Monday, January 25, 2010

New Intron Research Reveals Same Old Contradictions

In eukaryotes the DNA genes are sometimes interrupted by non coding segments. These intragenic regions, or introns, are cut out of the transcribed DNA before the copy is sent to the ribosome for translation into a protein. Naturally evolutionists have always believed introns are a result of evolution, but their explanations are strained. As one recent paper explained, understanding why such introns exist and their evolutionary origins is “a problem that has proved a conundrum for the past 30 years.”

Indeed, while it may have initially seemed to evolutionists that introns were inserted into genes during the course of evolution, findings of introns at conserved insertion sites, in various species, tell evolutionists that some of the introns are ancient, and were present in the earliest eukaryotes. But this suggests that the super complex editing machinery that splices the introns is also ancient. This is yet another example of early complexity whereas evolution predicts simple beginnings.

One virtue of this ancient origin view is that introns could be cast as evolutionary enablers in the origin of proteins narrative. After all, the expressed regions (exons) between the introns tended to conveniently be protein domains which can be rearranged and shuffled to modify the protein. As one of today’s leading textbooks explains, “It is believed that the organization of DNA coding sequences as a series of such exons separated by long introns has greatly facilitated the evolution of new proteins.” Or as one paper put it, by the 1980s “it had become a textbook dogma that introns were retained from a primordial RNA world in order to speed evolution by exon shuffling.”

It is yet another example of the tremendous serendipity in the evolution genre as evolution creates itself. Evolution creates everything from genes, chromosomes and alleles, to horizontal gene transfer, epigenetics, and now introns, so that, yes, evolution can occur. And evolutionists never think twice about the unlikely story they have contrived.

But the ancient origin view cannot explain many introns which don’t fit the pattern. Evolutionists view those as of more recent origin. In fact, evolutionists have constructed a battery of explanatory devices in their attempt to fit the data to their theory.

Perhaps introns are mostly ancient and exons arose within them, providing new genes. Or perhaps introns were mostly introduced later, during the course of evolution, interrupting the genes. And perhaps many introns were lost in the course of evolution, or perhaps introns slide around. And maybe introns served as sponges to reduce the deleterious impact of mutation showers.

As usual the genre elaborates from a rich set of devices and mechanisms, and it is often difficult to parse the empirical data from the theoretical constructs. Consider these passages from a recent paper which demonstrate how deeply immersed evolutionists are in their theory and how far they have departed from empiricism:

The fact that the alternative splicing products were of the cassette type (i.e., exons that are alternatively included/skipped from the mature transcript) did not question the emerging conceptualization of introns as definite DNA segments. Yet seeking to identify mechanisms for the rapid evolution of protein-coding sequences, records were cited of so-called cryptic donor/acceptor splice sites, and speculations were advanced that splicing-altering mutations could cause extensions/contractions of exons at intron junctions.

Interest in intron sliding models diminished on the belief that intron sliding could not be a frequent phenomenon. Under the notion of introns as fixed genomic segments, intron sliding is perceived as uncommon because it calls for the simultaneous occurrence of two mutations. Other paths, by a series of two or more short-range extension/contraction events of intron–exon boundaries, were deemed likely to be deleterious at the protein level. Such events would be feasible when the aberrant mRNAs contained premature stop codons that could be targeted by nonsense mediated decay.

Evolutionists think nothing of extreme speculation that amounts to little more than story-telling. And now, new intron research is adding more confusion to the narrative.

The intron patterns are now forcing evolutionists to switch from their view that intron insertions are random events. Sound familiar?

Evolutionists view biology as a fluke, and like the Epicureans and their veering atoms, evolutionists believe unguided events just happened to create the most complex structures known. Everything from mutations to genome insertion events occur at the roll of a die.

This is the evolutionary view even though so often it is falsified by reality. For everything from mutations to, yes introns, show patterns. And when these patterns cannot be fitted into the common descent model, then evolutionists must admit that the events do not occur at random.

Introns are yet another example of how evolution is less of a revealing explanation than merely a tautology. Whatever we find in nature, evolution will explain it no matter how strained is the narrative.

103 comments:

  1. Cornelius Hunter: Evolutionists think nothing of extreme speculation that amounts to little more than story-telling.

    When you make such comments, it seems as if you really don't get this whole science thingy. What you call "speculation" is a tentative assumption made in order to test its empirical consequences, that is, a hypothesis.

    ReplyDelete
  2. Cornelius:

    But this suggests that the super complex editing machinery that splices the introns is also ancient. This is yet another example of early complexity whereas evolution predicts simple beginnings.

    I suggest you look into the work of Michael Lynch who discusses mechanisms for the origins of introns in his book The Origins of Genomic Architecture, Chapter 9.

