Sunday, February 10, 2013

Craig Venter Discusses the Tree of Life

I don't know where this clip comes from or when it was made but it's being promoted on YouTube as "Dr. Craig Venter Denies Common Descent in front of Richard Dawkins!" The link was posted by someone in a comment to a previous post on Sandwalk.

Everything that Ventor says is correct. He didn't need to quibble about the universality of the genetic code but it's true that there are variants.

His point about the tree of life is correct, especially in a discussion about the origin of life. It's unfortunate that Richard Dawkins repeatedly makes such an issue about the tree of life because he's on shakey ground when he does that. I assume that Dawkins hasn't studied the problem. However, he's in good company since most scientists don't understand the problems with the early tree of life. The early history of life looks more like a bush with many interconnecting branches due to horizontal gene transfer [The Tree of Life].



266 comments:

  1. It doesn't even seem like he's denying it, he's more uncertain about to what degree the genetic code could be said to be evidence for it.

    Of course, the evidence for universal common descent doesn't stop at the genetic code, I know Douglas Theobald published a pretty comprehensive argument arguing for it via a different line of evidence.

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  2. Variants of the genetic code are quite numerous but slight. Far from underimining the essential unity of the code, they demonstrate that the code itself has undergone evolution in the past, and so can't have been created once and forever in a unique perfect form.

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  3. Single celled organisms are a web of life, not a tree, not even a bush. Multi- celled life is arguably more like a tree. So the diagram has more than one shape.

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  4. The clip comes from The Great Debate - What is Life? that took place in 2011, with such speakers as Richard Dawkins, J Craig Venter, Sydney Altman, Lee Hartwell, Paul Davies, Chris McKay, Lawrence Krauss, Roger Bingham.

    Peter McKay's comments starting at around 5:50 mark and Craig Venter's at around 7:40 mark all the way to 11:40 are quite amusing...

    To create life from scratch, Venter admitted, that he would have to "cheat" to some extent... Cheat??? What does he mean??? I won't tell you yet... ;)

    In response to Lawrence Krauss' question regarding what the minimum gene set would be to create life from scratch, Venter responded not only that there wouldn't be a minimal gene set for that, "there would multiple ones", but also, that ..."(he)is not so sanguine as some of his colleges (there), that there is only one life form on this planet..." ...which indicates what..??? You can view the rest here...and come up with your own conclusions...

    http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel

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  5. I don't read Dawkins as being overly concerned about the structure of the tree as opposed to its rooting. Does a bush/net mean more than one LUCA? The differences between codes are vastly over-hyped (eg EN&V, which links to the whole video, tries to lecture Dawkins that there are !!!17!!! variant codes). But any two codes differ by two or three bases at most - it is only by comparing all codes that one can determine that in all 9 (out of 64) codons vary. Which is still sod all, really.

    If there are separate origins, we might also wonder how the base pairs were arrived at - convergent evolution? There are theoretical other pairings that could exist, and the otherwise curious observation that methylUridine is the DNA base in every organism known - again, convergence?

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    1. I totally agree. It could be true that Dawkins does not know about the genetic code variants, but the point he wants to make to a wider public is that related to the root of the diagram that connects all life on Earth. There is considerably amount of evidences (e.g., biochemical and genetic) supporting that all life forms are related by common ancestry.

      It's also true that "genetic code" is sometimes not meant to be the correspondence between amino acids and triplets of nucleotides, but the sequence and type of bases in DNA. This is incorrect and very misleading but it is how I have noted it is sometimes treated in the media. Did Richard have this erroneous notion of genetic code in mind when he was speaking? Maybe...

      We have to keep in mind that Dawkins does not generally talk to evolutionists and the intentions of his speech is usually directed to a more general public.

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    2. @DEvoLUTIONIST Allan Miller, Sergio Andrés Muñoz Gómez

      Stop your idiotic speculations!!! Just because you can't swallow something, it does not make it wrong. Dawkins was at the table with the cream of the cream. Just read the list of speakers. Are you suggesting he forgot his basics? That's too bad. Professor Moran has already commented on Dawkins' stupidity...for the lack of better word...He just can't be somethings he is not... That's what happens to theoretical evolutionists when they spend 100% of their time promoting ideas others are testing in the lab. They forget what the test tube looks like... Amen!!!

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    4. John, what's with this assault on speculation anyway? Is there some intrinsic problem with speculation?

      I agree, we should not confuse said speculations with established facts, but please don't tell people to stop speculating. That's scientific defeatism. The dulling of curiosity, creativity and intellect.

      With respect to your requests for evidence of how organic compounds are made under natural conditions in the atmospheres, crusts of planets, and in outer space, I suggest you go and spend 10-15 minutes on google scholar. Here's a few suggested keywords: Spark-discharge, experiment, prebiotic chemistry, hydrothermal vent, geochemistry, photochemistry, abiotic synthesis.

      Mix and match them as you wish and see what turns up. Who knows, you jus might learn something about what work has been done in the field. Quick hint: Amino acids, amino acids everywhere. And primitive fatty acids, and sugars, and bases and... so on and so forth.

      PS: If your search comes back fruitless, you're an incompetent moron, or lazy, or both.

      EDIT: Spelling etc.

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    5. @John Witton Stop your idiotic speculations!!! Just because you can't swallow something, it does not make it wrong. Dawkins was at the table with the cream of the cream. Just read the list of speakers. Are you suggesting he forgot his basics?

      I'm suggesting - no, saying - that you are making something out of nothing. Venter did not say anything incorrect - and neither did Dawkins. This was a comparatively informal conversation. The title "Venter makes a fool of Dawkins" is just bollocks.

      Person A: "America and England use the same language"
      Person B: "They do not share the same language - there are many differences"
      Person A: "OK, I see what you mean - but they are clearly related ... aren't they?"

      That is the nature of Venter's "Mycoplasma" distinction. UGA codes for tryptophan instead of STOP. That's it. 63 out of 64 codons shared. I think you (and, for different reasons, Prof. Moran) are just indulging a little gratuitous Dawkins-bashing. I'm pretty sure he understands both HGT and the nature of 'different codes'.

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    6. @Allan Miller,

      I think you (and, for different reasons, Prof. Moran) are just indulging a little gratuitous Dawkins-bashing. I'm pretty sure he understands both HGT ...

      I'm pretty sure that Dawkins doesn't agree with those who question whether there's a tree of life. One of the most profound implications of the net of life is that it's consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species. In other words, there may not be a single LUCA (Last Universal Common Ancestor). Dawkins does not like that. It's not what he says on the lecture circuit.

      Dawkins is in good company. He signed a letter to New Scientist about the cover I showed in the post above. The other signers were Jerry Coyne, PZ Myers, and Daniel Dennett. Here's part of what they said ...

      Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.

      Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.


      The banyan tree is a good analogy but it's still not a net. And it's just not true what they say about HGT. The problem is, in fact, serious enough to obscure the branches.

      BTW, I alos opposed the cover of New Scientist but for different reasons.

      New Scientist Sheds its Last Ounce of Credibility
      Darwin Was Wrong?

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    7. One of the most profound implications of the net of life is that it's consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species.

      The most parsimonious interpretation of the data, per Theobald, is a single LUCA for protein-coding life. That is, obviously, based on molecular phylogenies, which at that scale preserve deep-time protein coding and fundamental RNA modules, but granted not every base. But we can also apply the principle of parsimony for the genes underlying the 55 invariant codons, and the fact that their invariance indicates they were already fixed in protein. We can also look at the minor variation among the other 9, and the commonality of DNA and RNA bases (which could be otherwise). Nowhere is there any direct support for a ‘multiple LUCA’ – especially if we are clear that LUCA is the last common ancestor. Retroviruses (for example) are not ancestors. So we dub an even more ancestral organism the last common gene ancestor: LUCGA.

      If we follow whole-genome copying back for every organism on earth, we appear to converge on LUCA. In doing so, we pass through symbiosis events whose partners had the same common ancestor, and undoubtedly see many other shorter fragment transfers joining the mainline flow. It is quite possible that, when we get to ‘whole-genome LUCA’, we still find genes in her descendants that did not come from her, but from a contemporary through HGT. But there is still a common ancestor of LUCA and that contemporary - LUCGA.

      If (as you must be) you are suggesting that genes from two completely independent origins, right back to first replication, could come together and function in the same individual, that’s quite a claim, with no evidence beyond the possibility provided by HGT. HGT (like sex) only works because the organisms are related, however distantly. Why would independently-originated DNA even be expected to use the same bases?

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    8. Yes, it would seem extraordinaryly unlikely to imagine that life originated twice independently, both evolved the same genetic code relatively simultaneously and then horizontally transferred seqeunces between them that just happened to work well in both "species" upon translation.

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    9. @Allan Miller,

      when I said ...

      One of the most profound implications of the net of life is that it's consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species.

      I meant exactly that. It does not mean "evidence for" and it does not mean that I support the idea of multiple origins of life. I mean exactly what Craig Venter meant in his talk.

      The old tree of life based on ribosomal RNA has a single common ancestor. The modern net of life, based on a large number of genes, does not. Therefore it is not scientifically correct to say that all modern species descend from a single common ancestor. You can say that, based on currently available scientific evidence, there was probably a single origin of life but that's not the same thing.

      @Rumraket,

      I'm a proponent of metabolism first. I think the evidence supports an origin scenario where nucleotides and the genetic code arose much later than cells that could carry out rudimentary energy metabolism and synthesis of small molecules like simple amino acids.

      I think there was a time when a simple genetic code accounting for only a few amino acids began to operate. That process could have evolved independently around many different thermal vents. There would be a great deal of redundancy in the primitive code and this would be compatible with all sorts of gene swapping events.

      Not only that, but different self-replicating RNAs could have independently come into existence in different locations. If the primitive cells were mobile they could have fused during the RNA world to produce hybrids with a variety of active RNA catalysts.

      I support the Co-Evolution Theory of the Genetic Code. I imagine that primitive life went through a period of one hundred million years or so with primitive genetic codes encoding only a handful of amino acids.

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    10. I wonder if there is a slight confusion between gene trees and species trees going on here. Even if there was a lot of horizontal gene transfer, there could still be a simple species tree instead of a net, only it will be much harder to infer. Systematics classifies groups of species, not gene copies.

      ---

      Independently of that, I wonder if it is plausible that there could be different origins of life which are then able to intermingle; at a minimum, that would require some very fortuitous parallel evolution of the genetic code, otherwise you could not use some other progenitor's genes. Maybe there is just one best genetic code, but it seem implausible to me. And if you solve the problem by saying "metabolism first", well, was that really already "life" then or was it just chemistry, and origin of life happen later and still only once?

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    11. @Larry Moran,

      I appreciate the point, but when you chide Dawkins for doggedly clinging to some outmoded paradigm, you present no sound reason he should do otherwise. Theobald and clear commonality in most codons point to a single organism, and AFAIK no evidence points the other way. The HGT that muddies multi-gene trees is still in protein-coding organisms, and they still have mostly invariant codons, and ribosomes, and tRNA and aaRS, suggesting all the shuffling has happened since those were fixed. It's possible (though unlikely) that the genetic code itself was cobbled by HGT of codon assignments from multiple organisms, but even so, what were they most likely descended from - common, or different, ancestors?

      What went on before that 'bottleneck' organism from which we appear to have inherited a DNA-RNA-protein system already pretty well fixed is up for grabs, but there does appear to have been a genuine bottleneck, on the evidence. According to Theobald, the scrambled phylogenies still resolve on a single ancestor. And that's as far back as we can get.

      There is nothing in principle forbidding multiple origins - except the need for convergence of some kind to permit their merger. So I can accept it as a possibility, and I'm sure Dawkins would too. There's just no evidence for it.

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    12. @Allan Miller.

      Dawkins supplied his own rope for the hanging of Darwinism when he stated in his book that"...

      The genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means 'start reading here' or 'stop reading here,' is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization)...

      ...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." The Greatest Show On Earth (2009, p. 409-10)

      How many variants do we have so far? 23 or is it 24 now? Can't keep up...

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  6. To create life from scratch, Venter admitted, that he would have to "cheat" to some extent... Cheat??? What does he mean??? I won't tell you yet... ;)

    It only goest to show that it's quite impossible to design and create life. Which is just fine: life wasn't created.

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    1. @ Piotr Gasiorowiski
      Then what? It's easier for life to create itself? Why? Just because you chose to believe so? You may be suffering from a very acute case of DEvoLUSIONS... Regular shrink won't do it for you. You need a team and 24/7 observe room... I know a good one in Poland-Warsaw, but you are in Poznan :( too bad...

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    2. Easier? Perhaps, if you have a whole planet, a global ocean with more than a billion cubic kilometres of "primordial soup" and all imaginable local combinations of physical and chemical conditions, solar and thermal energy galore, and several hundred million years at your disposal. Craig Venter isn't so lucky, and he knows his limitations.

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    3. @Piotr
      Where did the soup come from? Give me a reasonable explanation and then I might buy it...Tell me though that you are not an IDiot and can explain that in naturalistic terms... If you decided to believe it, it is fine with me but what makes you feel better than creationists? (I'm not one of them...just in case..)

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    4. Where did the soup come from?

      "Organic" compounds such as amino acids, hydrocarbons, alcohols, carboxylic acids, purines and pyrimidines can form spontaneously throughout the Universe. They occur even in meteorites. And we are talking not about just a few distinct compounds but tens of thousands, and more:

      http://www.scientificamerican.com/article.cfm?id=murchison-meteorite

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    5. Venter is a "true" scientist not moron...How he interprets his findings is his choice. But you can only interpret misspellings which puts you in what category? Howlers and nie znam polkie slowa but idiots is good enough,,

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    6. @ Piotr
      "Organic" compounds such as amino acids, hydrocarbons, alcohols, carboxylic acids, purines and pyrimidines can form spontaneously throughout the Universe. They occur even in meteorites. And we are talking not about just a few distinct compounds but tens of thousands, and more"

      Where did the organic compounds come from? Show me a testable theory or idea that will prove their appearance from nothing and then their formation into organized molecules and then to living, simple organisms...I'm sure you are not bluffing, because that would be inexcusable... Can't wait...

