Carl Woese – Evolution Skeptic

Carl Woese

b. July 15, 1928
d. December 30, 2012

“Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.”

“I have concerns about scientists thinking that they’re God when it comes to biology.”

“A future biology cannot be built within the conceptual superstructures of the past. The old superstructure has to be replaced by a new one before the holistic problems of biology can emerge as biology’s new mainstream.”

“I do not like people saying that atheism is based on science, because it’s not. It’s an alien invasion of science.”

  • Carl Woese

Suzan Mazur: Why do you think NAI chose to give you and your team $ 8M, since you are known as a challenger of Darwinian dogma? Is NASA finally acknowledging the Darwin approach is wrong?

Carl Woese: I would hope so because that’s very clear from our NASA Astrobiology Institute grant application.

Suzan Mazur: You’ve described the “disconnect between Darwinists, who had taken over evolution, and microbiologists, who had no use for Darwinian natural selection.” Do you have anything to say about the recent decision of Huffington Post to block publication of microbiologist James Shapiro’s response to Darwinist Jerry Coyne following Coyne’s attack on Shapiro’s thinking about a reduced role for natural selection in evolution?

Carl Woese: I think that’s immoral. Science must be free to examine what it sees. If you’re going to say everyone must follow the Darwinian line, that’s not free science.

Carl Woese, evolution skeptic.

390 thoughts on “Carl Woese – Evolution Skeptic

  1. colewd:

    What evidence supports the existence of a universal common ancestor?

    The extremely closely matching twin nested hierarchies of the fossil and genetic records. The same answer you were given the last dozen times you asked the same question.

    My little niece like to keep asking the same question over and over when she doesn’t like the answer too. Of course her excuse is she’s only five. What’s your excuse?

  2. Frankie: No, Alan, it is strong evidence for a common design.

    You have to have evidence for any design before you can claim common design. You don’t have evidence for either. FrankenJoe fails again.

  3. Alan Fox: But relatedness is falsified by such things as different code translations, differing chirality and so on. The fit for common descent is narrow. “Common design” (whatever that means – as you’ve never expanded on that mantra) has no entailments. It’s unfalsifiable.

    The almost universally common genetic code fits the theory that all life shares a common ancestor.

    Of course common design has entailments- similarities should abound. Linnaean classification is based on the concept of a common design. Common design is observed in engineering and construction. It is a well known concept. We even have ways of telling when people copy designs illegally. There is plagiarism, copy right and patent infringements, knock offs, etc.

    Please tell us why common descent says the genetic code cannot change over the duration of billions of years.

  4. The problem with common ancestry is that you don’t have a mechanism capable of accounting for all of the changes required to get from prokaryotes to the diversity observed. All of your “evidence” assumes common ancestry is true

  5. Sal: “One can’t shove a eukaryotic gene “as is” into a prokaryote like E. Coli and expect it to make protein.”

    Except for that nagging little fact that there is a large biotechnology industry that does just that.

  6. There is plenty of evidence for ID and ID is not anti-evolution. What we lack is a methodology to test the claim that blind and mindless processes did it. And all the alleged evidence for universal common descent is absent a mechanism. Why is that?

  7. Frankie: Of course common design has entailments- similarities should abound.

    You haven’t established any design occurred let alone common design. You might as well claim “MAGIC!” which is all ID proposes now.

  8. There isn’t any evidence that the proposed mechanisms of natural selection and drift are up to the task. No one knows how to test the claim that they are. And all the foot stomping and name calling is never going to change that.

  9. stcordova: Not if the intermediates are infeasible

    But are they?

    thus it’s stronger evidence for common design

    No, because you also need to contrast it with multiple independent origins of the code by chance, and multiple independent origins of the code by some sort of biased stochastic process.

    This isn’t a dichotomy. There isn’t just Common Descent vs It Was All Designed By A Single Designer, among the logical possibilities. Each of those hypothesis would have to be evaluated against the evidence.

    I suppose if one rejects that possibility, one is stuck invoking infeasible transitions (like prokaryote to eukaryote, single celled creatures to animal multicelled creatures, etc.)