    Dave Wisker

    ReplyDelete
  3. Zachriel,

    What is the hypothesis for blind, undirected processes?

    There is no way that blind, undirected processes can account for such a thing as alternative gene splicing, which is what introns allow for.

    Also there isn't any way for blind, undirected processes to conjure up editing and splicing machinery- both require knowledge- knowledge of what is supposed to be edited and knowledge of what needs to be spliced.

    ReplyDelete
  4. Joe G: What is the hypothesis for blind, undirected processes?

    That doesn't parse well in scientific terms. However, we can propose and test a number of evolutionary mechanisms, including those having to do with natural sources of heritable novelty, as well as selection.

    For instance, the Lederberg Experiment demonstrates that at least some mutations are random with respect to fitness. Other hypotheses can be tested having to do with divergence from common ancestors.

    ReplyDelete
  5. "These intragenic regions, or introns, are cut out of the transcribed DNA ..."

    Cornelius, it's hard to take your essay seriously when it starts off with such a glaring error.

    ReplyDelete
  6. Dave:

    ====
    "But this suggests that the super complex editing machinery that splices the introns is also ancient. This is yet another example of early complexity whereas evolution predicts simple beginnings."

    I suggest you look into the work of Michael Lynch who discusses mechanisms for the origins of introns in his book The Origins of Genomic Architecture, Chapter 9.
    ====

    If your point is that speculation, underwritten by the belief that evolution is true, is easy to find, then I agree with you. Otherwise, I'm not sure what your point is.

    ReplyDelete
  7. Zachriel:

    "When you make such comments, it seems as if you really don't get this whole science thingy."

    Yeah, I have this old-fashioned view that science is about investigating nature rather than promoting as fact silly 19th century religious beliefs that make no sense. That's just me I guess ...

    ReplyDelete
  8. Um, Cornelius, introns are not removed from DNA. Kids learn that in, like, 3rd grade nowadays :-) .

    ReplyDelete
  9. "But this suggests that the super complex editing machinery that splices the introns is also ancient"

    Wow, I didn't know that the intron splicing was super complex. No natural process can produce super complex stuff, no way. Maybe complex stuff, but not "super complex". And it's machinery. Nature doesn't make machinery.
    Good work Cornelius. This is some excellent science writing here.
    You are a great example of how all scientists should be: Objective, Hard Working (lot's of research), and free of any religious influence. I hope to be a scientist like you one day

    ReplyDelete
  10. Art:

    "introns are not removed from DNA ..."

    But of course I didn't say that (I said transcribed DNA). Unfortunately this is typical.

    ReplyDelete
  11. This comment has been removed by the author.

    ReplyDelete
  12. TheFroman:

    "religious influence ..."

    Can you elaborate on your sarcasm, or are you just making things up?

    ReplyDelete
  13. What is the hypothesis for blind, undirected processes?

    Zachriel:
    "That doesn't parse well in scientific terms."

    I know. That is what we have been saying for decades yet that is exactly what the theory of evolution postulates.

    Natural selection is blind and the mutations are undirected genetic accidents.

    ID is in opposition to that premise.

    Zachriel-
    "However, we can propose and test a number of evolutionary mechanisms, including those having to do with natural sources of heritable novelty, as well as selection."

    Ummm "evolutionary mecahnsims" is a misdirecting equivocation- "evolution" has several meanings.

    This has been pointed out to you many times and you still do it.

    Do you think that your deception helps your cause?

    Also the Lederbergs didn't know about the communication that goes on between bacteria.

    We now know more than they did. "built-in responses to environmental cues"- see "Not By Chance" by Dr Spetner.

    ReplyDelete
  14. "Can you elaborate on your sarcasm, or are you just making things up?"

    Oh, I'm just making things up. You are free from religious influence. Anyone can see that. I'm sure you have asked yourself many times if its possible that your religious views are influencing your science, and I'm sure that every time the answer is "no". Right?

    ReplyDelete
  15. TheFroman-

    Does their atheistic thinking influence those scientists who are atheists?

    How does an atheist deal with the fact that natural processes only exist in nature and therefor cannot account for its origins, which science says it had?

    ReplyDelete
  16. TheFroman:

    So evolution is claimed to be an undeniable fact, religious arguments are made to prove it, (even though the science fails to show it is a fact), and it is the person who points this out who has the religious ax to grind, even though you can't actually provide any details. After all, anyone who doubts the fact of evolution must be a zealot, right? Unbelievable.

    ReplyDelete
  17. Hello Joe G,

    "Does their atheistic thinking influence those scientists who are atheists?"
    You mean does their atheistic worldview influence their scientific work? Probably not. Same for religious scientists. Science works.