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    7. The tests have been done, maybe if you at least bothered to spend 10 minutes on google scholar, you'd see countless of examples of experiments in prebiotic chemistry that demonstrate organic compounds can be created in a whole host of naturally occurring conditions.

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    8. @John Witton: I'm not responsible for you basic education deficiency. If you are generally as science-illiterate as your postings may suggest, I'm afraid you may be beyond help. But perhaps you are just feigning complete ignorance for the sake of successful trolling. In that case you might want to read this summary of progress in prebiotic chemistry achieved by the early 2000s:

      http://www.oup.com/us/pdf/Rigoutsos/I-SampleChap.pdf

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    9. Piotr, Rumraket, correct me if I am wrong, but.....
      JW's challenge included, "and then their formation into organized molecules - and then to living, simple organisms"

      He is not interested in experiments that resulted in pistons and exhaust pipes. He would like to see a testable THEORY or IDEA that produces an automobile. Oh, and perhaps an automobile that gives birth to little tiny automobiles that go on to produce MORE automobiles.

      Prebiotic chemistry, for all it has accomplished, has not accomplished the equivalent of that.

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    10. His original question (before he started shifting the goalposts) was about the origin of the "primordial soup". There is no problem with that. Organic molecules including amino acids and other compounds regarded as the "building blocks" of life have been found in meteorites and samples of comet dust. Carbon atoms link with one another to form lattices so easily that pretty complex carbon compounds are produced spontaneously in interstellar and protoplanetary environments.

      Living system as we know them were not simply assembled overnight from simple parts -- so much is certain. There is no testable theory of prebiotic chemical evolution on Earth as yet. There are some loose ideas and insights. So what? If we ever learn more, it will be thanks to biochemical research, not to theological speculation or psychedelic visions.

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    11. Sorry, Piotr, perhaps I'm only responding to Rumraket then, who said 'the tests have been done'.
      He wrote this directly below JW's comment that said, "Show me a testable theory or idea that will prove their appearance from nothing and then their formation into organized molecules and then to living, simple organisms."

      The tests have not been done.

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    12. Rumraket, apparently, doesn't read very well, at times. Either he just skims over portions of what has been presented to him or he doesn't understand their implications. Or he bluffs.

      But he likes to use the word 'fuck' a lot. I guess that's a plus?

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    13. You're right, I did skim over his post and didn't notice the latter part about watching life crawl out of the test tube. My apologies for that. Though Piotr still has a point about shifting the goalposts, because his demands kept growing.

      With respect to creating life, that haven't been done yet of course, we haven't created life from scratch.

      But the problem is that I get you're among a set of people to whom this appears a fruitless search? What's your suggestion here, should we just give up and declare goddidit?
      Then when we've done that, shouldn't we do the same with cancer research, the total amount of hours spend reseaching astronomically outweighs the total amount of hours spend doing lab-work in prebiotic chemistry? You prepared to stop that too?

      Now more to the point of what mr. Witton was asking about, a testable hypothesis at the very least, I suggest he start here:
      http://www.ncbi.nlm.nih.gov/pubmed/12594918

      Several tests of that specific hypothesis are ongoing.

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    14. Rumraket writes,
      "But the problem is that I get you're among a set of people to whom this appears a fruitless search? "

      You 'get' that? Um, no.

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  7. A great line from Dawkins, in that it encapsulates the hubris of scientism. The clip doesn't show what he is referring to, but that isn't important - probably some discussion of developing life in a laboratory. Dawkins reveals that he is perplexed that it should be considered an 'ethical problem' and goes on to say that he can see how it might be considered a 'problem of expediency' in that one 'might fear that it would escape and overrun the world or something, but ETHICAL problem?'

    To Richard Dawkins, scientists need not be concerned with the ethics of experiments that might, in his own words, overrun the world? The fact that he doesn't consider this an issue of ethics is very telling, in that he is sort of a poster child of 'scientism', the very existence of which of course he denies. He says that 'scientism' is merely a charge made by people from other disciplines such as philosophy and theology who are upset that they have 'lost'.

    This is a very clear example of why the scientific imperative - to know at all costs, because knowledge is that important - though not wrong in and of itself, needs to be tempered by other disciplines that are much more closely focused on outcomes, consequences, right, wrong and morals. It is why Larry Moran's vision of a '21st century based on reason and science' needs to be looked at with concern and skepticism.

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    1. You've said nothing about why it sould be considered an ehtical problem either, other than the thing about overrunning the world, which you even concede he acknowledged. Then what the fuck is the problem again?

      Another theist with a Dawkins obsession. In other news, water is wet.

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    2. 'other than that thing about it overrunning the world'
      Priceless.

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    3. Rumraket, sometimes it is good practice to reverse a situation, in order to see if perhaps our prejudices are showing in terms of leniency or harshness toward something that someone has said.
      For example, let's say that YOU heard an evangelist say the following:

      "I don't see how converting native tribes to Christianity at gunpoint is an ethical problem. I mean, it may be a problem of expediency, in that the natives are more likely to resent and resist the conversion if it comes through force. But an ETHICAL problem? We are talking about the poor creatures' eternal SOULS! It would only be an ETHICAL problem if were to consider NOT doing it!"
      See? He admits that the natives won't like being converted. So what the fuck is the problem again?

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    4. Rumraket, since your comment indicates that -and I hope I'm wrong - you haven't given consideration to the ethical issues related to the potential for massive harm to the environment or any citizens thereof resulting from scientific experiments, let me happily inform you that numerous professors at the University of West Virginia, from a variety of disciplines have given a lot of thought and consideration to it. Given the question, What Role Should Ethics Play in Science? - they put their thoughts into essays which can be found here.
      http://thequestion.blogs.wvu.edu/questions/2009/12/1/what-role-should-ethics-play-in-science-
      You might be interested in hearing their views.

      One of the professors, from the Chemistry department, wrote this
      " Finally, a scientist is responsible to the public and the environment. Their public comments must be made with care and accuracy. Scientists must serve the public interest and safety, understand and anticipate the environmental consequences of their work, and minimize pollution."

      I agree with him. If there is a chance that an experimental life form might be released into the larger environment with unknown consequences, that is far from an issue of 'expediency'. It is an issue of ethics.

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    5. What an utterly ludicrous pile of nonsense to throw at me. Are we held at gunpoint at the possibility of creating life?

      I really don't see what it is you want to argue about, there's a difference between saying merely creating cellular life is intrinsically an ethical issue(i don't see why it would be), and saying that said created life could potentially be harmful.

      The thing is, considerations of the latter is already established procedure at all accredited universites. I know, I've worked at several. Work is happening routinely with potentially dangerous chemicals and organisms and all sorts of procedures are in place with respect to protecting both the lab workers themselves, and not releasing various forms of pollutants into the environment. Don't get me wrong, mistakes happen and people can be lazy and uncareful, but that's not what we're talking about.

      There's nothing about the subject discussed in the video that merits any greater or special considerations than are already happening in university research faculties the world over. I get it, religious people hate Richard Dawkins and can't help hammering on every little utterance the man makes, but it gets boring pretty quickly. It's a storm in a teacup. Get a better hobby.

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    6. Wow. You really don't get it. Creating life is an ethical issue. You are way out of the mainstream if you don't think that. You are way out of the mainstream if you don't think that people who are hesitant about it are so for religious reasons only. I guess you didn't live in the 20th century.

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    7. Rumraket writes,
      ' Don't get me wrong, mistakes happen and people can be lazy and uncareful, but that's not what we're talking about.'

      No. That's what we are talking about.

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    8. Then your argument has no specific relevance to creating life, it's a more general concern about proper laboratory operation.

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    9. of course! But the greater the potential for harm, the greater the concern. Thus, the greater degree of ethics involved. If history has provided examples of (it has) things that, when tested in the lab are 'failsafe', have proven to be quite otherwise when put into the greater world of people doing work -and that includes human tendencies of laziness, cutting corners, laxness, forgetfulness, etc. - then it absolutely becomes an ethical, rather than logistical, concern as to whether or not experiments should go forward.

      It doesn't mean they SHOULDN'T go forward, necessarily. It just means that the question as to whether or not they should is inherently ethical.

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  8. @Peter Gasiorowski

    Holy schnikes!!! I have to admit that I expected pretty much anything but Stanley L. Miller's famous experiments in relation to the prebiotic soup... This is what happens when one has never been to the lab and relies on others to do the work for him, so that he can sleep better with the belief he wants to believe in... What a pity...
    I have to admit,that I've neglected to read all the 54 pages of blubber...
    ...I actually only read the first sentence and I've had enough...

    " The origin of life remains one of the humankind’s last great unanswered questions, as well as one of the most experimentally
    challenging research areas."

    I've asked for testable theories or ideas and the first sentence says there aren't any...

    Well, if your "faith" in the origin of life is based on theories that are based on others theories that can't be tested, you might as well become a believer, because I guarantee you, that this kind of belief requires more faith than the belief in Supernatural or ID.
    However, to continue the fun, I have found a really humorous and yet educational video of Professor Robert Shapiro, who at one point in his scientific career earned a nickname "Dr. No", for obvious reasons revealed in the video...

    http://www.youtube.com/watch?v=ku9wUbbPVYg

    Enjoy!!!

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    1. I have to admit,that I've neglected to read all the 54 pages of blubber...
      ...I actually only read the first sentence and I've had enough...


      Fuck you, then.

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    2. I wonder why there are some people that defend this tree of life concept so dogmatically? It does not work, its not science and everywhere you look its being uprooted! Here is a published article in nature that compounds the problem!

      http://www.nature.com/nature/journal/v493/n7432/full/493305f.html

      With 83% of the tree of life data missing or unable to backup the claim and only 17% verifiable are you content that the tree of life is true? Is 17% good enough evidence for you? Not for me, no sir my standards for belief in something is at a bar much higher than 17%.

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    3. For those really interested here is a good source!

      http://opentreeoflife.org/

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    4. Andre, this is approaching trolling behavior. There's a difference between saying the old tree analogy has been overturned by webs at the base of single-celled organisms, and claiming that 83% of the tree of life is missing.

      You didn't understand the publication you cited. It's not that 83% of the tree is missing(as if there's millions of species for which we don't have data at all or someting to that effect), it's that of the roughly 6200 papers surveyed in your reference, many of the publications are old and nobody apparently bothered to save their data.

      More to the point, many of the missing published phylogenies are sub-kingdom phylogenies intended to resolve the trees within, for example, fungi(a lot of which could be at such low levels as phyla). Apparently a lot of people didn't bother saving their alignment data, so we can't go back and check wether those phylogenies are correct.

      But there's a significant difference between not being able to verify their data and see how baker's yeast relates to Saccharomyces pastorianus, and claiming that the basis for resolving the interrelationships between kingdoms and domains are gone. Quick hint: They aren't. We still know roughly how distantly related you are to fungi, compared to how distantly related you are to plants, and so on.

      You're still a mammal, a primate and a great ape. The evidence for this isn't gone and it's pretty unambigous.

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    5. 17% x 6193 papers = 1053 papers confirming common ancestry.

      Papers supporting special creation: 0

      Yeah, that's good enough evidence for me.

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    6. I wish I was as gullible as you, ignorance is bliss they say and you prove that!

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    7. Rumraket.

      An ape you say? 45 000 000 base pairs present in us that chimps don't have equally they have the a considerable amount difference from us too! I very much doubt that you can say so if the evidence is inconclusive.

      I need to make my position clear I'm not opposed to common ancestry it is possible but there is not enough evidence to call it a fact, evidence is currently circumstantial at best. If you believe otherwise you're on the wrong track my friend!

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  9. Rumraket,

    This is additional evidence that the tree concept is a man made ideology that is wrong and its needs to be redone! If the data is missing and only 17% remain is the 17% good enough to substantiate or backup the claim that the tree of life in any form is real? No it isn't!

    So call me what ever manes you like.... sticks and stones love, sticks and stones...

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    1. Thank you for confirming a second time that you don't understand the reference you give.

      This is what IDcreationism makes of men's minds.

      Delete
    2. Fortunately, the Discovery Institute has retained every scrap of work it has ever done on bifurcating phylogeny, and it is available ... somewhere ... to blow the entire concept sky-high.

      Delete
    3. I'm not sure why the IDiots try to make an issue of common ancestry, anyway. Common ancestry should be fully compatible w/ ID, which does not require that every species be specially created - Oops, sorry! - I mean "designed." All that ID requires is that God - Oops, sorry! - the "Designer" come down and fiddle with the genomes of extant organisms to create irreducibly complex structures and cause speciation events, things which the IDiots believe lie beyond "the edge of evolution." Acceptance of common ancestry is supposed to be one of the things that distinguishes ID from creationism. And the IDiots are always insisting that, no siree Bob, ID is most definitely not creationism. Aren't they?

      Delete
  10. @John Witton
    I've asked for testable theories or ideas and the first sentence says there aren't any...
    You were given one in this very thread you idiot.

    I guess it's true what they say, in this day and age, ignorance is a choice.

    ReplyDelete
    Replies
    1. Creationist troll-by-numbers. "I'm going to wind you people up good, testable hypothesis, ideology, James Shapiro".

      Coming soon, a whinge about ad hominem and a taunt. Yawn. Next!

      Delete
    2. @Allan Miller
      It's only trolling if you have proof for it...Since there is none...and just as many arguments...your faith remains to be a DEvoLUSION ...What else can it be called???

      Delete
  11. To All DEvoLUSIONISTS:

    "In the interim, looking for topics to get amused with, I got into the question of the origin of life, and knowing the DNA chemistry that I did know — and helped write — I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

    I'm always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words "To be or not to be, that is the question," that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth.

