is though to have appeared spontaneously.

      Sorry but, yes, all of that is claimed, by evolutionists, to have originated spontaneously.

      Rather, the easiest history of evolution was a lengthly, highly inaccurate, non-purposeful period of construction that eventually produced those instructions out of elementary things where none existed.

      You just defined "spontaneous."

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    8. High fidelity replication did not appear spontaneously.

      We had no instructions, a lengthly period of highly inaccurate non-purposeful period of replication, then eventually, after much time, high-fidelity replication.

      I don't know how you get "spontaneous" out of that. Again...

      "Those elementary things are simple chemicals, such as short strands of RNA, that can perform only low-fidelity replication and therefore do not exhibit the appearance of design."

      Or are you disagreeing as to what is referred to by "the appearance of design"?

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    9. It's not even clear we would consider the first replicators part of a species since it did not exhibit high-fidelity replication. So how could a species appear spontaneously?

      Why don't you start out by explaining what would be a non-spontaneous appearance of an species, then point out how evolution doesn't fit that explanation? Please be specific.

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    10. I don't know how you get "spontaneous" out of that.

      Perhaps you don't know what "spontaneous" means. It does not mean rapid. Recall that a chemical reaction evolves to a lower energy state (lower Gibbs energy, which accounts for entropy as well as bonding energies) *spontaneously*. It may take a century, but it will move to the lower Gibbs energy spontaneously (on its own, without external energy / forces applied).

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    11. Scott:

      The evolutionist's claim that evolution is a fact entails the claim that it is a fact that the universe is at a lower Gibbs energy with all the millions of species, compared to a world where they did not evolve. That is absurd.

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    12. Cornelius Hunter

      Recall that a chemical reaction evolves to a lower energy state (lower Gibbs energy, which accounts for entropy as well as bonding energies) *spontaneously*. It may take a century, but it will move to the lower Gibbs energy spontaneously (on its own, without external energy / forces applied).


      Apparently they never covered endothermic and endergonic reactions at your school.

      How do you think photosynthesis works?

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    13. Cornelius Hunter

      The evolutionist's claim that evolution is a fact entails the claim that it is a fact that the universe is at a lower Gibbs energy with all the millions of species, compared to a world where they did not evolve.


      Reference please. Which "evolutionist" every claimed that, and where?

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    14. Cornelius: "Perhaps you don't know what "spontaneous" means. It does not mean rapid."

      Unless you can point to a theory of evolution that posits the first primitive replicators formed in deep interstellar space, where it is completely cold and dark (as opposed to a young earth or another planet like it) can you see why I might ask for clarification?

      Cornelius: "Recall that a chemical reaction evolves to a lower energy state (lower Gibbs energy, which accounts for entropy as well as bonding energies) *spontaneously*. It may take a century, but it will move to the lower Gibbs energy spontaneously (on its own, without external energy / forces applied)."

      Yet, what's missing here is what you mean by "on it's own, without external / forces applied" in the context of evolution. Again, can you see why I've asked for clarification by via a contrasting example? To repeat...

      I wrote: "Why don't you start out by explaining what would be a non-spontaneous appearance of an species, then point out how evolution doesn't fit that explanation? Please be specific."

      It doesn't matter what label we put on it. Nor does it need to be exhaustive. We merely need a clarification on what you mean by "spontaneous" that is sufficient to make progress on the issue at hand. You do want to actually make progress, right?

      Delete
  16. Mapou, we have been over this before. If you can't keep up with the adults intellectually, maybe you should find some other kids to play with.

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    1. No you haven't. You are just lying as usual. Mr. Dirt Worshipper.

      I will never tire of repeating it because I know it hits you idiots where it hurts the most. LOL

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    2. What does the Flying Dirt Monster's asteroid smell like today, dirt worshipper?

      ahahaha...AHAHAHA...ahahaha...

      Delete
  17. I love the fact that Darwinists are in retreat, desperately trying to defend their dying secular religion. Good riddance to the greatest scientific hoax of all time.

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    Replies
    1. There is another great scientific hoax out there but I must agree that Darwinism takes the cake.

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    2. Mapou: "There is another great scientific hoax out there..."

      Let me guess. Relativity?

      It amazes me that a man who can't string two sentences together without being abuses is smarter than two of the top scientis of the last century and a half. Who should I believe?

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  18. In the end, the proof of the pudding is in the eating. In 1952 Stanley Miller succeeded in producing a few amino acids from inorganic chemicals. More than 60 years later, nobody has managed to create any form of life given the most elaborate laboratories imaginable. All they can do is blah-blah on and on over why abiogenesis is, according to them, possible. An RNA world, parallel combinations, many viable outcomes, etc., etc. This is all just speculation and so much hot air. If life can arise by chance, surely somebody should be able to do it in a laboratory. It stands to reason that well trained chemists in well equipped labs should be more capable than blind chance. Maybe blind chance is not such a good bet.

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    1. well its better u religi9us do stick to what u all do best ... like molesting little kids ... for abiogenesis on pre-biotic earth is cracked , thanks to the max planck institute in 2013 .....and we engineered ouselves nucleobases in 2010 to speedup ""time"" for a test of the last reaction of abiogenesis ...the moment life happens after the long chain of reactions called abiogenesis....and managed to have life emerging without our guidance...we just let the nucleobases fight it out among themselves and life emerged ... and it was an even more complex life as ur skyfuhrer made ...for we r just out of 4 nucleotides ... xna is 6 nucleotide based .... it evolves prospers and has promising medical applications as well ..


      end of god ... for the gazillionth time ..... har har har har har

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