    "How does an atheist deal with the fact that natural processes only exist in nature and therefor cannot account for its origins, which science says it had?"
    I don't have any issues with this, so I cannot give you an answer. Ask an atheist.

    ReplyDelete
  18. So, Cornelius, you are claiming that after a gene that encodes RNAs with introns is transcribed, the introns are removed from the DNA. This is what you wrote, and what you seem to be defending.

    No matter how you cut it, your statement is silly. And wrong.

    ReplyDelete
  19. Art,

    Transcribed DNA is RNA.

    So Cornelius is not claiming what you said he is.

    So no matter how you cut it all you are doing is twisting what was posted into something you want it to say.

    ReplyDelete
  20. TheForman,

    So only Cornelius has religious biases.

    Got it.

    ReplyDelete
  21. Art:

    ===
    So, Cornelius, you are claiming that after a gene that encodes RNAs with introns is transcribed, the introns are removed from the DNA. This is what you wrote, and what you seem to be defending.

    No matter how you cut it, your statement is silly. And wrong.
    ===

    When writing about science for the public one tries to avoid jargon when it doesn't really help. For instance, I tried to avoid "exon" (but ended up using it in this post). In the sentence you referring to, I thought it would be better to discuss "DNA" and copies of DNA, rather than introduce the term mRNA and the details that it entails.

    I make no claim about my writing skills, but I don't think that was a bad choice.

    ReplyDelete
  22. Joe G: Ummm "evolutionary mecahnsims" is a misdirecting equivocation- "evolution" has several meanings.

    Evolution refers to changes in the heritable traits of a population. Now you know.

    Joe G: Also the Lederbergs didn't know about the communication that goes on between bacteria.

    That's funny. Joshua Lederberg won the Nobel Prize for discovering that bacteria can mate and exchange genes. In any case, there is no communication between the bacterial plates, so that is not a valid objection to the finding that the mutations involved are random with respect to fitness.

    ReplyDelete
  23. Zachriel:
    Evolution refers to changes in the heritable traits of a population.

    That is one definition. There are several.

    And I am sure no one debates that.

    You can also say that evolution is the change in allele frequency over time.

    We have been down this road before also.

    It appears that you enjoy being willfully ignorant:

    http://intelligentreasoning.blogspot.com/2006/09/biological-evolution-what-is-being.html

    So ID is not anti-evolution and Creation is not anti-evolution.

    I am sure you will do everything in your power to correct all those forums who say otherwise.

    But all of that misses my point.

    IOW once again all you can do is provide a distraction.

    According to the theory of evolution natural is selection is blind and allegedly all mutations are genetic accidents.

    Zachriel:
    Joshua Lederberg won the Nobel Prize for discovering that bacteria can mate and exchange genes.

    I know what he did.

    I also know that doesn't address the type and range of communcations that we now know exists.

    I take you don't know either.

    Your ignorance is not a refutation.

    Zachriel:
    In any case, there is no communication between the bacterial plates, so that is not a valid objection to the finding that the mutations involved are random with respect to fitness.

    Why does there have to be communication between the plates?

    My scenario doesn't require that.

    IOW all you have is equivocation and a strawman.

    You must be very proud of yourself.

    ReplyDelete
  24. I am sure the following would be news to the Lederbergs:

    Quorum sensing


    how bacteria communicate

    ReplyDelete
  25. Joe G Why does there have to be communication between the plates?

    The Lederberg Experiment is a very simple and elegant experiment. It shows that the relevant mutations occur whether or not the bacteria have been exposed to the antibiotic, that is, the mutations are random with respect to environmental fitness. Here's the link again:

    http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml

    Quorum sensing is irrelevant to the results.

    ReplyDelete
  26. I know what the Lederberg experiment was.

    Why is quorum sensing irrelevant?

    There is also electromagnetic chatter- April 2009 PLoS ONE- Daniel Fels Swiss Tropical Institute.

    So there are communications going on on each plate.

    And as far as anyone knows part of these communications are finding out who has what defensive strategy for survival. Then if something isn't covered "orders" are sent out to "get-r-done".

    But anyway your response didn't address the question.

    Here is the question again:

    Why does there have to be communication between the plates?

    My scenario doesn't require it Mr Strawman.

    ReplyDelete
  27. Zachriel,

    In case you are unable to click on the links I provided- perhaps you like to cut-n-paste:

    http://www.pharmainfo.net/reviews/quorum-sensing-communication-between-bacteria

    http://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html

    Ignoring what I post isn't going to make the evidence go away.

    ReplyDelete
  28. So, Cornelius, you think that a good way to communicate with the lay public is to make statements that are laughably wrong.

    I don't share that opinion. I think most people who read these discussions can handle the fact that intron removal happens with RNAs, and not DNA.

    (Look! I didn't even have to use the term "exon" to convey the simple fact that intron removal involves RNA and not DNA.)