    None of these transitions have been shown to be infeasible, and in fact the overwhelming support for the phylogenies they fit into is evidence that not only aren’t these transitions infeasible, they actually happened in biological history.

    Besides, the genetic code isn’t universal as there are alternate codes, and even then it’s really only the general codon table. Also various species have alternate start codons. It’s only universal when it’s not….

    Right, but this is one of those cases where if you actually look at the details (tRNA and aaRS phylogenies), what emerges is that these alternative codes are recently(in geological terms) evolved adaptations of the standard code. You can’t just ignore this data or that evolution explains it much better than any ad-hoc design hypothesis you can come up with.

    One can’t shove a eukaryotic gene “as is” into a prokaryote like E. Coli and expect it to make protein.

    That’s not because of the genetic code, that’s because eukaryotic genes usually contain introns that bacteria have no way of removing, and because they use different enhancer and promoter sequences. When it comes to the genetic code itself (the correspondence of codons to amino acids), the mapping is fine. All the amino acids map to the same codon, and all the codons that mean “start” in the standard genetic code, also mean start in E coli.

    While exceptions to the universality of the code exist, they are minor deviations and as a general rule, on can IN FACT expect to move a gene from one organism to another and get the same protein out the other end. Exceptions to this usually have to do with methods of initiating transcription and mRNA processing, not with the mapping of codons to amino acids.

    If you think I’m overstating the case, one should hear the exchange between Craig Ventner and Richard Dawkins. Ventner (a practical scientist) had his doubts….

    The exchange about what? You mean we should take the less than 1 minute quips from a public discussion, talking about whether there is a tree or a bush of life, of which one asked a question and the other failed to answer it, to be authoritative on this matter?

    https://www.youtube.com/watch?v=MXrYhINutuI This shit is what you’re talking about? Where Dawkins asks a question of Craig and he doesn’t answer and also doesn’t in the full video?

    Craig doesn’t make anything clear. None of the terms are defined. What does he mean by another “form” of life. He points out metabolic differences between different domains. Does that make them another “form” of life? Surely he doesn’t mean they’re not longer cellular life? Doesn’t the idea of a domain merely constitute another branching? Doesn’t he in fact use the term “deep branching” himself? What publications are there on this by Venter et al? I found this: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

    Abstract
    Background

    Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.

    Methodology/Principal Findings

    We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.

    Conclusions/Significance

    Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.

    It seems to me there’s nothing in here about the genetic code not implying common descent, and the short exchange of words between Dawkins and Venter was actually more confusing than informative. In fact I think they talked past each other. Dawkins was concerned with whether there is universal common descent (and whether the genetic code implies this), while Craig was conserved with whether the root of the tree of life is a bush rather than a single stem. It seems neither of them got what the other one was saying.

    Do you take this confusion between them to be an authoritative statement that the genetic code does not imply universal common descent? If so, I don’t think you know what constitutes proper academic rigour.

  10. stcordova,

    One can’t shove a eukaryotic gene “as is” into a prokaryote like E. Coli and expect it to make protein.

    What, because of the insurmountable differences between their genetic codes? Which happen also to be the difference between nuclear and mitochondrial codes in us.

    What do you think of the evidence that Tryptophan-coding UGG evolved from a STOP (see your ‘atypical’ thread)? Why did the Creator make so many similar-but -different ciliate codes?

  11. Adapa: Actually we do.Science has known the mechanisms of evolution for many decades.Just because you’re ignorant as mud doesn’t make everyone else ignorant too.

    But, heaven forbid we ask FranjenJoe about the mechanisms behind ID.

  12. Frankie:
    The problem with common ancestry is that you don’t have a mechanism capable of accounting for all of the changes required to get from prokaryotes to the diversity observed. All of your “evidence” assumes common ancestry is true

    Actually we do. Science has known the mechanisms of evolution for many decades. Just because you’re ignorant of them doesn’t make everyone else ignorant too.

  13. Acartia: But, heaven forbid we ask FranjenJoe about the mechanisms behind ID.

    [IDiot Mode]

    ID isn’t about mechanisms! ID is about the design!