    Christian de Duve, the Nobel laureate, once wrote a letter to Nature which was headed, 'Did God Make RNA?' Because it's hard to think of any other manner in which RNA out of purely abiotic chemistry would assemble itself on the early Earth. Seeing this area called prebiotic chemistry, I decided, my major attention still being funded by National Cancer Institute, and devoted to how chemicals can rip apart DNA as a hobby essentially, I started publishing papers which disassembled — deconstructed, if our German friend wants — so-called prebiotic chemistry, and showed that in every case the result was due to the flagrant interference of the investigator in biasing the results to attain the results that he wanted..."-ROBERT SHAPIRO is professor emeritus of chemistry and senior research scientist at New York University. http://edge.org/conversation/robert-shapiro-life-what-a-concept

    ReplyDelete
  12. Some more proof for DEvoLUSIONS for so-called testable prebiotic chemistry ;)

    "..At one point I went and spoke to the now, unfortunately, late Stanley Miller, and asked him about the circumstances of his famous Miller-Urey experiment — the one with the electric lightning and amino acids were formed — and he handed me a biographical piece he himself had written to something called the Transactions of the Copernican Society or something like that, and he described how in building his apparatus he was concerned with questions of safety, because if you take a flask and you mix it with methane and hydrogen and ammonia, the most likely result is BOOM, with flying glass in all directions, which is definitely not publishable.

    With regard to safety, he built a certain apparatus, let it run for a number of days, and at the end of the days he looked at what he'd found and he found the class of chemicals called hydrocarbon — the stuff that makes up the lakes on Titan but no amino acids whatsoever. And he looked at this and he said, this isn't interesting. And he threw it out. He redesigned the equipment: he said, I was over-cautious. This is not likely to explode. He interchanged the spark and the condenser and he re-ran the experiment, and this time he got amino acids and not hydrocarbons, and he said, Ah ha! And he published.

    Thus we have the famous Miller-Urey experiment showing the inevitability of amino acids on the primitive Earth. And of course the apparatus itself has no resemblance whatsoever to the primitive Earth. One of the popular magazines said that if his apparatus had been left on for a million years, something like the first living creature might have crawled out of it. And I say, if he'd left his apparatus on for a million years, he would have run up one hell of an electric bill. But nothing further would have happened because the spark was in the atmosphere and he'd used up all of the chemicals with carbon in the atmosphere, and the amino acids, which aren't volatile — they don't fly, so to speak — were safely ensconced in the water solution, and the water solution was a collection of non-volatile compounds, well, and the volatile compounds ended up in — so when an experiment goes wrong in organic chemistry you get a black gook and you reach for the potassium bichromate and sulfuric acid — mixed together it's a called cleaning solution — that cleans out about 90 percent of the failed organic experiments that are ever run..."-ROBERT SHAPIRO is professor emeritus of chemistry and senior research scientist at New York University

    ReplyDelete
  13. And more....
    "Since then, so-called prebiotic chemistry, which is of course falsely named, because we have no reason to believe that what they're doing would ever lead to life — I just call it 'investigator influenced abiotic organic chemistry' — has fallen into the same trap. In the proceedings of the National Academy of Sciences about two months ago there was a paper — I think it was theoretical — they showed that in certain hydro-thermal events, convection forces and other attractive forces, about which I am unable to comment, would serve to concentrate organic molecules, so that organic molecules would get much more concentrated in the bottom of this than they would in the ordinary ocean.

    Very nice, perhaps it's a good place for the origin of life, and interesting finding, but then there was another commentary paper in the Proceedings by another invited commentator, who said, Great advance for RNA world because if you put nucleotides in, they'll be concentrated enough to form RNA; and if you put RNA in, the RNA will come together and form aggregates, giving you much more chance of forming a ribosome or whatever. I looked at the paper and thought, How did nucleotides come in? How did RNA come in? How did anything come in?

    The point is, you would take whatever mess prebiotic chemistry gives you and you would concentrate that mess so it's relevant to RNA or the origin of life — it's all in the eye of the beholder. And almost all of prebiotic chemistry is like this; they take chemicals of their own selection.

    People were talking about Steve Benner and his borate paper where he selected, of his own free will, the chemical formaldehyde, the chemical acid-aldehyde, and the mineral borate, and he decided to mix them together and got a product that he himself said was significant in leading to the origin of RNA world, and I, looking at the same thing, see only the hands of Steve Benner reaching to the shelf of organic chemicals, picking formaldehyde, and from another shelf, picking acid-aldehyde, etc. Excluding them carefully. Picking a mineral which occurs only in selective places on the Earth and putting it in in heavy doses. And at the end getting a complex of ribose and borate, which by itself would be of no use for making RNA, because the borate loves to hold onto the ribose, and as long as it holds onto the ribose it can't be used to make RNA. If it lets go of the ribose, then the ribose becomes vulnerable to destruction by all the other environmental agents.

    The half-life of pure ribose in solution, a different experiment and a very good one, by Stanley Miller is of the order of one or two hours, and all of the other sugars prominent in Earth biology have similar instability.

    I was publishing papers like this and I got the reputation, or the nickname in the laboratory of the prebiotic chemist, of 'Dr. No'. If someone wanted a paper murdered, send it to me as a referee. And so on. At some point, someone said, Shapiro, you've got to be positive somewhere. So how did life start? And do we have any examples of authentic abiotic chemistry, not subject to investigator interference?"-Robert Shapiro
    http://edge.org/conversation/robert-shapiro-life-what-a-concept

    ReplyDelete
  14. Robert Shapiro is a proponent of metabolism-first hypotheses, like Larry Moran is. I also gave you a reference to such a hypothesis in this thread Witton, you troll-gimp.

    Tell me, what do you think you achieve citing Shapiro in a thread chuck full of people who agree with him? lol

    ReplyDelete
    Replies
    1. On a related note that really is a very nice interview with Shapiro, thoroughly enjoyed it.

      Delete
    2. @Rumraket
      "Robert Shapiro is a proponent of metabolism-first hypotheses, like Larry Moran is. I also gave you a reference to such a hypothesis in this thread Witton, you troll-gimp.

      Tell me, what do you think you achieve citing Shapiro in a thread chuck full of people who agree with him? lol"

      They are not idiots. They very well know that the hypothesis RNA first is flawed, because it doesn't explain where the energy came from to fuel the production of the first RNA molecules. Besides, researchers have never located a piece of RNA that can replicate itself from scratch, or how nucleotides formed and so on.
      Just because he, or others for that matter, believe in metabolism first, it doesn't mean they can prove it. It makes sense, even to Shapiro, but there is no scientific proof for it. It is all speculative optimism stretching their faith to the limit.

      Delete
    3. @Witton,

      They very well know that the hypothesis RNA first is flawed, because it doesn't explain where the energy came from to fuel the production of the first RNA molecules.

      Ah, bullshit. "it doesn't explain where the energy came from"! Ignorance. In Powner's work on pyrmidines, the energy is UV radiation. That comes from the sun.

      Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Matthew W. Powner, Béatrice Gerland & John D. Sutherland. Nature 459, 239-242 (14 May 2009) doi:10.1038/nature08013.

      Delete
    4. It's hilarious to see Witton quote Shapiro's attacks on the RNA-first hypothesis, which are lucid and educated, but then when it comes to Witton trying to construct arguments of his own, he just embarasses himself as the uneducated ignoramus he is. Hahahahaaa..

      Witton, just stick to quoting Shapiro okay? At least we'll have something intelligent to read.

      Delete
    5. @Rumraket

      How about this? "Origins: A Skeptic's Guide to the Creation of Life on Earth-by Robert Shapiro??? What do you think?

      Delete
    6. Witton: They very well know that the hypothesis RNA first is flawed, because it doesn't explain where the energy came from to fuel the production of the first RNA molecules.

      Again, I repeat: Ah, bullshit. "it doesn't explain where the energy came from"! Ignorance. In Powner's work [cited above] on pyrmidines, the energy is UV radiation. That comes from the sun.

      Delete
  15. @Peter Gasiorowski wrote:
    "It only goest to show that it's quite impossible to design and create life. Which is just fine: life wasn't created."

    You have no clue what you are talking about...Nobody is trying to design or create life. Venter and others are trying recreate life that must've been designed, unless someone proves this otherwise...

    ReplyDelete
    Replies
    1. Venter and others are trying recreate life that must've been designed, unless someone proves this otherwise.

      God of the Gaps is the default hypothesis? Right.

      All creationist arguments depend on either:

      1. Factually false statements, or

      2. Redefinition of the scientific method.

      Here it's 2.

      Delete
    2. @Diogenes
      Firstly, take back ALL you accused of on the other blog, that Professor Moran said on this one WAS ALL TRUE. Then, and only then, I will show you what an idiotic DEvoLUSIONIST you are...

      You wrote:
      "Witton, you're a liar or an idiot.

      Craig Venter denies common descent, says the tree of life is a joke...
      http://www.youtube.com/watch?v=-bMQkAqxNeE


      That video does not say what you say it says, so you're lying or an idiot. Venter doesn't deny common descent, so the title of this video is another creationist lie. Shocking... I'm shocked.

      Everybody knows there's a lot of HGT among bacteria, not among animals and plants. Animals and plants, eukaryotes still form a tree of life and Venter knows it. He even described the bacteria he found as "deeply branching". "Branching" means Venter knows there's a tree.

      Witton, are you a regular at Uncommon Descent?"

      Remember...??? Or the side effects from psychotropic drugs for your DEvoLUSIONS make you selectively forgetful?

      Delete
    3. @Witton,

      You take back what you said.

      You were wrong, and the video proved it.

      I agree with what Venter said in the video.

      Let me repeat my words.

      Me: "Witton, you're a liar or an idiot.

      ...That video does not say what you say it says, so you're lying or an idiot. Venter doesn't deny common descent


      I was right. Venter does not deny common descent in the video.

      You said Venter denied common descent. You're either lying or an idiot.

      Me: so the title of this video is another creationist lie. Shocking... I'm shocked.

      The title of the video is indeed another creationist lie.

      Me: Everybody knows there's a lot of HGT among bacteria, not among animals and plants. Animals and plants, eukaryotes still form a tree of life and Venter knows it.

      Again, I'm 100% correct. Venter talking about the "bush" of life refers to bacteria. I said "animals and plants."

      Me: He even described the bacteria he found as "deeply branching". "Branching" means Venter knows there's a tree.

      Again, correct.

      I was right and Witton was wrong.

      Now you, Witton, said Venter denied common descent in the video.

      I demand you take back what you said.

      Delete
    4. @Diogenes
      I understand you have a problem seeing or accepting things the way they are...That's not my problem.

      Here is the transcript of the video

      Venter:"I'm not so sanguine as some of my colleagues here, that there's only one life form on this planet.
      0:03We have a lot of different types of metabolism
      0:08different organisms
      0:10I wouldn't call you the same life form as the one we have that lives in pH 12 base
      0:14That would dissolve your skin if we dropped you in it.
      0:18I've got the same genetic code. We all have a common ancestor. You don't have the same genetic code
      0:23In fact, the mycoplasmas use a different genetic code that would not work in your cells.
      0:28So there are a lot of variations on the theme... But you're not saying it belongs to a different tree of life from me,
      0:32are you?
      0:34I think that the tree of life is an artifact
      0:38of some early scientific studies that aren't really holding up...
      0:44...the tree...? uh...
      0:45There may be a bush of life…
      0:47Uh... right
      0:48Uh... bush... right... I don’t like that word...
      0:52but that's only... I can see that...
      0:55So there's not a tree of life
      0:59In fact, from our deep sequencing of organisms in the ocean
      1:02out of now... we have about sixty million different
      1:07Uh... unique gene sets
      1:10we found 12 that look like a very, very deep branching... perhaps forth domain of life
      1:16Uh...
      1:17That is obviously extremely rare that only shows up out of those few sequences.
      1:22But it is still DNA based uh... but you ... the diversity we have
      1:26in the DNA world... I'm not so sanguine whether we’re ready to throw out
      1:30the DNA world...
      1:32Maybe ...uh like Richard was saying... what we're going to find is the same
      1:35molecules and the same base systems wherever we look...
      1:40You in fact had a comment... you wanted to make...Richard, right?
      1:41Oh...
      1:42Well, we’d rather moved on... I mean... I was just going to say, I can’t imagine why anyone would think that
      1:47it was an ethical problem...
      1:48I can see why you would think it was
      1:51a problem expediency... You might
      1:54fear that it would escape and
      1:55run around the world or something... but...
      1:58ethical problem...? I can’t see that... But now I'm intrigued by Craig’s saying... bang...! bang...!
      2:16I’m intrigue by Craig saying that tree of life is a fiction...
      2:23The DNA code of all creatures that have ever been looked at is
      2:27all but identical and that
      2:30surly means...
      2:32that they're all related...???"

      Here is Venter's quote from 2007 proving his been doubting commons descent even then. The video just reaffirms his doubts.
      "I have come to think of life in much more a gene-centric view than even a genome-centric view, although it kind of oscillates. And when we talk about the transplant work, genome-centric becomes more important than gene-centric. From the first third of the Sorcerer II expedition we discovered roughly 6 million new genes that has doubled the number in the public databases when we put them in a few months ago, and in 2008 we are likely to double that entire number again. We're just at the tip of the iceberg of what the divergence is on this planet. We are in a linear phase of gene discovery maybe in a linear phase of unique biological entities if you call those species, discovery, and I think eventually we can have databases that represent the gene repertoire of our planet.

      One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common. J. CRAIG VENTER"

      Obviously, even the above won't have any affect on you...Not that I expect anything like that from you...

      Delete
    5. I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me.

      Hmmm. It's counterintuitive to everyone! That's maybe why it wasn't discovered by Stone Age Man. Mycoplasma differs from us by one codon assignment out of 64. If that's grounds to infer separate origins, I'll eat every hat on the planet.