    JoeG, your proposal that the transcription apparatus includes some sort of deoxyribonucleotide oxidase, to convert the transcribed DNA to RNA, poses many interesting questions. But they are interesting in the same sense that a pondering of the impact of flying pigs is interesting.

    ReplyDelete
  29. Joe G: Why is quorum sensing irrelevant?

    We have clonal bacteria. We spread them on a plate. We let them grow into colonies. We expose the plate to antibiotics. Some live and some die. By propagating the survivors, we can show that they are antibiotic resistant, that is, there is a heritable variation for antibiotic resistance.

    One hypothesis is that the bacteria adapt in response to exposure to the antibiotic.

    So we repeat the experiment. We have clonal bacteria. We spread them on a plate. We let them grow into colonies. Only this time, we stamp the plate, that is, make a copy of the plate. Now we have two plates with the same pattern of colonies on each plate. We expose one plate and take note of which colonies live and which die. We then expose the second plate. The exact same colonies live and die. That means the heritable variations were there *before* exposure.

    Some bacteria mutate resistance and some don't. This happens whether or not the mutations are an advantage to the organism. Mutations are random with respect to fitness.

    ReplyDelete
  30. Zachriel: The exact same colonies live and die.

    Another way to say it is that the results of the first plate allow us to predict what will happen to the second plate. So even though the bacteria on the second plate have never been exposed to antibiotics, we can tell which ones are resistant and which ones aren't.

    ReplyDelete
  31. Art:
    JoeG, your proposal that the transcription apparatus includes some sort of deoxyribonucleotide oxidase, to convert the transcribed DNA to RNA, poses many interesting questions.

    Not my proposal. I never even thought such a thing.

    IOW Art that you for proving my point that you can take what is posted and twist it to suit your needs.

    ReplyDelete
  32. Why is quorum sensing irrelevant?

    Zachriel:
    We have clonal bacteria. We spread them on a plate. We let them grow into colonies. We expose the plate to antibiotics. Some live and some die. By propagating the survivors, we can show that they are antibiotic resistant, that is, there is a heritable variation for antibiotic resistance.

    Nope no response to the question in that bit of subterfuge.

    Zachriel:
    One hypothesis is that the bacteria adapt in response to exposure to the antibiotic.

    Nope- that doesn't have anything to do with what I am saying.

    Zachriel:
    So we repeat the experiment. We have clonal bacteria. We spread them on a plate. We let them grow into colonies. Only this time, we stamp the plate, that is, make a copy of the plate. Now we have two plates with the same pattern of colonies on each plate. We expose one plate and take note of which colonies live and which die. We then expose the second plate. The exact same colonies live and die. That means the heritable variations were there *before* exposure.

    That is what I am saying.

    Ya see in order to defend yourself you have to be ready before the thing you are defending against happens.

    Do you know anything about strategy or are you a liberal?

    Zachriel:
    Some bacteria mutate resistance and some don't. This happens whether or not the mutations are an advantage to the organism.

    Exactly- they don't all make ready for the same thing.

    Variation is the key to survival. Put all your eggs in one basket and a single selection pressure can wipe you out.

    So it makes sense to communicate and diversify- it's a strategy thing that you don't understand.

    Zachriel:
    Mutations are random with respect to fitness.

    I understand the propaganda.

    But as far as anyone knows they weren't random in any respect at all.

    ReplyDelete
  33. Joe G: There is also electromagnetic chatter- April 2009 PLoS ONE- Daniel Fels Swiss Tropical Institute.

    Is that supposed to be a citation? Perhaps you are referring to Fels, Cellular Communication through Light, PLoS ONE 2009.

    We'll rework the Lederberg Experiment. We take clonal bacteria and spread them on a plate. We allow them to grow into colonies. Then we stamp the plate (make a copy). We take one plate and send it into a mine shaft a mile underground. We take the other plate and load it on a rocket and a few minutes later it's in orbit on the other side of the planet. We then expose the plate deep in the mine to antibiotics and note which colonies live and which die. The colonies in orbit have never been exposed to antibiotics before, yet we will now reliably predict which colonies are resistant and which are not.

    Joe G: But as far as anyone knows they weren't random in any respect at all.

    Even if you were to claim that variation is part of the "design," the Lederberg Experiment still demonstrates that the mutations are random with respect to fitness. You probably don't understand what "random with respect to" an independent variable means. It means uncorrelated.

    Meanwhile, other experiments show that mutations have a variety of natural causes.

    Joe G: Nope no response to the question {about quorum sensing}.

    In fact, quorum sensing is irrelevant to the results. If you believe otherwise, instead of loading your comments with bile, you might try to explain how the results are explained by quorum sensing.