    [/IDiot Mode]

  14. And for those without a dictionary- design is a mechanism. Intelligent agencies manipulating nature for a purpose is a mechanism.

    Evolutionary algorithms model evolution by Intelligent Design and have a known mechanism- targeted search/ active search for solutions

  15. Frankie,

    Joe, you’re painting yourself into a corner. Why would such an incredible designer limit herself so? Take for example cognition and the associated substrate – nerve conduction velocity is about 120 m/s – glacial compared to what actual human designers can do. Obviously this is somewhat compensated for via parallelization, but one can’t but help recognize life has a terrible internal bus. Was the designer so incompetent? What capable designer only (poorly) uses one tool from a limitless toolbox?

  16. Allan Miller:
    stcordova,

    What, because of the insurmountable differences between their genetic codes? Which happen also to be the difference between nuclear and mitochondrial codes in us.

    What do you think of the evidence that Tryptophan-coding UGG evolved from a STOP (see your ‘atypical’ thread)? Why did the Creator make so many similar-but -different ciliate codes?

    Tryptophan- the structure of which made Doug Axe think that blind processes are impotent for being able to create. So how does blind and mindless processes account for tryptophan?

  17. It’s just another day at Creationism Central. They’ve been trying to make capital out of Venter and Dawkins’s mutual confused looks in that short clip for years.

    If Venter thinks a 1-codon difference is profound, he is a bit ill-informed.

    I posted this already, showing a bewildering array of differences in ciliate codes, including one with no STOPs. That’s the difference, usually, a STOP here or there. And it’s usually the same small group of codons involved.

    It certainly seems like ciliates are genetically related, and the variations evolved.

    What persuades one otherwise?

    What’s the Design reason for the differences?

  18. The nested hierarchy of a common design makes it easy to control and not get confused as to what organism gets what parts. As for nerves, do you realize what would happen to us if the impulses traveled at the speed of light? Have you even thought about it? Others have and what we have is the best for living tissue

  19. Alan Fox,

    Of course not. Multicellularity has evolved via intermediates from unicellular organisms. Again the bizarre question…

    Again this is a “just so” story without empirical support. Where did the complex genetic information come from to accomplish this task. The blind watchmaker or a trial and error process worked through these sequences to function?

    The fact that you think this is a bizarre question is telling. You just have not thought through the difficulty of coming up with the sequences that are required for these transitions. My question was based on needing the genetic information to make this story feasible.

    If I ask you to come up with the code to transition a single celled organism to a multicellular one and gave you 10 protein experts and all the computer power in the world do you think you could solve this in a year, 10 years, 100 years?

    So your answer is it happened on its own from cell division and variation leading to what?

  20. Frankie:
    And for those without a dictionary- design is a mechanism. Intelligent agencies manipulating nature for a purpose is a mechanism.

    How is the physical manipulation of matter done in the ID scenario? Sooner or later your Designer has to work with the physical layer. Evolution doesn’t need to manipulate matter to achieve preconceived goals because there are no preconceived goals. It’s just the normal laws of chemistry and physics making changes more or less randomly

    Must be MAGIC! Right Joe?

  21. Allan Miller,

    If Venter thinks a 1-codon difference is profound, he is a bit ill-informed.

    Should I let Craig know that Miller consulting services are available to clean up his basics on biology 🙂

  22. stcordova,

    Also various species have alternate start codons.

    That’s right – including little ole us! We use CUG in certain proteins. ‘Cos it’s better there. It’s what the Designer would have wanted.

  23. There isn’t any evidence that the laws of physics and chemistry can produce the diversity of life starting from populations of prokaryotes. There isn’t any evidence that the workings of a cell can be reduced to the laws of physics and chemistry and there is no way top test the claim that random, as in happenstance, mutations can produce protein machines let alone the diversity of life.

    Testability is the hallmark of science and UCD doesn’t have that

  24. colewd:
    Alan Fox,

    Where did the complex genetic information come from to accomplish this task.

    From the process of genetic variation and selection interacting with the environment. The same answer you got the last dozen times you asked the same question.

    Do you have OCS in normal life too?