      If he is dredging up protein coding organisms by the bucketful, he is finding organisms with ribosomes, and I'm betting they will have sequence commonality and convergence on a tree (subject, of course, to the usual stochastic noise, particularly in the genes made by those ribosomes). If there are separate origins, that should show up on phylogenetic analysis. Either way, it simply means there is more than one 'tree' (with some interbranch connection, leading many to say "that's not a tree! Trees don't do that!"). There are statistical tests for this kind of thing - you need to do more than have a hunch. Find me a non-protein organism and I may sit up. Or one with a really different code.

      Delete
    6. @Allan Miller
      I posted this on the other blog:
      "Dawkins supplied his own rope for the hanging of Darwinism when he stated in his book that"...

      The genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means 'start reading here' or 'stop reading here,' is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization)...

      ...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." The Greatest Show On Earth (2009, p. 409-10)"

      You wrote: "Find me a non-protein organism and I may sit up. Or one with a really different code".

      Hmmm...I don't think you really know the meaning of "really different code"...

      Would finding non-DNA organism make you sit up? Maybe... for a while until you came up with an excuse..

      Delete
    7. @Witton,

      You're wrong-- you said Venter denies common descent, and you have no evidence of that, including in the video, which some lying creationist labelled "Venter denies common descent"

      Dawkins asks straight out whether mycoplasma, which has a genetic code that differs from ours by one codon, is on a different tree:

      0:28So there are a lot of variations on the theme... But you're not saying it belongs to a different tree of life from me,
      0:32are you?

      Venter does not say that it belongs to a different tree, nor that it belongs to a different bush. He says it belongs to the same bush as we belong to, but they're intertwined.

      0:34I think that the tree of life is an artifact
      0:38of some early scientific studies that aren't really holding up...

      [snip]

      0:44...the tree...? uh...
      0:45There may be a bush of life…

      A bush. Not them on a different tree than us, nor them on a different bush than us.

      Back to Venter:

      1:10we found 12 that look like a very, very deep branching... perhaps forth domain of life
      1:16Uh...
      1:17That is obviously extremely rare that only shows up out of those few sequences.

      "Deeply branching" into WHAT!? A fourth domain of life is not a separate tree and not a separate bush. It is "deeply branching" into OUR tree or OUR bush, take your pick, we are inter-twined with them.

      So the creationist who labelled the video "Venter denies common descent" was lying.

      More obviously, Venter never gets close to challenging that all eukaryotic life forms a tree. That includes animals, vertebrates, mammals, apes.

      So humans and apes are of COMMON DESCENT, humans and mice are of COMMON DESCENT, humans and fish are of COMMON DESCENT, humans and arthropods are of COMMON DESCENT, humans and fungi are of COMMON DESCENT, humans and plants are of COMMON DESCENT, etc.

      As for your additional Venter quote: "One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common."

      In this quote Venter, does not assert that evidence proves there is no universal comment ancestor, and even if he did, it would not be a "denial of common descent" as you claimed, because we and they are intertwined on the same bush, assuming his speculation (not evidence) is correct that there are "multiple COMMON ancestors."

      From Venter speculating, without evidence about multiple common ancestors you assert that he denied common descent. NO, you put those words in Venter's mouth.

      You and apes are of COMMON DESCENT and you cannot find any major scientist denying that-- not even Michael Behe!

      If YOU deny common descent, then you go arge with Michael Behe, who called it "trivial"!

      Delete
    8. @John Witton

      You wrote: "Find me a non-protein organism and I may sit up. Or one with a really different code".

      Hmmm...I don't think you really know the meaning of "really different code"...


      Of course I do. You think I am somehow unaware of the constraint on codon changes? That's precisely why a 'really' different code - no commonality at all, for example - would support a case against universal common descent, or at least push it very deep. But this does not mean that we are forced to conclude that codons can never change. In particular, almost all variant codons function as STOP in one or more lineages. It appears less damaging to piss around with the ends of your protein than something in the middle. Do you think Venter thinks that a single different codon means separate origins down to the roots? Do YOU think that?

      Would finding non-DNA organism make you sit up? Maybe... for a while until you came up with an excuse..

      Lots of things would make me sit up. You starting to get a proper grasp of the science you purport to teach others would be one. But yeah, a non-DNA organism would be conclusive proof of more than one tree of life. Absolutely. Just bring it in to show and tell, and I will happily embrace the 'two-trees' model. I only 'cling to the tree' because that's where all the fucking evidence points!

      Delete
  16. I'd like to stick up for the RNA world - not the most popular view hereabouts, but IMO retaining substantially more merit than Metabolism First, despite acknowledged difficulties.

    See here for an informed (rather than cut 'n' paste gibbering) view of the difficulties and interesting perspectives. Worth it for the title alone: The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)

    http://www.biology-direct.com/content/7/1/23

    Although polymerisation of both peptides and nucleic acids requires energy, it is packaged in the molecules in the latter case - and most notably, in that central denizen of 'metabolism', ATP, an RNA monomer.

    One thing that has some people stumped is the belief that RNA must be single strand. In fact, it hybridises readily, which provides a potential mechanism for 'crystallisation' of both homochiral ribose and bases that pair from a broader spectrum mix of activated sugar-phosphate molecules with various side groups. Molecular stability may be the early criterion for survival, rather than early development of a lengthy polymerase. Complementary sequences stabilise each other. Double strands are less bendy, and hence can grow more before cyclising restricts growth, and being pinned in place, hydrolysis by the 2' -OH is less the fatal issue than it might be to a free single strand.

    Prebiotic peptide bonding contains no obvious mechanism for repeat specification, where base pairing gives it for free.

    Also worth noting that, although ribozymes are weaker and are commonly believed to need significant length, there is a 5-nucleotide ribozyme that will aminoacylate an acceptor stem. I find that a more plausible mechanism of moving towards generating the peptide bond (and 'freezing' amino acid homochirality) than anything I've heard from the Metabolism-First-ers.

    ReplyDelete
    Replies
    1. Explain to me again where the bases come from? What about the ribose - where does that come from? Did someone "poof" it into existence? As for nucleotides .... not possible.

      Delete
    2. Explain to me again where the bases come from? What about the ribose - where does that come from? Did someone "poof" it into existence? As for nucleotides .... not possible.

      You'll note that I have not yet come to the attention of the Nobel Committee for solving every last issue.

      Am I am misunderstanding your intent in using 'metabolism'? Clearly, monomers initially have to arise abiotically. If you want to call that metabolism then yeah, 'metabolism' came first - well, duh!

      But it usually is taken to mean something more, particularly when placed in opposiition to the RNA world. Some complex chemical system that does not simply fall into some thermodynamic well is capable of synthesising all the bits and pieces - not just a few nucleic acid monomers, but repeatable catalytic peptides as well - and then - poof! - it assembles into coordinated units out of which Life somehow crystallises and makes a D-ribose genome ... something like that.

      Any vagueness you may direct at 'RNA world' is equally directed right back. How on earth does nucleic acid 'take over' the co-ordination of pre-existing 'metabolism'? Nah. For my money (which is not very much), 'metabolism', as I would use the term, is something nucleic acid genomes generate as part of the survival/replication thing. I know about non-enzymatic Krebs cycles etc. That simply means that 'controlled' living pathways exploit the thermodynamically favourable.

      I'm also well aware you have to get a nucleic acid 'genome' in the first place, and before that just a few oligonucleotides, and before that monomers, but I think complementarity and hybridisation provide a potential means of 'selecting' short double stranded RNA from what is bound to be an impure mix of products, and chemical stability an early 'selector' of structure, rather than exotic function.

      Delete
    3. Fascinating story, almost as good as Doctor Seuss! Now tell me the story on how it became "alive"!

      Delete
    4. And once you've told me that story please tell me how chemicals got consciousness!

      Delete
    5. Hey Gross, weren't you earlier denying that you have a problem with the origin of life? If you don't, what's this silly trolling supposed to achieve?

      In response to your last question Andre, let's see the reverse: Got any examples of disembodied minds around? You know, minds existing in the absense of physical brains? No? Then please relax your compulsion to argue from your ignorance.

      Delete
    6. Rumraket,

      Speculation is something anybody can do, you me, the Pope but that does not make it true now does it? Here is something I would like to say to you take this anyway you want, Life seems to be rather supernatural in this natural world we live in don't you think? If it was natural why the difficulty in recreating it? Why the difficulty in understanding it and why the difficulty in figuring out how it started? Sure you can just say to me that science will find out one day but that's just another god of the gaps answer.

      Did you hear what Dr Craig Venter said in the interview? He does not believe we will EVER know. That is a pretty strong statement for a guy that knows allot more than you and me about these things. Fact is this life is currently a supernatural entity in this natural universe the lack of science's power to prove it as natural backs my claim.

      Delete
    7. Rumraket writes
      'Got any examples of disembodied minds around?'

      Do you not see that your question is philosophical, rather than scientific? Look, we have one universe; just one. No other to compare it to. It's origin, and the origin of life, remain mysterious.
      Therefore, it either did, or did not, emerge through some form of 'mind'. That it did, or didn't, hasn't been proven or demonstrated either way. If it DID, then EVERYTHING in it it emerged through consciousness, and so everything from an asteroid to a Steven Spielburg movie and a Verdi opera emerged through consciousness. Hence, there would be no 'examples', as you put it, of something that came into existence through any other agency than consciousness.
      If it DIDN'T, then, as you write, there would be no 'examples of disembodied minds around'.
      You are merely stating your preference in terms of which scenario you choose to believe, in the face of inconclusive evidence. You have no more of a 'slam dunk' than Andre does.

      Delete
    8. Rmuraket as for minds please define exactly what you mean? Will it help you if I point out that people who has had a Hemispherectomy retain their memories even after half of their brains have been removed?

      http://en.wikipedia.org/wiki/Hemispherectomy

      Now you know what's interesting about this? It means the brain has redundancy. You can figure out what redundancy means, once done try and fit a goalless, directionless, and chance processes into the mix to see if it works..... Good luck you're going to need it. To get you going here is what redundancy means in this context!

      http://en.wikipedia.org/wiki/Redundancy_(engineering)

      Delete
    9. Andre Gross Yeah where did it come from?

      Yeah! Where? Huh? Huh? It just pinged into existence, the way things do when someone wills it.

      Delete
    10. Allan

      Seriously where did it come from? If there is a materialistic explanation with proper supporting evidence I'll gladly believe it, so where did it come from?

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    11. Speculation is something anybody can do, you me, the Pope but that does not make it true now does it?
      Noone here's claiming their speculations are statements of truth that you must believe.

      Here is something I would like to say to you take this anyway you want, Life seems to be rather supernatural in this natural world we live in don't you think?
      Uhh no, not even remotely. Life is chemistry, chemisty is natural. What drugs are you on and where can I get it?

      If it was natural why the difficulty in recreating it?
      Depends on what you mean by "recreate". Do you mean recreate via a plausible, unintelligent natural process, or just intentionall construct a cell? There's a difference betweeen the two.
      In case of the latter: Cells are extremely small, it's very hard to manipulate molecules effectively without having to rely on forces that dominate at the atomic scale. That really is the main obstacle here.

      Why the difficulty in understanding it and why the difficulty in figuring out how it started?
      Because it's very small and very complicated. We can't directly observe an entire cell down to the atomic level. We have pretty good knowledge of all the different chemical reactions involved, but to really assemble it all into a big picture of an entire cell is beyond extant computer technology. We have to work with generalizations and so on, we are still not at the quantumcomputer level.

      The challenge with understanding life is mainly due to the challenges facing computational chemistry in sufficiently large, spatiall distributed systems.

      Sure you can just say to me that science will find out one day but that's just another god of the gaps answer.
      I don't know what science will ultimately find out, but my approach here is diametrically opposite of what you accuse me of. I don't claim to know stuff on the basis of some obscure faith in what we will know in the future, nor do I demand that you believe in any particular speculative hyppothesis.

      What I will say, however, is that science is the best tool we have for finding answers to your questions. Faith is useless here.

      You're the one doing god of the gaps, bozo, because you're the one who just above asserted life appears supernatural on no other basis that we haven't figured it out in every detail yet.

      How dare you accuse ME of god of the gaps when offering that very method of argumentation yourself? It's pathetic.

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    12. Did you hear what Dr Craig Venter said in the interview? He does not believe we will EVER know.
      And one could dig in to what he means by what it is we will never know? If he's saying we will never know how life, of any kind, can originate, then I don't hold much respect for that view, because it's nothing than opinion. He can offer nothing in support of such a statement.

      From a certain different perpective I actually agree with Craig venter though. We will never be able to say with great certainty how life DID originate. The evidence for the earliest stages of life on our planet are simply gone. But it is possible we will alight on a natural process by which we can say life could have originated.

      Notice here, I'm not demanding that you believe anything in particular. But I'm also not the idiot standing on the sidelines screaming we should give up because we don't know yet and therefore it "appears supernatural". It's a joke.

      Fact is this life is currently a supernatural entity in this natural universe
      Pure, unadulterated, counter-factual blind assertion. Everything we've come to know of life so far has been natural physics and chemistry. Whatever supernaturalism you percieve must be hiding in the things we don't know yet.

      Do tell me, what is the history of observed phenomena for which we found actual supernatural explanations? None? ZERO? Yeah.

      Disease, epilipsy, infection, fever, heartattacks, viruses and bacteria, earthquakes, storms, weather, lightning, the sun(what is it, where does it come from?) the day and night cycle. Countless millions upon millions of unexplained phenomena through the ages turned out upon closer inspection to be the products of nature. Physics and chemistry every last single one of them.

      Who knows, maybe you're right and a supernatural designer is hiding in the origin of life. History tells me I souldn't lend much credence to that possibility, so I won't, and I'll be rational not to.

      the lack of science's power to prove it as natural backs my claim.
      Also, you have an invisible dragon in your garage. You borrowed it from Carl Sagan.