    ReplyDelete
  34. Zachriel,

    You are as clueless as ever.

    And if you say quorum sensing is irrelevant it is up to you to demonstrate why.

    And when you say:

    Meanwhile, other experiments show that mutations have a variety of natural causes.

    Proves that you are clueless- design is a natural cause.

    As I said and you have ignored communication is what set the variety-making mechanisms in motion.

    IOW saying that the mutations are "random with respect to" anything is based on ignorance.

    As Dr Spetner wrote in 1997- "built-in responses to environmental cues" and those cues come from the plate and the communcations by other bacteria.

    Now what part of that don't you understand?

    As for "bile" you deserve everything you get.

    I was against your banning form UD but now I remeber what a butthead you are and understand Clive's reasoning.

    Bacteria communicate- something the Lederbergs did not know about.

    That you think ignoring tat fact helps your case is truly amazing.

    ReplyDelete
  35. Ya see in order to defend yourself you have to be ready before the thing you are defending against happens.

    Do you know anything about strategy or are you a liberal?


    Do you understand that?


    Exactly- they don't all make ready for the same thing.

    Variation is the key to survival. Put all your eggs in one basket and a single selection pressure can wipe you out.

    So it makes sense to communicate and diversify- it's a strategy thing that you don't understand.


    Do you understand that?

    Or do you think your ignorance of what I am saying is meaningful discourse?

    ReplyDelete
  36. Joe G: As for "bile" you deserve everything you get.

    It dilutes the reading value of the thread for everyone to have to wade through your inane ad hominem.

    Joe G: As Dr Spetner wrote in 1997- "built-in responses to environmental cues" and those cues come from the plate and the communcations by other bacteria.

    That can only explain the correlation between the plates if there is communication between the plates. You do understand that the question is how to explain the correlation between the plates when they have yet to be exposed to antibiotics? In others words, some develop antibiotic resistance and some don't—regardless of the environmental fitness of that trait.

    Joe G: IOW saying that the mutations are "random with respect to" anything is based on ignorance.

    The experiment shows that the mutations are random with respect to fitness to the environment. Some develop antibiotic resistance even if never exposed to antibiotics.

    Joe G: Bacteria communicate-

    Yes, they do. But that doesn't explain the results. Indeed, we could do the same experiment by separating the individual colonies or bacteria and have a comparable result.

    ReplyDelete
  37. Joe G: So it makes sense to communicate and diversify- it's a strategy thing that you don't understand.

    As already stated, that's irrelevant. Even if the bacteria are superintelligent beings that sense the environment and communicate with one another, they can't sense the antibiotics if they've never encountered them before. They may spread out their variations as a hedge not knowing what they might encounter, but the variations are random with respect to fitness.

    ReplyDelete
  38. Zachriel,

    You don't even address what I am saying.

    And it isn't irrelevant if the bacteria communicate and the mutations occur as a result.

    That would mean that the mutations occurred for a reason and they are not random in any respect.

    They don't need to sense the anti-biotics before responding.

    They just have to be prepared for any eventuality.

    That is why they are not all the same.

    Ya see the debate is about are all mutations genetic accidents.

    You are trying to muddy the waters with the empty claim of "random with respect to fitness".

    But what is fitness if not survival and reproduction?

    And if the mutations allow the organisms to survive and reproduce then how can anyone say they are random with respect to that?

    And when I say that bacteria communicate I am only talking about the bacteria on any given plate.

    Again my scenario does not require bacteria to communicate between the plates.

    Now I have told you that several times and you still can't get that through your thick skull.

    As for diluting the tread your tripe has done just that.

    Anti-biotics- what are they made from?

    IOW what was the anti-biotic the Lederbergs used?

    I bet it can be found in nature and bacteria have encountered it before.

    ReplyDelete
  39. But anyway I am blogging about your refusal to understand what I am saying:

    Zachriel and the Lederberg Experiment

    ReplyDelete
  40. Variation is the key to survival. Put all your eggs in one basket and a single selection pressure can wipe you out.

    So it makes sense to communicate and diversify- it's a strategy thing that you don't understand.


    What part of that don't you understand?

    ReplyDelete
  41. Joe G: You are trying to muddy the waters with the empty claim of "random with respect to fitness". But what is fitness if not survival and reproduction?

    It means some bacteria will have a given variation, some won't, and the difference is not due to the whether or not the variation makes the particular organism more fit.

    Joe G: So it makes sense to communicate and diversify- it's a strategy thing that you don't understand.

    We can show that mutation occurs whether or not the organisms communicate.

    Joe G (from his blog): That woudl mean the mutations are nit genetic accidents but part of some "built-in response to environmental cues".

    That is precisely what we show does not happen. The resistance is not due to environmental cues, but occurs regardless of the exposure to antibiotics.