  25. colewd,

    Allan: If Venter thinks a 1-codon difference is profound, he is a bit ill-informed.

    Cole: Should I let Craig know that Miller consulting services are available to clean up his basics on biology

    I would happily discuss with him.

    In a dispute between one expert and another, you side with Expert A. Why? Couldn’t be because Expert B is – spit – Dawkins, could it? And Venter is on every Creationist site from here to Tuesday disagreeing with him.

  26. Frankie: Tryptophan- the structure of which made Doug Axe think that blind processes are impotent for being able to create. So how does blind and mindless processes account for tryptophan?

    So what has Douglas Axe have to say about tryptophan?

  27. Frankie:
    The nested hierarchy of a common design makes it easy to control and not get confused as to what organism gets what parts. As for nerves, do you realize what would happen to us if the impulses traveled at the speed of light? Have you even thought about it? Others have and what we have is the best for living tissue

    Wow. That’s special. Feel free to link to what “others have” thought. Obviously the whole system would be different – one does not put wings on a car to get a plane. But it highlights why it wasn’t designed but evolved – evolution had to work with what was there already.

  28. Adapa,

    From the process of genetic variation and selection interacting with the environment. The same answer you got the last dozen times you asked the same question.

    Do you have OCS in normal life too?

    So why the big conference in London to extend the synthesis? You really don’t realize that the “just so” story is dying.

  29. colewd: Again [evolution of multicellularity] is a “just so” story without empirical support.

    What could possibly be a first step to multicelluar organisms? Could you conceive of the idea of single-celled organisms sticking together rather than separating? Just needs some component in the cell membrane to evolve that is a bit “sticky”. Maybe clumping together gives some slight adaptive advantage depending on the niche. Doesn’t need a vast number of changes.

    ETA a Nature paper for you to have a look at.

  30. Allan Miller,

    In a dispute between one expert and another, you side with Expert A. Why? Couldn’t be because Expert B is – spit – Dawkins, could it? And Venter is on every Creationist site from here to Tuesday disagreeing with him.

    Ok. Whats you’re hourly rate? 🙂

  31. colewd,

    So why the big conference in London to extend the synthesis? You really don’t realize that the “just so” story is dying.

    What was the most significant development to come out of this conference you know so much about?

  32. colewd,

    Ok. Whats you’re hourly rate?

    I spy a joke, but don’t see how it follows from what you quoted. I guess you had to be there. Why is Venter right and Dawkins wrong? Why is a one-codon difference fatal at all conceivable stages?

  33. colewd:
    Adapa,

    So why the big conference in London to extend the synthesis?You really don’t realize that the “just so” story is dying.

    LOL! The imminent death of evolution, the longest running failed prediction in the 150+ year history of YECkery. 😀

    Why don’t you tell us the mechanism the Designer used to physically manipulate matter? Let me guess, GAWD “spoke” things into existence.

  34. Frankie: And for those without a dictionary- design is a mechanism. Intelligent agencies manipulating nature for a purpose is a mechanism.

    Sorry FrankenJioe, but that is not the definition of design. Try again.

  35. Frankie: The nested hierarchy of a common design makes it easy to control and not get confused as to what organism gets what parts.

    The designer can get confused? That might be news to most of the ID proponents.

  36. Frankie: That it is evidence for design- intentional design.

    So what does Douglas Axe have to say about tryptophan? Is it written down somewhere? The bare claim “tryptophan is evidence for ‘intentional design'” is not much of an argument, is it?

  37. colewd:
    Allan Miller,

    Should I let Craig know that Miller consulting services are available to clean up his basics on biology

    Yeah he can talk to me too, it seems he’s not aware of the statistical basis of phylogenetic inference. Apparently Venter thinks all individual gene-trees should agree. Which is a rookie mistake. Douglas Theobald directly addressed this misconception in his 29 Evidences for macroevolution and common descent.

  38. Alan Fox,

    What could possibly be a first step to multicelluar organisms? Could you conceive of the idea of single-celled organisms sticking together rather than separating? Just needs some component in the cell membrane to evolve that is a bit “sticky”. Maybe clumping together gives some slight adaptive advantage depending on the niche. Doesn’t need a vast number of changes.