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    13. @AndyBoerger

      I don't claim to have a slam-dunk. The difference between me and Andre Gross is that I'm not jumping to conclusions. The purpose of my question was to show that despite what he might think, his position is no better than mine on the face of it. Both of us don't know how consciousness works.

      But as I also just told Andre above, the history of supernatural claims are pretty poor. Really, the origin of life, consciousness and the universe are the 3 last gaps for god.

      God knows where you'll find gaps to hide your gods in should we solve any of of them. Heck, half the worlds religious population is still in denial about the origin of species, so I guess that sort of answers my own question. The last refuge of supernaturalism: Just pure denial.

      In the mean time, society, technology and science just keeps moving on and so you're sitting here on the internet, telling people about supernature through the use of a computer, living your relatively famine and disease-free lives with all sorts of goods and infrastucture provided to you.. by what? By empirical science, using methodological naturalism. Prayer, incantation and wishful thinking has provided none of that to you.

      The sheer irony of it...

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    14. @rumraket
      You assume that wherever science has discovered something you have discovered something God does not do. What you've actually discovered though is the method by which God does His work. This was the view of all the founders of modern science and it's only via a crude semantic trick that you can make the claims you make, and only your ignorance of the history of science that allows you to make them with a straight face.

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    15. That's great Luther, the unfalsifiable argument that all that happens is the will of god.

      Carl Sagan's dragon is hiding in your garage too?

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    16. @It's no more unfalsifiable than the claim that the earth exists. And one might argue that someone (eg, you) arguing that the earth doesn't exist because there's only actually this oblate spheroid (not an earth) has missed the point somewhere along the line. Or consider someone objecting to evolution by saying that common descent is true, and yes there's natural selection, and variation/mutation etc, but no such thing as evolution. No more so than a dragon.

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    17. @Rumraket wrote:
      "Who knows, maybe you're right and a supernatural designer is hiding in the origin of life. History tells me I souldn't lend much credence to that possibility, so I won't, and I'll be rational not to."

      You are not the only one who, facing the difficult question regarding the origin of life, caved in...Dawkins did so too...

      Richard Dawkins admits to Intelligent Design too...

      http://www.youtube.com/watch?v=BoncJBrrdQ8

      You contradict yourself like a typical DEvoLUTIONST who is so blind, that can't even see his arguments are childish and of an uneducated moron...
      In the end you have nothing... Slum-dunk is not attainable...not in your case... You're just too ignorant to the facts that all you have is nothing...

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    18. Rumraket, there is no 'irony', just a line of defense that I have seen before, and is quite illogical.
      It basically goes, because we have all this neat technology that comes from scientific studies, and you are actually using it now to communicate, therefore science is better.
      Well, there are so many ways to combat this, that I will strive for brevity.
      1.) So what? Technology comes from peoples minds, and a theist believes that peoples minds derived through the greater mind of 'god'. The more important part of our argument is not the devices we are using to have it, but the even MORE amazing technology we are using to form our thoughts and express them. Science still doesn't have conclusive evidence for how we came to be, so moot point.
      2.) No music for you, my friend! Nearly all music that people in the west listen to has its roots in religious purposes. From Bach's choral compositions, church music, etc., leading eventually to gospel music and the 'revivals' that gave birth to rock and roll. So it would be 'ironic' of you to continue listening to music, and enjoy it, while maintaining your position, perhaps.
      3.) People who create beneficial technology can be theists as well as atheists. They may even arrive at their choices, for example to pursue careers in medicine, pharmacology, etc. out of a desire to make the world better and ease suffering, and that choice may have been influenced by the spiritual side of their nature. Do you maintain that such people don't exist?
      You seem intent on making this an 'a or b' argument, but it isn't. There are many people, including in the professions that use technology to improve lives, that do not live their lives in conflict, or think that they have to choose one side or another.

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    19. Rumraket, another thing you may wish to consider is the "irony' of an atheist who is fully committed to a naturalistic explanation of human origins arguing emphatically that "empirical science, using methodological naturalism" has been a net good.

      You, after all, are the one who likes to argue that we are just apes. More generally, we share the same DNA with all other living creatures, and we are after all just variations on the Mammalian Success story that has been going on since the end of the age of great lizards.
      So.....how has all this technology and empirical science improved the lives of OTHER apes? We use it to decrease their living spaces. We have used them for medical, space, and other experiments. What about whales, our cousins? Our sonar technology is disrupting their very sophisticated communication and homing abilities, resulting in increases in stranding incidents.
      If we are not special, just animals like all others, then we would have to consider our OWN advantages in relation to the net loss to other specie. No way around this. We can justify, but not actually excuse, our behavior. We are all organisms that have evolved differently. And this one type of organism that calls itself human is using empirical science to absolutely NO benefit - and lots of detriment - to other species.
      What criteria are you using to take them OUT of the equation? Surely not specialness. Surely you wouldn't like the idea that humans have used technology to create a kind of 'priest class' of elites that act in their own interests, solely? Why, that sounds like pretty much the only thing you seem to think religion does! The sheer irony of it.....

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    20. to paraphrase Orwell, all animals are evolved equally, but some animals are more equal than others, perhaps?

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  18. I'll just comment on one, the rest of the stuff is based on your very own feelings, I don't care how you feel honestly, Let me say it again, the fact that matter is alive and can contemplate its aliveness is supernatural. Life is supernatural, hence the reason science can't say jack or shit about it.

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    1. So denial it is. Good, glad we got that settled.

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    2. There is no denial, but what I don't have is a feeble mind that swallows whatever crap people call fact, you sir have made yourself guilty of that. There is no natural explanation for life and there never will be, and when the day comes when life is created in a lab you will know that only a tinkerer could ever do it not some natural process that given some time suddenly had a chance..... Those beliefs are fairyland stuff, the very idea that non-intelligence could in fact create or give rise to intelligence is not only absurd its unreasonable. But for people like you its the easy way out, no intelligence needed because why should I ever give thought to what it really means.... Good luck with that false world I lived it for 34 years and it was a so hollow.

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    3. http://www.dailygalaxy.com/my_weblog/2013/02/cosmic-dust-a-source-of-life-in-the-milky-way.html#more

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    4. Lol, yes and we think there is life on the moon, mars, and everywhere else. Question is... have we found it.... A resounding no, stop feeding yourselves bullshit...

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    5. @Andre Gross

      Even if we find life on Mars, it will be almost positively of our kind. The problems is, we will not know whether it has develop there or it came from the Earth, as both planets pollute each other enormously...

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    6. @Andre gross
      "One huge blind, counter-factual blind assertion following another".

      Ok Andre, whatever you say. I can't "cure" you of your need for easyer non-answers. To you life is just inexplicable because it just is because.. well you don't understand it. Great. Not only is it circular reasoning, you're a science-stopper guy, so let's give up and declare goddidit.

      Do me a favor, show some intellectual consistency: The next time you suffer some kind of severe injury or illness, pray. If you run out of food, pray. If you're thirsty, pray. Don't take antibiotics, don't get surgery, don't go to the supermarket, don't drink tap-water. Rely on supernature to provide you what you need. It worked so well during the black plague.

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    7. The black plague, had the doctors followed basic bible instructions on hygiene they would not have lost some many lives... Sometimes truth is stranger than fiction!

      http://www.hope-of-israel.org/bihealth.htm
      http://home.sprynet.com/~pabco/tw0172_health.htm

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    9. How enlightening, and to think, all the health problems could have been solved by listening to the Bible. All we had to was use soap and water and bury shit... Wow, the whole time-- right there...

      Where's the chapter on performing heart surgery? Or perhaps better or cheaper and more efficient ways to have clean water? I mean, desalination is a bitch and a child dies every few minutes from not having clean water. Good call God..

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    10. The bible argument is the most colossally stupid argument I've read in my life. Priests, monks and nuns were running AMOK in the 1300's, scouring their scriptures for signs of "what this could be?" and what to do about it. Everybody thought something in between "it must be punishment from god" to "the work of the devil".
      Contemporary historical accounts are rife with chapters on monks and preachers teaching and engaging in how to lash yourself bloody and into shreds in atonement for god's punishment, complete with section after section of biblical support of these mad ideas.

      But hey, historical revisionism is just another tool in the creoretard arsenal.

      Andre, it's becoming apparent to me that not only your biology education is severely lacking, but you're simply a complete ignoramus in general.
      Here, I bothered looking up something for you, read it and learn:
      http://en.wikipedia.org/wiki/Black_Death#Consequences

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    11. Of course, it's always easy for some internet idiot to sit here now 700 years of scientific discoveries later, casually cherrypick the "correct" bibleverse that would have saved everyone if only they'd read it the way Andre could.

      Oh Andre, if only we could send you back. What utterly colossal, brain-fucking-dead, religious bullshit.

      "The Black Death led to cynicism toward religious officials who could not keep their promises of curing plague victims and banishing the disease. No one, the Church included, was able to cure or accurately explain the reasons for the plague outbreaks. One theory of transmission was that it spread through air, and was referred to as miasma, or "bad air". This increased doubt in the clergy's abilities. Extreme alienation with the Church culminated in either support for different religious groups, such as the flagellants, which from their late 13th century beginnings grew tremendously during the opening years of the Black Death, and later to a pursuit of pleasure and hedonism. It was a common belief at the time that the plague was due to God's wrath, caused by the sins of mankind; in response, the flagellants traveled from town to town, whipping themselves in an effort to mimic the sufferings of Jesus prior to his crucifixion."
      http://en.wikipedia.org/wiki/Consequences_of_the_Black_Death

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  19. @Andre

    Allan

    Seriously where did it come from? If there is a materialistic explanation with proper supporting evidence I'll gladly believe it, so where did it come from?


    I'm not asking you to believe anything. What's it to me? In its most abstract form, science is a set of puzzles for people who like puzzles. You don't have that intellectual curiosity, don't study it. ID sounds like a game show where the only answer is 'Design'. Who wrote Hound of the Baskervilles? Design. What force holds quarks together? Design. How can a reaction be made to go against its thermodynamic gradient? Design. It's incurious.

    There are some hard-won facts about atoms, molecules and energy, and any attempt to get to the bottom of this puzzle must take account of them. But - however it happened - it is also a fact of history. You want ‘proper supporting evidence’ for something about the ‘dirty chemistry’ of a few square inches somewhere on earth some 4 billion years ago? I can give you reactions that produce ribose, adenine, or even activated nucleotides, from simple precursors. Whether they have any relation to ‘the’ origin of Life, who can really say? But such things do indicate that it is not impossible to generate the building blocks abiotically. There is an element of ‘choreography’, especially in the nucleotide case, but dynamic systems will be closer to reality than static ones.

    My own view is that a vital ingredient is to link chemistry to a more local source of energy than is readily generated from ‘out here’. We’re looking for manipulations at the molecular level, and the forces at this scale are massive. You can heat a reaction mixture, but you’re jiggling every damned atom. Likewise adding UV – which is used in the Powner/Sutherland synthesis, but is very hard on nucleic acids. But Life seems to apply energy ‘surgically’. For primary sources - most notably chemotrophy - it typically uses the energy of electrons passing along gradients of electronegativity to generate an electrochemical gradient, and that is coupled to activation of molecules against their thermodynamic gradient. There is nothing in principle forbidding the operation of such a physical system outside of living organisms.

    But you will no doubt return to ‘hahaha Dr Suess’ mode. All that can be done is to probe the properties of matter. It may be that the answer does not lie within the properties of matter, but that does not mean all 'materialist' speculation is bunk. But if one’s pet theory goes against a known property, it’s not an ID JAQ-er who is going to go after you, but another scientist. And their analysis will be far more penetrating.

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    1. Even though you've made some false accusations about design, which the informed can spot a mile away, I still want to think you for the post. So we have always maintained much like your post here that life is in the hardware. Ever consider that the secrecy might be sitting in the software? Matter is matter, chemicals are chemicals and atoms are atoms. I'm putting my money on the software. What is a computer without its operating system? What is a living creature without its operating system?

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    2. Here is a perfect point in case that ID not evolution is true.

      http://www1.umn.edu/news/news-releases/2013/UR_CONTENT_429344.html

      Design, directed, manipulated, purpose,they used their minds to do all this but then, say; evolution did it.... shameful that people don't even give their own intelligence credit for this. How much longer before somebody realizes that if you take the tube and chuck it in the ocean or soil nothing will happen only through tinkering did they achieve these results.

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    3. From the aticle;

      "Seelig created the fledgling enzyme by using directed evolution in the laboratory. Working with colleague Gianluigi Veglia, graduate student Fa-An Chao, and other team members, he subsequently determined its structure, which made its debut December 9 as an advance online publication in Nature Chemical Biology. Lab tests show that the enzyme (a type of RNA ligase, which connects two RNA molecules) functions like natural enzymes although its structure looks very different and it is flexible rather than rigid. Seelig speculates the new protein resembles primordial enzymes, before their current structures evolved."

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    4. Directed Evolution? is that not an oxy-moron? Does directed evolution not mimic theistic evolution?

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    5. No, it mimics natural selection.

      Theistic evolution postulates god is the cause of fortuitous mutations, not that god is the orchestrator of selection. At least sensu Kenneth Miller's version of theistic evolution.

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    6. Are you honestly that daft? When I direct selection it is no longer natural selection. There is no mimicking.... The same goes for the idea that a non-intelligent force (aka natural selection can somehow mimic intelligence to give things the appearance of design its a total bullshit story and you know it!

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    7. You are part of nature you tard. There's no difference in principle between a human being picking a dog he likes for breeding, or a female bird picking a beautifully coloured male to mate with.
      Birds and human beings are part of nature, they both select what they like. In this respect it doesn't matter that the human being knows that it will be making a new dog family tree from the two dogs in question, the important fact here is that something was selected. Just because the bird might not be consciously aware what will ultimately result from it's choice of mate doesn't make the act of selction of desirable traits any less analogous. They're both natural and they're both selection, so it's natural selection.

      QED.

      This lesson brought to you by the Rumraket-educates-Andre-Gross foundation, a charitable organization providing free education where need is great.