    ReplyDelete
  42. Zachriel:
    It means some bacteria will have a given variation, some won't, and the difference is not due to the whether or not the variation makes the particular organism more fit.

    What does being more fit mean?

    Is it all about survival and reproduction, as I said?

    Because if it is then variation is key to that for the reason provided.

    Zachriel:
    We can show that mutation occurs whether or not the organisms communicate.

    The Lederbergs didn't do that. As I said they didn't even know about the communications I linked to.

    So who, exactly, showed that and how did they do it?

    Zachriel:
    The resistance is not due to environmental cues, but occurs regardless of the exposure to antibiotics.

    Excuse me but their environment is made up of more than the selection pressure- ie exposure to anti-biotics.

    Ya see it is as I said, you, being a liberal have no idea what strategy is.

    You wouldn't know how to stage a defense.

    Thankfully bacteria aren't subject to liberalism's mind-numbing effects.

    As I said you defend by preparing, variation is the preparation and communication helps direct the variation.

    ReplyDelete
  43. Joe G: Excuse me but their environment is made up of more than the selection pressure- ie exposure to anti-biotics.

    Then be specific.

    In any case, the point of the experiment is that the bacteria on the second plate have never been exposed to antibiotics, yet we can predict which ones have resistance and which ones don't. This demonstrates that the mutations occurred without regard to exposure to the fitness effects of antibiotic resistance. That means, by definition, that the mutations are random with respect to fitness for that environment.

    ReplyDelete
  44. Excuse me but their environment is made up of more than the selection pressure- ie exposure to anti-biotics.

    Zachriel:
    Then be specific.

    So you have been arguing against something that you didn't understand?

    You should ask first.

    The environment includes everything on the plate, which means other bacteria- you know the bacteria who are sending and receiving signals.

    Zachriel:
    In any case, the point of the experiment is that the bacteria on the second plate have never been exposed to antibiotics, yet we can predict which ones have resistance and which ones don't.

    But that doesn't have anything to do with whether or not the mutations were directed or just genetic accidents.

    Zachriel:
    That means, by definition, that the mutations are random with respect to fitness for that environment.

    You have never gotten around to define what you mean by fitness.

    If you define fitness by survival and reproduction then variation is not random with respect to it.

    Variation would be a very sound defense plan.

    And communication lets all the individuals know what variation already exists.

    Once you know what you have then you can tell what you need.

    ReplyDelete
  45. JOe G: But that doesn't have anything to do with whether or not the mutations were directed or just genetic accidents.

    It doesn't matter if the bacteria are superintelligent and supercoordinated. It doesn't even matter if they are consciously directing the variation in order to enhance the group's chance of survival. There is still no correlation between the mutation for antibiotic resistance and the presence of antibiotics.

    Joe G: You have never gotten around to define what you mean by fitness.

    Traits that provide a differential reproductive advantage in a given environment.

    ReplyDelete
  46. But that doesn't have anything to do with whether or not the mutations were directed or just genetic accidents.

    Zachriel:
    It doesn't matter if the bacteria are superintelligent and supercoordinated. It doesn't even matter if they are consciously directing the variation in order to enhance the group's chance of survival.

    Actually it matters quite a bit to the debate- the debate which you keep ignoring.

    Zachriel:
    There is still no correlation between the mutation for antibiotic resistance and the presence of antibiotics.

    It doesn't matter.

    A good defense is one that is ready BEFORE the selection pressure comes.

    It is called planning.

    Planning is something unwelcome in the theory of evolution.

    You have never gotten around to define what you mean by fitness.

    Zachriels:
    Traits that provide a differential reproductive advantage in a given environment.

    So survival and reproduction, just as I have been saying.

    Some out-reproduce others- for a variety of reasons.

    So you say "random with respect to fitness" yet it is obvious that the variation is key to fitness as you have defined it.

    Go figure...

    ReplyDelete
  47. Joe G: Actually it matters quite a bit to the debate- the debate which you keep ignoring.

    You took issue with the statement that mutations are random with respect to fitness. That is the claim we are trying to resolve.

    Joe G: A good defense is one that is ready BEFORE the selection pressure comes. It is called planning.

    That's fine, but you ignored my repeated argument. The bacterial overlord can be directing that the bacteria produce variations, but those variations are still random with respect to fitness.

    Joe G: Some out-reproduce others- for a variety of reasons.

    One of those reasons can be shown to be due to inherited traits, the fitness depending on the environment the organism finds itself in.

    Zachriel: Traits that provide a differential reproductive advantage in a given environment.

    Joe G: So you say "random with respect to fitness" yet it is obvious that the variation is key to fitness as you have defined it.