    You need to evolve proteins that can allows cells to communicate. Then you need to evolve the systems that will allow the cells to form a multicellular cell cycle so you need apoptosis in addition to DNA repair.

    Did LUCA have DNA repair?

    Then you need a system for oxygen to get to all the cells. This is the respiratory system.

    Then you need a central nervous system and muscles to move.

    Do you think humans currently have the capability to come up with the DNA sequences for a respiratory system?

    How about just the sequences for an oxygen/co2 transport protein?

    How about the ability of the cells to differentiate during animal development?

    Cells sticking together is not a multicellular organism. You need to organize DNA with 4^500000 possible ways to arrange and build all this. So how did all that DNA become arranged to build the first multicellular organisms we observe in the fossil records?

    Do you agree it requires a pretty complex design just to get to a Cambrian animal?

  39. Adapa,

    LOL! The imminent death of evolution, the longest running failed prediction in the 150+ year history of YECkery. 😀

    Why don’t you tell us the mechanism the Designer used to physically manipulate matter? Let me guess, GAWD “spoke” things into existence.

    Just to understand. Are you claiming the RMNS and genetic drift account for all life’s diversity?

  40. Adapa: Why don’t you tell us the mechanism the Designer used to physically manipulate matter? Let me guess, GAWD “spoke” things into existence.

    He’s already done that: according to Bill, Jeebus downloads genetic “information” into reproductive cells so that dinosaurs give birth to birds, lancelets to vertebrates and monkeys to people. Pregnant women, get ready cause you’re gonna shit bricks one day

  41. Allan Miller: In a dispute between one expert and another, you side with Expert A. Why? Couldn’t be because Expert B is – spit – Dawkins, could it? And Venter is on every Creationist site from here to Tuesday disagreeing with him.

    It’s become apparent that Venter is emphatically not an expert in the logical basis of phylogenetic inference.

    Listen to this https://youtu.be/EcUD_6dKJ7k?t=45m58s

    Dawkins asks Craig Venter repeatedly about the impact of HGT on molecular taxonomy, as he calls it, as a field, and Venter either manifestly doesn’t understand what he’s being asked, or actually doesn’t understand the logic of making phylogenies using statistics.

    As Theobald writes in 29+ Evidences for Macroevolution – The Scientific Case for Common Descent:

    The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:

    “Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.” (Penny and Hendy 1986, p. 414)

  42. colewd:
    Alan Fox,

    You need to evolve proteins that can allows cells to communicate.

    Why do you say that?

    Then…

    Exactly! Things don’t need to happen all at once. Did you look at that Nature paper I linked to?

    …you need to evolve the systems that will allow the cells to form a multicellular cell cycle so you need apoptosis in addition to DNA repair.

    You also need cell differentiation , Hox genes and so on! But not all at once!

    Did LUCA have DNA repair?

    You already asked this. Why would an organism that had no DNA need a system to repair it? There have been detailed responses from other posters on this.

    Then…

    Exactly! You don’t need everything happening at once!

    …you need a system for oxygen to get to all the cells.This is the respiratory system.

    You are familiar with the cube-square law.? It depends how big you are.

    Then you need a central nervous system and muscles to move.

    Bacteria move without muscles. Octopuses manage to be good problem solvers without a brain.

    Do you think humans currently have the capability to come up with the DNA sequences for a repertory system?

    What’s a repertory system? As I don’t think humans had a hand in the processes that led to the diversity of life we see on Earth, why would I worry?

    How about just the sequences for an oxygen/co2 transport protein?

    How about the ability of the cells to differentiate during animal development?

    Cells sticking together is not a multicellular organism.You need to organize DNA with 4^500000 possible ways to arrange and build all this.So how did all that DNA become arranged to build the first multicellular organisms we observe in the fossil records?

    People have been over this with you. Evolution is not a search and doesn’t need to check every theoretical sequence for functionality. It just needs to stumble across one that works well enough.

    Do you agree it requires a pretty complex design just to get to a Cambrian animal?

    The environment had nearly three billion years to design the Cambrian organisms. It didn’t happen all at once.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.