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    9. For my response to Gross' ridiculous denial of the evolution of new complexity in that paper on the de novo evolution of an enzyme, see below, the next thread.

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  20. "For decades, naturally occurring enzymes have been tweaked by industry to make industrial processes and products more effective. The ability to create enzymes from scratch using a natural process opens the door to a vast array of new products that provide business opportunities and improve quality of life without harmful environmental effects."

    I wonder how is intelligent selection natural selection? I wonder? If a mind chooses how the hell can it be blind undirected chance? This brain is baffled?

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    1. Mutations happen randomly.

      Natural selection is just a term for the mechanism that "selects among mutants".
      Bacterial mutants that do better out-compete mutants that do worse, and so they come to dominate the population. We say that they have been "selected". This happens naturally in nature, and human beings can reproduce the same effect in a laboratory. We just replace a bacterial with a test-tube and let a human being make a new "generation" of enzymes from the best enzymes of the previous.

      Nobody and nothing has to operate with foresight and intention for this to work. All it requies is that some enzymes have higher catalytic activity than others. They do, due to random mutations.

      This is the same kind of "microevolution" that leads to antibiotic resistance and a new flu and cold every year, which creationists constantly advertise that they accept.

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    2. * It should read "we just replace a bacterial cell with a test tube.

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    3. Don't you think that "selection" in natural selection is a bit of a misnomer? Since when did non-intelligence have the capability to "select?" How does this non-intelligent force know that its selection was the right one? That's right it does not yet somehow it was capable of building a creature with a trillion cells that each do about a 100 000 chemical reactions in each one of those trillion cells every second..... Go dumb force you can do it! Fek you need allot of faith to believe that!

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    4. Andre, it's true.
      Mutations occurring, and the ones that confer some advantage remain, is a natural and easy to grasp concept.
      But that dynamic, plus a simple transfer of genetic material through nearly neutral mutations, being tasked to explain the vast complexity and organization and diversity of life we see on Earth (and leaving Earth aside, really just an average square acre of tropical rain forest) is a huge stretch of the imagination.
      It is like asking the same mechanism that changes 'my hat fits.' to 'my, that fits!' to go on to change either of those sentences into the fully developed, complex, mysterious and tragic heroine that is Anna Karenina.

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    5. Andy of course mutations are true, I'm not disputing that. Take some time and go through the literature and what you'll find is mutation are almost always bad not good. It does not logically follow that majority bad mutations can be supressed by a possible minority few. That is pure lala land stuff!

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    6. Andre your portrayal is an oversimplification. Most mutations are nearly neutral, not lethal. So yes, a few good mutations can indeed outweigh the effect of many very slightly deleterious mutations. It's all relative of course. How deleterious are they? How beneficial are they? It's not as black and white as you describe it.

      Carriers of sufficiently many deleterious mutations die. The key word there is 'sufficiently'.
      That's why so many individuals die, and indeed why many species go extinct. That's also partly why evolution is slow from a human point of view. It takes hundreds of thousands, sometimes millions of generations to fix relatively few good mutations

      Good mutation are rare, but after enough generations one inevitably arises and gets "selected for", in the sense that the carrier out-competes non-carriers, in terms of reproductive success.

      @Andyboerger
      Yes, it would be a stretch of the imagination if we didn't have the evidence for it in significant molecular phylogenies for countless genes that demonstrate not only that it happened, but in some sufficiently detailed cases, also how it happened.

      See http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001446
      Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
      Karin Voordeckers equal contributor, Chris A. Brown equal contributor, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere mail, Kevin J. Verstrepen mail

      And for enzyme evoluion in general: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002403
      Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
      Nicholas Furnham mail, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton

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    7. ZOMG now its all relative!!!


      Mutations are almost only bad if you want proof of this look at the increase of cancers (mutations)

      http://www.medicalnewstoday.com/articles/246061.php
      http://articles.latimes.com/2012/jun/01/science/la-sci-sn-world-cancer-incidence-20120601

      Please spare yourself from trying to defend the indefensible, mutations are killing us not making us better!

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    8. If you're not sure what cancer is I hope this helps you!

      http://www.sanger.ac.uk/genetics/CGP/cosmic/

      Please stop the idea that mutations are beneficial its not they are fucking us up!

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    9. Rumraket, your examples only argue for increasing complexity. They do not argue for the emergence of consciousness. When you reply to me, there will be a remarkable electromagnetic relay of information from your brain to your fingertips to the computer in front of you. You will type out words without even thinking about how implausible an act you are performing. Your mind sends signals, in the blink of an eye, to your fingers, which tap as they are directed, to form words, that we have developed, to express concepts, that we don't really know the source of. Send me a million papers, or please send me just ONE that describes how consciousness emerged through mechanistic evolutionary processes.

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    10. ...that PROVES it, not just one that supplies a theory for it from someone who is already committed to purely mechanistic processes 'explaining' everything and struggling to provide a theory for accomplishing this.

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    11. Andre: You're not really dealing with anything I'm saying beyond making oversimplistic caricatures of it and making blind, black/white declarations about the nature of mutations. I can't be bothered entertaining your idiotic gish-gallop and lack of formal education in biology. It's clear to me from our exchange that you have zero intention of open discussion, you just wish to throw assertions out there and stick up for your worldview the facts be damned.

      Long story short: the nature (good/bad) of mutations depend on environment. If you have a mutation that gives you a thick coat of bodyhair, that's probably not going to serve you well if you live in a hot desert. This should be patently obvious to any rational person. And you can find me a trillion examples of bad mutations and all you'll have accomplished is to demonstrate an ability of selective reading and volitional ignorance.

      @Andyboerger
      I did not claim to know, or be able to explain, how consciousness evolved. You spoke about the organization and complexity of life, so my references were supposed to cast light on what we've discovered about evolution in that respect.
      Yes, the brain is a wonderful organ, and we still don't know much about it. It is extremely large for an organ, outrageously complex in it's functions, burns a lot of energy and requires constant mental effort not to degrade into senility.
      But look at what you're doing, it seems to me that you're effectively conceding that it is possible the brain is somehow the source/generator of consciousness. That it is possible that somehow in this unbelievably comple, living organic "computer", consciousness emerges. The brain is made of cells and tissues, which are made of polymers of atoms and molecules, which obey natural physical and chemical laws.

      To your last poin: You don't have a theory either. Just some vague reference to some unobserved soul-entity that just works. How? Nobody knows. How does it interact with the brain? Nobody knows. If the brain is made of material, and he soul can interact with brain-material, why can't it interact with other matter which the brain is made of(carbon, hydrogen, oxygen, nitrogen etc. etc.)? If you think it can, why is there no critically robust evidence of souls interacting with matter anywhere in science?

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    12. @Rumraket
      You writing what you just wrote is an example of soul interacting with matter. We see billions of examples of it every day. All of which are in principle inexplicable in terms of any material processes. Unclear what more you like in the way of evidence.

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    13. Rumraket asks, " why is there no critically robust evidence of souls interacting with matter anywhere in science?"

      excellent question, and the short answer is I don't know.

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    14. @Rumraket
      How is it question begging? The soul/mind (whatever you want to call it) interacts with matter in a way that is in principle inexplicable via any material processes. That's not to beg the question, it's to answer it by giving you billions of examples of exactly the thing you say there's no evidence of. How much more evidence would you like? Humans are not describable in purely material terms - deal with it.

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    15. It's an honour to be called a Gish Galloper...

      Duane Gish had over 300 public debates with atheists and won every single one of them! Thank you!

      http://www.conservapedia.com/Duane_Gish

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    16. Gross is amazingly audacious in trying to cite lab experiments of de novo enzyme evolution via Darwinian methods, as an example of "Intelligent Design"!

      Creationists have been shitting their pants for decades each time a study like that comes out, where new complexity and new function and new sequences and new INFORMATION are CREATED by Darwinian algorithms.

      Response: they just totally redefine the scientific method. Like many losers, they just want to change the rules.

      Here's creationist logic.

      Creationist: "Evolution is disproven, because new complexity and new function NEVER appear by random mutation and selection in lab experiments!"

      Scientist: "Here are a DOZEN experiments where new complexity and new function appeared by random mutation and selection in lab experiments."

      Creationist: "Evolution is disproven, because because new complexity and new function OFTEN appear by random mutation and selection in lab experiments! After all, all lab experiments are intelligently designed."

      Hmm. That's not what creationists said before the 1960's, before the time when scientists had many examples, in vitro, in silico, and in the wild of evolution of new complexity.

      The creationists have totally redefined every part of the scientific method.

      In the 1950's, before we had so many examples of new complexity and new function evolving in lab experiments, creationists cited that to DISPROVE evolution.

      The creationist argument, up to about, say, late 1960's, was:

      "If something happens reproducibly in the lab, that proves it is a NATURAL process. Evolution of new complexity CANNOT be seen in lab experiments, therefore evolution is disproven."

      But starting from the 1970's onward, creationists started shitting their pants when scientists produced example after example of evolution of new complexity. The creationist argument then became:

      "If something happens reproducibly in the lab, that proves it is an INTELLIGENTLY DESIGNED process. Evolution of new complexity CAN be seen in lab experiments, therefore evolution is disproven."

      Now the first step in this sort of experiment, typically, is to add a mutagen to increase the rate of totally random mutations. Explain to me, Gross, how increasing the rate of random mutations is "intelligent design"?

      Delete
  21. Enjoy your mutations!

    http://www.sanger.ac.uk/genetics/CGP/Publications/#2004

    ReplyDelete
  22. andre said:

    "Please spare yourself from trying to defend the indefensible, mutations are killing us not making us better!"

    So, 'God' designed and created the mutations that "are killing us", or did
    'God' just design and create the "better" stuff?

    ReplyDelete
    Replies
    1. God does not exist according to you so I'm not sure why you're invoking Him... anyway. The degredation we are experiencing is consistent with the biblical narrative if you must know, everything that has a beginning must have an end. Our genetic information has become worse, findings from the Cambrian prove that we are in fact getting simpler not more complex. I'll post the supporting paper later.

      Delete
    2. http://www.sciencedaily.com/releases/2012/10/121010131436.htm

      " Because the brain anatomy of branchiopods is much simpler than that of malacostracans, they have been regarded as the more likely ancestors of the arthropod lineage that would give rise to insects. However, the discovery of a complex brain anatomy in an otherwise primitive organism such as Fuxianhuia makes this scenario unlikely. "The shape [of the fossilized brain] matches that of a comparable sized modern malacostracan," the authors write in Nature. They argue the fossil supports the hypothesis that branchiopod brains evolved from a previously complex to a more simple architecture instead of the other way around."

      Delete
    3. Oh, so "we" = Branchiopoda! I see! You are a water flea and have a water flea's brain anatomy. That indeed explains a lot.

      Delete
    4. Hey we all came from the same warm little pond according to you....

      Delete
    5. Of course we do, I was just referring to your interesting assertion that "we" are simpler than our Cambrian ancestors. Evolution is not unidirectional, from simple to complex. Simplification does happen, but showing an example of such a thing in a lineage very distantly related to ours is a far cry from proving simplification to be the rule.

      By the way, what does the Bible narrative have to say about the evolution of crustaceans? Of all the biblical references to arthropods the one I remember the best is the claim that locusts are four-legged and therefore can be eaten.

      Delete
    6. This might come as a suprise to you, it says WALKING on all fours, you are aware that locusts do not walk with their jumpers right? I mean as a scientific litarate you knew that hey?


      http://en.m.wikipedia.org/wiki/Kosher_locust

      You can do better....

      Delete
    7. Have you ever actually seen a locust (or any other grasshopper) walk? I have, and they do indeed use their "jumpers", by which you mean their rear legs. I can't imagine why you would think otherwise, unless of course you're desperate to save biblical literalism.

      Delete
    8. So much for biblical zoology:
      http://dsc.discovery.com/tv-shows/other-shows/videos/superswarm-locust-plagues.htm

      Delete
    9. Yes I have the front four legs are for walking and the jumpers get placed as they walk, but are not considered feet, see it every day of my life.

      Delete
    10. andre said:

      "God does not exist according to you so I'm not sure why you're invoking Him... anyway."

      But "God" exists, according to you, and you're claiming that "God" is the designer-creator.

      "The degredation we are experiencing is consistent with the biblical narrative if you must know, everything that has a beginning must have an end."

      So you're admitting then that you believe that "God" designed and created the mutations that "are killing us". Gee, what a loving, merciful designer-creator "God" is. Not.

      "Our genetic information has become worse, findings from the Cambrian prove that we are in fact getting simpler not more complex. I'll post the supporting paper later."

      Hilarious! You refer to the bible and then say that you'll find a scientific paper that shows "degredation" (sic) and that "Our genetic information has become worse". Let's see you find a scientific paper that verifies the stories in the bible about a man living inside a fish for three days, and goats having striped/spotted/speckled offspring just because they mate near striped sticks, and dead zombies (including "Jesus") walking around, and people living for 900+ years, etc., etc., etc.

      Oh, and if "we are in fact getting simpler not more complex" based on "findings from the Cambrian", maybe you can also find a scientific paper that shows that "we" were around during the Cambrian. Were more complex, less degraded, better humans barbecuing trilobites on Sunday afternoons during the Cambrian?

      Delete
  23. Just in case you want to cry wolf I posted the original Jewish source on the verse, you know to eliminate any meaning errors that come with translations, Jews will know what Jews said so the source is accurate.

    ReplyDelete
  24. Andre, if you want example of a beneficial mutation look up salivary amylase copy number variations. Adaptation to a heavily starch-filled diet.
    http://en.wikipedia.org/wiki/Copy-number_variation

    Or how about the mutation that makes it possible for you to digest lactose after lactation stops?
    http://en.wikipedia.org/wiki/Lactase_persistence

    Those are two standard examples of beneficial mutations known to have occurred in the human population within a few ten thousand years.