    Fitness is defined as a differential advantage. Some bacteria have variations that can affect their fitness. Actual fitness depends on the environment. But those variations occur regardless of the given environment. They are *uncorrelated*. Hence, by definition, variations are random with respect to fitness.

    ReplyDelete
  48. Zachriel:
    You took issue with the statement that mutations are random with respect to fitness. That is the claim we are trying to resolve.

    I take issue with most of the stuff you post.

    And "random with respect to fitness" is vacuous- it has no heuristic value.

    Not only that variation is key to fitness.

    A good defense is one that is ready BEFORE the selection pressure comes. It is called planning.

    Zachriel:
    That's fine, but you ignored my repeated argument.

    You are ignoring everything I say. I have told you that a) your "argument" is meaningless and b) variation is key to fitness so far from being random with respect to it, variation provides it.

    Zachriel:
    Fitness is defined as a differential advantage. Some bacteria have variations that can affect their fitness. Actual fitness depends on the environment.

    And what is the environment? The plate the bacteria reside.

    The plate that includes all the bacteria and their communication networks.

    Zachriel:
    But those variations occur regardless of the given environment.

    You don't know that.

    Ya see the environment includes the other bacteria and their communication networks.

    And my premise is that it is via those communication networks that the variation takes place.

    That is what planning means.

    IOW they are correlated.

    So the bottom line is Zachriel thinks his ignorance is meaningful discourse.

    Sweet...

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  49. Joe G: And "random with respect to fitness" is vacuous- it has no heuristic value.

    Let's start with fitness. Fitness is a measure of an organism's reproductive advantage over others in a population of such organisms in a given environment. For instance, we can show that some bacteria survive and reproduce better in antibiotic environments, so it seems we can provide a relative measure of fitness. Do you agree?

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  50. Zachriel:
    Fitness is a measure of an organism's reproductive advantage over others in a population of such organisms in a given environment.

    Advantage? Are we playing tennis?

    How does one gain that adavantage?

    Is there more than one reason?

    What happens when cooperation is involved- as opposed to competition?

    Zachriel:
    For instance, we can show that some bacteria survive and reproduce better in antibiotic environments, so it seems we can provide a relative measure of fitness.

    So if we choose which to kill we can control who live.

    Got it, but it sounds a lot like artificial selection.

    If we supply the selection pressure we can determine who dies.

    Zachriel:
    Do you agree?

    Yes I agree that artificial selection exists and can cull at the will of the agency applying it.

    But anyway variation is key to fitness- by your defintion.

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  51. Fitness is a very basic concept in biology. Most readers are already familiar with it. (Your questions are obviously not meant to clarify the issue.)

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  52. I know what fitness means in biology.

    And by your definition variation provides fitness and therefor is not random with respect to it.

    As for clarifying the issue you don't want that as your position counts on subterfuge.

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  53. Joe G: I know what fitness means in biology.

    Great! Please provide a scientific definition of biological fitness, that is, one that provides an unambiguous measure. Thanks!

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  54. Fitness is a measure of an organism's reproductive advantage over others in a population of such organisms in a given environment.

    Do you agree?

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  55. I don't know how scientific that is or if it allows for unambiguous measure- the source is very sketchy...

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  56. Joe G, you had said you knew "what fitness means in biology," but for whatever reason, you didn't bother to provide a definition. Here is a typical definition from Wikipedia:

    "Fitness (often denoted w in population genetics models) is a central idea in evolutionary theory.describes the capability of an individual of certain genotype to reproduce, and usually is equal to the proportion of the individual's genes in all the genes of the next generation. If differences in individual genotypes affect fitness, then the frequencies of the genotypes will change over generations; the genotypes with higher fitness become more common. This process is called natural selection."

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  57. It seems there are issues with "fitness" in biology:

    Stanford Encyclopedia of Philosophy on Fitness

    It looks like it is a nonsense term in an evolutionary context.

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  58. Zachriel,

    I provided the definition of fitness YOU posted.

    And if you have issues with it take it up with yourself.

    The definition you just provided from wikipedia is "an empty, unfalsifiable tautology bereft of explanatory power"*

    * from the Stanford encyclopedia

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  59. Joe G: It looks like it is a nonsense term in an evolutionary context.

    But you already said you knew what it meant!

    Indeed, there can be difficulties with the definition. That's why a scientific definition has to be specific and unambiguous. We have to show a correlation betwee the traits of an individual organism and the differential reproductive potential compared to others in the population and in a particular environment. Are we okay with that, or will you continue to maintain to our readers that fitness can never be a valid scientific metric?

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  60. Joe G: The definition you just provided from wikipedia is "an empty, unfalsifiable tautology bereft of explanatory power"*

    That is not correct. The Wikipedia definition includes the important word "capability," which refers to those characteristics that lead to a reproductive advantage.