    Thus, the claim you made earlier, that there are no beneficial mutations, has been shown false directly. Also, you keep ignorantly dismissing the case for actual numbers. Drift can fix neutral and weakly deleterious alleles in the population, paving the way for crossing of valleys in "fitness landscapes". Here, the strenght of the effect of selection, population size etc. all contribute to the effect. Again, no black/white caricatures as you keep making.

    Better to make caricatures of course, than deal with the actual science behind it, because if you did it would butt-fuck your mindless assertions.

    ReplyDelete
    Replies
    1. I'll bite, I have said before almost all harmful, you missed that no doubt... tell me how did 45 000 000 beneficial base pair differences between our closest relatives and ourselves become fixed in less than 8 000 000 years? That is 5.65 positive mutations per year fixed in the population.... Say does evolution happen faster with less genetic information or will it happen faster with more.? What about the more bad ones (scientific fact) and the neuteral ones. Surly at this rate of beneficial mutations we would have seen over 1400 of these since Darwin... Where are they?

      Delete
    2. Nowhere near 45 million of them are beneficial you gimp. They're mostly neutral. Ever heard of integenic regions, introns, noncoding DNA? Do you know what it means to evolve at a neutral rate? Oh god, do you know ANYTHING about biology?

      Go take a fucking introductory course on basic genetics and molecular biology before you attempt these kinds of arguments. Consider that friendly advice.

      Delete
    3. You know the Richard Lenski long-term evolution E. coli experiment right? Over 600 mutations have been fixed in the E. Coli population, and that's over the course of about 20 years.

      Almost all of them are nearly neutral. Many bad mutations happened too, and the carriers of those mutations got out-competed. That would be analogous to your cancer mutations in some respects. Yet despite the majority of mutations being bad or neutral, the E. coli still managed to fix 600 mutations, weed out carriers of the bad ones and evolve citrate metabolism.

      Delete
    4. 45 000 000 million differences are neutral? Lol... And about Lenski, go have a look he is reporting loss of fitness in his colonies no gains.....

      Delete
    5. Not all of them you idiot. You're sitting here right now with roughly 150-200 mutations in your genome, and you're not dead, and you haven't(I hope) "devolved". So yes, the vast majority of mutations are effectively neutral.

      And yes, once a species adapts to one environment, it's fitness will be worse in other environments. Otters, despite being mammals, are terrible runners compared to deer, for example. And Dolphins are even worse.
      You're a terrible fish, now 380 million years after your ancestors left water, but an excellent terrestrial mammal.

      The E. coli in Lenski's experiment has adapted to the growth-medium and temperatures used in the experiments. In that environment it has higher fitness than it's ancestors, though in the environment the ancestor is adapted to, it's worse in comparison to it's ancestor. That's how evolution works, species adapt to local conditions over generations, when mutations happen in their genomes than confer them an advantage in the local environment.

      That's what, the 4th time I give you basic education in biology and all you've got to respond with is a caricature and a demonstration of the lack of biology education. I couldn't ask for a better demonstration of the Dunning Kruger effect.

      Delete
    6. I think it's time to invoke Grey's Law:

      "Any sufficiently advanced incompetence is indistinguishable from malice."

      Delete
    7. A tiny defect causes this

      http://www.seattlepi.com/national/article/Tiny-defect-behind-rapid-aging-disease-1112411.php

      Delete
  25. Woah!!!! slow down sugar! Extraordinary claims require extraordinary evidence remember!

    1.) Please provide evidence that mutation rates can become fixed in a population in such a very short period please.

    2.) If cancer will increase by 75% in 2030 please provide evidence that most mutations are neutral, something killing you is not neutral!

    3.) Please provide evidence that my great great great great great granddaddy was in fact a fish!

    4.) Please provide evidence that a beaver's great great great granddaddy was in fact some Savannah runner please!

    5.) Please provide evidence that a dolphin was a fish that came to land hated it and went back evidence please!

    6.) It's clear that you don't really know how the Lenski experiment works can I give you some supplemental material?

    http://www.lehigh.edu/bio/pdf/Behe/QRB_paper.pdf

    Now I know you don't like Behe but do yourself a favour read it, for some reason you believe I only ready creationist or ID material and that is simply not true I read all of it and only after that do I make a decision. I'm doing exactly what Charles Darwin has taught us to do and so should you! This philosophy that you embrace is bull dust!

    “A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question."

    Charles Darwin

    And since its just been Darwin Day you should really try it! Oh one more thing... ignoramus!

    ReplyDelete
    Replies
    1. Check this Gem!

      http://www.nydailynews.com/life-style/health/human-beings-stupider-research-article-1.1200985

      Delete
    2. 1. Not mutation rates, just mutations, you gimp. Keep banging the rocks together Andre. The long-term E. coli experiment in itself is evidence that most mutations are neutral.

      2. The ratio of mutations to cancer-causing mutations is still much greater in total. Deal with it.

      3. Nested hierarchies in comparative anatomy, biochemistry and molecular biology.

      4. I don't claim it is.

      5. Dolphins fall into nested hierarchies as everything else does. Oh and, whale fossil record is excellent. Google it.

      6. Boldfaced lie. Here's the fitness data for the experiments:
      http://myxo.css.msu.edu/ecoli/relfit.html
      It is even explained what the numbers mean so a complete know-nothing, proud gish-galloper like you can follow it.

      They all increase. You lose, deal with it. b>



      "Mutations in the human brain are making us stupider, new research shows" - With people like you around the evidence is pretty compelling.

      Delete
    3. 1.) You are wrong.

      2.) No its not

      3.) Really? It's easy to explain comparisons, why not take a stab at the differences rather?

      4.) You said it!

      5.) It's not because we recently found a whale fossil that predates the ancestor!

      6.) The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski's research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. ... In the most open-ended laboratory evolution experiment (Lenski 2004), in which no specific selection pressure was intentionally brought to bear, all of the adaptive mutations that have been so far identified have either been loss-of-FCT or modification-of-function mutations, and there is strong reason to believe that most of the modification-of-function mutations diminished protein activity.

      (Michael J. Behe, "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution'," Quarterly Review of Biology, Vol. 85(4) (December, 2010).)


      In short; in the Quarterly Review of Biology, Behe pointed out that citrate can already be utilised by E. coli under low-oxygen conditions, and hypothesized that a simple modification of gene-regulation was likely responsible for the observed phenotype. That says it but here is the most telling indication..... After 50 000 generations they are still e-coli, sick and weak e-coli but yes still e-coli!

      Delete
    4. I'm having a whale of a time aren't you?

      http://www.dna.gov.ar/INGLES/DIVULGAC/ARQUEO.HTM

      "Based on this find, today we dare say that the evolution (from terrestrial to aquatic animals) and distribution that the “semi-aquatic whales” have undergone in the southern seas have been much more quickly than previously thought. This statement takes into account that the Protocetidae reported in the Indian-Pakistan region (of terrestrial origin and with 4 developed feet) where assigned an age of 53 million years, while the "Antarctic archaeocete" (already fully acquatic), has been assigned an age of 49 million years."

      Evolution sure happens fast hey! what happened to the notion of slight and small modifications over a long period of time? Everything so sudden! Whats up with that? They must be liars for Jesus! Yes!

      Delete
    5. You know when people say "have undergone in the southern seas have been much more quickly than previously thought" they are actually saying we fucked-up and we're sorry for misleading you... because just before the discovery that contradicted the previous one the old one use to be the fact of the matter!

      Delete
    6. 1. No I'm not. Read the fucking papers Andre. Over 600 mutations have been fixed in the E. coli over the course of 50.000 generations, and the key mutations that conferred increases in fitness have all been worked out. Incidentally, they are very few compared to the total amount fixed. That means the rest are mostly neutral. It's just a fact, a plain, undeniable fact.
      Fuck, even Behe accepts this fact. His disagreement in your quote is only with what the nature of the beneficial mutations are, because he claims they're just "modification of function" mutations. That's irrelevant with respect to the 600 total mutations that have been fixed but do nothing. They're neutral. You lost, time to move on.

      2. Yes it is. The average cell has hundreds of mutations, it happens every time the cells in your body divide. Mutations are a fact of life. Once in a rare while a bad one arises which is a cancer-causing mutation. Think about it. The cells in your body are dividing your entire life, and they will mutate at every generation. Again, the average cell has 150-200 mutations. That's how many mistakes slip through during replication of your total 3.2 billion base-pair genome, so the error rate is actuall impressively low. Yet, they still happen. But if as you say, most mutation were bad, you'd develop cancers every day. You don't. Countless trillions of cells are replaced by new ones by cell division in every tissue of your body, every waking hour of your life. They simply are mostly neutral, the only alternative is everyone would die to cancer shortly after birth. They don't, so you're wrong.
      Simply, empirically wrong. Deal with it.

      Delete
    7. 3. Evolution is a stochastic process, it predicts more similarities between more closely related species, and less similarities(both in number and degee) for more distantly related species.
      That means there will be differences yes, this is a prediction of evolution. But if you are close enough related (like chimp-human), the similarities will outnumber the differences, and so on and so forth.

      All species we know of fall within the predicted nested hierarchies. Morphologically, biochemically, genetically. The differences between species aren't refutations of evolution, they're expected, because they too fall within the nested hierarchies.

      Mate, if you're going to criticize the theory, learn what it is first.

      4. No I didn't, I made a comparison between two mammals, one which is highly adapted for terrestrial locomotion and one that isn't. I never claimed Otters evolved from deer. Time to put on the glasses so you can actually read, Andre.

      5. The fossils in the whale evolution cladogram aren't postulated to have evolved from each other. One is not the ancestor of the next one. It seems you don't understand cladograms either.

      Again, evolution predicts multiple coevolving lineages because individual populations will occasionally become fragmented, with one subpopulation following one trajectory and another going another way. That's why you don't necessarily see the fossil transition in perfect sequence, because you're not guaranteed to find your transitional fossils in perfect temporal sequence.

      Even today, multiple mammals exist as contemporaries which are all showing different degrees of adaptation to aquatic lifestyles. Again, I'm not postulating that one evolved into the other, but notice that right now, both Otters, Seals, Deer and Dolphins exist. All mammals, all showing different levels of adaptation.

      6. Your quote of Behe is irrelevant with respect to the fitness claim you made. You said they all show lower fitness, my reference constitutes a direct empirical falsificaion of your claim. Behe's talking, again, about what to call the mutation involved(modification of function, novel function or loss of function). But that's not what we're discussing. We're discussing fitness, you claimed they had lower fitness, you were wrong. Admit it.

      Delete
    8. Hey Andre, when was 4-5 million years "fast" and "sudden" ?

      Sticking to aquatic mammal generation times I googled Dolphin generation time and found numbers between 5-7 years. That gives you between 571.429 and 1.250.000 generations, in a sexually reproducing species(recombination is another source of variation in addition to mutations, not available to asexually reproducing bacteria).

      Delete
    9. One could compare that with the split between the brown bear (fully terrestrial) and the polar bear (semiaquatic, spending most of their time at sea).They began to diverge about 4-5 million years ago, but the split was gradual and gene flow continued until about 150 thousand years ago (occasional interbreeding still happens in the wild).

      Delete
    10. First Gross tells us there are fully-formed whales that are older than transitional whale fossils.

      Next, Gross tells us that Pakistani protocetidae are 4 million years older than Antarctic archaeocetidae.

      What the fuck?

      We have the transitional fossils. For many decades, creationists said that ANY TRANSITIONAL FOSSILS BETWEEN LAND ANIMAL AND WHALE WERE IMPOSSIBLE.

      YOUR CREATIONIST HEROES, INCLUDING MICHAEL BEHE, SAID TRANSITIONS TO WHALES DID NOT EXIST.

      We have the fossils. You have egg on your face.

      Delete
    11. I think Gross' point was that since we have whale fossils that are older than the so called transitional fossils the so called transitional fossils can't be transitional at all.

      Delete
    12. Rapey: we have whale fossils that are older than the so called transitional fossils

      NO WE DON'T. RE-READ GROSS' SOURCE. IT DOES NOT SAY THAT.

      If that's Gross' point then he's dead wrong, and Gross' own source proves it!

      (To get technical, the passage cited by Gross mentions an Archaeocete from 49 mya. This is compared to Protocetidae from 53 mya.

      Protocetidae (e.g. Rhodhocetus) is a SUBSET of Archaeocetes.)

      To have an Archaeocete appear AFTER Protocetidae is not necessarily out of order.

      In fact this particular find is IN ORDER, because it is not just an Archaeocete-- Gross' own source identifies it as from the Basilosauridae, e.g. like Dorudon (not to be confused with Basilosaurus sensu stricto.)

      Why didn't Gross cite the very next paragraph? From Gross' source:

      "Concisely, this find is relevant as it confirms the presence of " archaeocetes" in the Antarctica. But what is most relevant of the Antarctic " archaeocete" is that it is the most ancient record of an “aquatic whale” in the world (dated 49 million years back). It belongs to the Basilosauridae, group from which all present cetaceans were originated. Another important fact that emerges from this find, is that the archaeocetes’ diversification time, that is currently estimated in 15 million year, is brought to fewer million years (4 million years)."

      But of course the "4 million" number above assumes that the Protocetidae, e.g. Rhodhocetus, evolved at the same time as the oldest fossils of Protocetidae, which is unlikely.

      Luther Flint: we have whale fossils that are older than the so called transitional fossils the so called transitional fossils

      NO WE DON'T.

      So will Gross and Luther Flint take back their false claims? DO NOT CHANGE SUBJECT. DO NOT GISH GALLOP.

      Delete
    13. @Paedo
      Yes we do. We have whale fossils from around 50 million years ago with many of the so-called "transitional" fossils from later than that.

      I demand (demand I say) you take back your lies.

      Delete
    14. Rapey: We have whale fossils from around 50 million years ago with many of the so-called "transitional" fossils from later than that.

      Really? "Many", oh really? So, name three then.

      Are you saying that the first appearance of transitional forms is younger than the first appearance of fully aquatic whale fossils?

      Yes or no. Are you saying that the first appearance of transitional forms is younger than the first appearance of fully aquatic whale fossils?

      Rapey: many of the so-called "transitional" fossils from later than that.

      "Many", eh? Then name three. Name three transitional fossils that first appear after the first appearance of fully aquatic whale fossils.

      Delete
    15. @Paedo
      I'm saying that we have fossils evidence of whales that are older than many of the fossils that were said to be transitions on the way to whales. And there are. Now dry yer eyes.

      Delete
    16. Notice how Gross and Rapey evade a simple question, directly relevant to the topic that they, Gross and Rapey, brought up!

      YOU brought up the subject? Why are you avoiding answering a simple, yes-or-no, direct question relevant to the topic you brought up?

      Me: Are you saying that the first appearance of transitional forms is younger than the first appearance of fully aquatic whale fossils?

      Rapey: I'm saying that we have fossils evidence of whales that are older than many of the fossils that were said to be transitions on the way to whales.

      EVASION! EVASION!

      That's not an answer to what I asked!

      Simple question re: an issue that you creationists presented as crucial, critical, relevant to your point! Creationists won't answer!

      And Gross was dead wrong when he cited this website as proof that fully aquatic whales make their first appearance before the first appearance of transitional forms! Gross' own source contradicts Gross and Rapey!

      Me: "Many", eh? Then name three. Name three transitional fossils that first appear after the first appearance of fully aquatic whale fossils.

      And another question: Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of transitional forms? Will you admit that Gross' cited source says nothing of the sort?

      Delete
    17. @Paedo
      I'm saying that we now have a fully aquatic whale from around 50 million years ago when it used to be thought (presumably on account of "transitional" fossils although they may just have made it up) that "transitional whales" were still amphibious at 45 million years ago and that the final transition to being fully aquatic took place during the few millions years after that. This means that whatever fossils they had, if any, from 45 million years ago (the amphibious "whales") were not transitional because there already were whales (whale whales) several millions years before that.

      And all you caps, and all your bold text, and all your italics, and all your (whalelike) spouting is merely the bluff and bluster of a religious fanatic throwing a hissy fit because the world didn't match your religious view of how it should be.

      And I'm not really interested in what Gross' source doesn't say because it doesn't say a lot of things. I'm interested in what the source does say. See the difference?

      Delete
    18. Well, the source says that tentative analysis suggests that a fully aquatic early whale from a land-dwelling ancestor may have taken as little as 4 million years. How long does it usually take, in your experience? Is that quicker than normal?

      Delete
    19. @Miller
      What else could they say? We have land mammals and then whales 4 million years later, and since one had to evolve into the other it must have happened in that time. It's not like they worked this out using anything akin to science/maths.

      Delete
    20. Gross and Rapey show that the reason why creationist have not contributed to science in 120+ years is because they're dishonest, pathological liars.

      Their biggest lie is pretending to care about science!

      I asked four direct questions relevant to Gross' and Rapey's alleged interest in whale fossils. I got zero answers-- just outright lying and evasion.

      Here are simple questions no creationist dares to answer!

      1. Me: Are you saying that the first appearance of transitional forms is younger than the first appearance of fully aquatic whale fossils?

      Rapey: Rapey: I'm saying that we have fossils evidence of whales that are older than many of the fossils that were said to be transitions on the way to whales.

      EVASION. Creationists cannot contribute to science because they're too dishonest to answer a simple question.

      Instead we get Rapey changing his story, changing his story, changing his story...

      Rapey's New Lie: we now have a fully aquatic whale from around 50 million years ago when it used to be thought (presumably on account of "transitional" fossils although they may just have made it up) that "transitional whales" were still amphibious at 45 million years ago...

      No, this is not what Rapey just said! His new lies contradict his old lies!

      Rapey's Old Lie: we have fossils evidence of whales that are older than many of the fossils that were said to be transitions on the way to whales.

      So Rapey changed his lie. Compare again:

      Rapey's New Lie: around 50 million years ago when it used to be thought (presumably on account of "transitional" fossils although they may just have made it up) that "transitional whales" were still amphibious at 45 million years ago...

      What happened to the fossils? Rapey changed it to "presumably on account of "transitional" fossils".

      Rapey's Old Lie: whales that are older than many of the fossils that were said to be transitions on the way to whales.

      The old lie was fossils. The new lie is "presumably on account of "transitional" fossils although they may just have made it up."

      "They" made it up? Who's they? Scientists? Scientists didn't make up any fossils-- Gross and Rapey made up the fossils!

      Yes, Gross and Rapey made up imaginary fossils! Where are they? Where are the citations to the scientific literature? Name these fossils!

      Maybe they're along the Paluxy River, in Texas, where you creationists found your fraudulent man-tracks alongside dinosaur tracks? Maybe they're in Calaveras, like the Calaveras fraudulent man-skeleton you creationists promoted as from dinosaur times?

      Maybe they're in Freiberg, like the Freiberg "black skull" you creationists fraudulently said had been turned to coal by Noah's Flood (actually a sculpture made from coal)?

      Maybe they're in Coso, California, like the "Coso artifact" (actually a 1920's era spark plug) that you creationists fraudulently said was from pre-Noah's Flood?

      Maybe they're in Peru, like the "Ica Stones" with modern pictures of dinosaurs that you creationists fraudulently promoted as proof that ancient man coexisted with dinosaurs?

      Maybe they're at Mount Ararat, where every decade, creationists promote two or three different fraudulent discoveries of Noah's Ark?

      Where are the fossils you made up, Gross and Rapey? No citations to the scientific literature? No references? No journals?

      Where are the fossils you made up, Gross and Rapey? Your fever dreams? Your imagination? Anywhere outside your hypoxic brains?

      Delete
    21. @Paedo
      I answered your question. Previously it was thought (either on the basis of fossils or story-telling or some combination of both) that amphibious "whales" evolved into aquatic whales between around 45-43 million years ago. Now we have a fully aquatic whale from 49 million years ago. Thus, whatever the 45 million yer old amphibious whales" were they were not transitions to whale whales because whale whales had already been doing their whaley thing for at least 4 million years.

      And, fwiw, I'm not a creationist, so you're baking up the wrong tree there. You, on the other hand, are a religious fanatic. Look at how uncontrolled your posts are. Look at the shrill tone and ALL THE CAPS you use. So what, whales didn't evolve in the way your religion demands, deal with it.

      Delete
    22. Rodhocetus can't be the direct ancestor of fully aquatic whales if it's younger than some of them, but there are very primitive, half-terrestrial whales (early pakicetids) older than both Rodhocetus and the earliest basilosaurid unearthed so far. The fact that some whales evolved into fully marine animals did not make all their cousins follow the same course or die out immediately. It's pretty obvious that at least some primitive whales lingered on, even for millions of years. A "transitional form" is any fossil we use to illustrate a certain morphological type, not necessarily the actual ancestor of anything modern (just similar to it). It may well coexist with more derived taxa. Fossil and modern species form a tree, not a linear sequence. After all, whales evolved from terrestrial artiodactyls, and there are still plenty of other terrestrial artiodactyls around -- deer, cattle, sheep, pigs, camels, giraffes, hippos, etc. They didn't all go to the sea.

      The fossil record is full of gaps, but every new discovery fills one of them. It can only get more complete.

      Delete
    23. @Piotr

      Rodhocetus can't be the direct ancestor of fully aquatic whales if it's younger than some of them

      But what is the evidence of that?

      Delete
    24. Previously it was thought (either on the basis of fossils or story-telling or some combination of both) that amphibious "whales" evolved into aquatic whales between around 45-43 million years ago. Now we have a fully aquatic whale from 49 million years ago. Thus, whatever the 45 million yer old amphibious whales" were they were not transitions to whale whales because whale whales had already been doing their whaley thing for at least 4 million years.
      Oh dear, another ignoramus who needs a lesson in basic biology. An organism can be a transitional species and still be contemporaneous with sister groups showing greater degree of transition into a different environment.

      Even if a fossil transition seems to be found in ordered temporal sequence, they're not postulated to be the direct ancestors of each other exactly because we can't actually know whether they are. That's why they're usually shown as sister groups on cladograms.

      The only requirement for a transitional form is to show predicted transitional features.

      When any given transition is postulated to have happened over some specific timeperiod, it is because that's what the evidence available to us showed. New evidence can always come and change the picture.

      Delete
    25. Rapey lies some more.

      Rapey: I answered your question

      No you did not. You have now changed your story for the third time.

      My question: Are you saying that the first appearance of transitional forms is younger than the first appearance of fully aquatic whale fossils?

      Watch how Rapey evades.

      Rapey's Lie #1: we have fossils evidence of whales that are older than many of the fossils that were said to be transitions on the way to whales.

      Many of the fossils that were said to be transitions. Fossils, of real whales, older than the first appearance of transitional forms. Got that? That's Lie #1.

      I asked for citations to the fossils.

      Rapey's Lie #2: around 50 million years ago when it used to be thought (presumably on account of "transitional" fossils although they may just have made it up) that "transitional whales" were still amphibious at 45 million years ago...

      In Lie #2, it's not "fossils" anymore. Now it's a daydream of Rapey's, "it used to be thought."

      Rapey's Lie #3: Previously it was thought (either on the basis of fossils or story-telling or some combination of both)

      Now it's either fossils or else "story-telling". Rapey can't keep his lies straight.

      Still no citations, no references, no science, just made up imaginary "fossils" like the Paluxy Man-Tracks: more creationist fraud.

      Let me re-state the questions no creationist dares to answer.

      1. Are there fully aquatic whale fossils older than the first appearance of transitional, semi-aquatic forms like Ambulocetus?

      2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

      3. Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of semi-aquatic, transitional forms? Will you admit that Gross' cited source says nothing of the sort?




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    26. @Flint

      @Miller
      What else could they say? We have land mammals and then whales 4 million years later, and since one had to evolve into the other it must have happened in that time. It's not like they worked this out using anything akin to science/maths.


      So what's the big deal? Why are you crypto-and-not-so-crypto-Creationists so group-hysterically lathered up about whales? I'll ask again in a more direct fashion: why is 4 million years too short? How long should it take?

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    27. @Rumraket
      Look, if the transition from amphibious "whales" to whale whales took place between 45-43 million years ago then there can't have been whale whales 49 million years ago. Or, the other way round, if whale whales existed 49 million years ago then the transition to fully aquatic whales couldn't have happened between 45-43 million years ago.

      And, if what you say about "transitional" fossils is true, then a rabbit in the Cambrian is no problem because all the transitional fossils would still be there, they'd just all occur (those we have found) a whole lot later. They'd still be transitional though you understand!

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    28. @Miller
      I'm not, I couldn't really care less about whales. I was just pointing out that the paedo had (deliberately) misinterpreted Gross and was clarifying his point out of the kindness of my heart.

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  26. Andre Gross 2.) If cancer will increase by 75% in 2030 please provide evidence that most mutations are neutral, something killing you is not neutral!

    Manfully resisting the many tasty lures proferred by our trolling chum, but this is particularly obtuse. Most mutations cause cancer? Even those ending up in gametes? Hahaha! Do they cause cancer in single-celled organisms?

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    Replies
    1. The man is just completely clueless. We're witnessing the effect of what happens when a man is fed all of his "science" information from a religious propaganda-mill.

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    2. Ultimately, I don't think he cares. There is a rash of people 'going forth' into the blogospahere armed with a troll-y attitude ("I was going to play you guys for a few more days") and the same photocopied sheaf of Things Evolutionists Can't Explain. They then pepper the stuff around, and the science-y types chase the bait in the belief that any rational peron would be embarrassed to knowingly make total howlers, and genuinely interested in consistency with hard-won facts. But it's a different mindset. The effort put into misunderstanding and misrepresenting by the more dogged trolls is huge. I really don't know what they get out of it. Furthering the inroads of The Wedge, or perhaps they hope Jesus will one day say "Yep, that's exactly what I wanted from you - keeping science buffs dancing. Come on in."

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    3. @Alla
      Wrote a long post that got lost to browsererror, oh well. Long story short is that I agree with what you say, I don't have any illusions about whether people like Andre can be "reached".
      I engage people like him mostly because I often find myself reading similar discussions between people more knowledgeable than myself and I would say I have benefitted from this greatly. I like to think I can contribute something to that effect myself, though I wouldn't pretend to be an expert on these matters in any respect.

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    4. Rumraket,

      I'm with you - I learn a lot from arguing the toss with people. I have been - shocking I know! - wrong about stuff in the past, and my general aim is to become less wrong. But if there is - as there appears to be - a concerted effort to hijack blogs, we're giving 'em precisely what they want. (There's not necessarily any harm in that - it's just words on a server!).

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    5. Rumraket,

      do you have any citations on what fraction of non-neutral mutations are beneficial vs. deleterious? I can think of a couple of examples, but I'd like to see more.

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    6. Luther doesn't understand the definition of a transitional fossil. He thinks it has to be both a temporal and a morphological transition, this is a common creationist mistake.

      @Diogenes
      Off the top of my head the old talkorigins archive had some good references on the frations of mutations that are neutral/deleterious/beneficial.

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    7. this is a common creationist mistake

      A common popular mistake, not necessarily creationist. But of course it's a common demagogic trick employed by creationists: "If man evolved from apes, why are there still apes?"

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    8. @Rumraket
      Perhaps, but there had better be transitional species that actually are transitions between, say, land based mammals and whales, or else the theory of evolution would be a non-starter. So, with that in mind, do you have any transitional species that are part of the actual transition from land mammals to whales? I'm assuming you have hundreds because, after all, the ToE is as well established as the idea the earth goes round the sun.

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    9. @Luther
      There are transitional species, as in fossils that show transitional features between aquatic and terrestrial mammals.
      There is no requirement or expectation that we should be able to find all of them in complete temporal sequence. That's a stupid creationist fantasy

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