    There is no doubt that fitness exists. We can demonstrate that by showing that some bacteria have resistance to naturally occurring antibiotics, and some don't. In antibiotic environments, the tendency of resistant bacteria to dominate the population is called natural selection.

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  61. Zachriel:
    But you already said you knew what it meant!

    I do and it has been nonsense since I first read about it.

    And the Stanford Encyclopedia agrees that it is nonsense.

    Perhaps you should take it up with them.

    Ya see the only way to check evolutionary "fitness" is AFTER reproduction.

    Yes some individuals leave more offspring than others.

    Howevber that can be for many reasons not related to biological make-up.

    As for anti-biotic introduction- that is artificial slection.

    And yes if we choose which die and which survive then we control the "fitness".

    Natural selection didn't have anything to do with it.

    But anyway again you provide nothing but a distraction.

    If variation leads to survival, which leads to reproduction, ie fitness, then variation is not random with respect to it.

    It is very simple actually.

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  62. Joe G: I do and it has been nonsense since I first read about it.

    You have explained your position well enough.

    You will convince exactly those people who agree with you that biological fitness is a nonsense concept and don't think it meaningful to say that antibiotic resistant bacteria are more fit in antibiotic environments. And yet, bacterial fitness and evolution are of crucial medical importance.

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  63. Zachriel,

    I provided a reference from the Stanford Encyclopedia to support my claim about fitness.

    You think that ignoring valid references and providing useless references- ie wikipedia- helps your case.

    Amazing.

    Saying that antibiotic resistant bacteria survive and reproduce better in antibiotic environments is meaningless because once you call bacteria "antibiotic resistant" it is a given that they survive and reproduce better in an antibiotic environment.

    IOW Zachriel once again you have proven deficient in the knowledge required to have an educated discussion about evolution and biology.

    ReplyDelete
  64. More for Zachriel to ignore:

    The Strength of Natural Selection in the Wild:

    "Natural selection disappears as a biological force and reappears as a statistical artifact. The change is not trivial. It is one thing to say that nothing in biology makes sense except in the light of evolution; it is quite another thing to say that nothing in biology makes sense except in the light of various regression correlations between quantitative characteristics. It hardly appears obvious that if natural selection is simply a matter of correlations established between quantitative traits, that Darwin's theory has any content beyond the phenomenological, and in the most obvious sense, is no theory at all."

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  65. Joe G: Saying that antibiotic resistant bacteria survive and reproduce better in antibiotic environments is meaningless because once you call bacteria "antibiotic resistant" it is a given that they survive and reproduce better in an antibiotic environment.

    It's not meaningless: it's giving a name to an observed phenomena, that some organisms can resist antibiotics, and some can't. In addition, we can show that antibiotic resistance is a *heritable* trait, and that in antibiotic environments, those organisms with this heritable trait have a reproductive advantage over those in the population without the trait. We call this reproductive advantage "biological fitness." And virtually everyone knows this.

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  66. We need to break this down to fundamentals. (This reminds us of the days of Sam of Ballyvourney, County Cork!)

    We have two strains of bacteria. If we expose these two strains to antibiotics, we note that one strain dies and one strains lives. We will call the strain that lives "antibiotic resistant." Okay so far?

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  67. Zachriel:
    If we expose these two strains to antibiotics, we note that one strain dies and one strains lives. We will call the strain that lives "antibiotic resistant."

    That is what I have already said.

    Also your example is an example of artificial selection. And virtually everyone knows this.

    AND-

    If variation leads to survival, which leads to reproduction, ie fitness, then variation is not random with respect to it.

    It is very simple actually.


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  68. I will bring it to you piece by piece if need be:

    1. The Classical Problem of Fitness

    The leading idea of Darwin's theory of natural selection is often expressed in terms first coined by Herbert Spencer as the claim that among competing organisms “the fittest survive.” If there is random variation among the traits of organisms, and if some variant traits fortuitously confer advantages on the organisms that bear them, i.e. enhance their fitness, then those organisms will live to have more offspring, which in turn will bear the advantageous traits. Whence descent with adaptive modification, i.e. evolution. Evolution by random heritable variation and natural selection will explain ever increasing adaptation to given environments, increasing diversity in the occupation of new environments, and the complexity of organisms and their parts as their lineages adapt to one another and to their environments.

    But what is fitness and how can one tell when a trait enhances fitness, or more to the point, when one organism is fitter than another? Opponents of the theory of natural selection have long claimed that the theory is so treated by its proponents as to define fitness in terms of rates of reproduction, thus condemning the principle of the survival of the fittest to triviality: the claim that those organisms with higher rates of reproduction leave more offspring is an empty, unfalsifiable tautology bereft of explanatory power. In the century and a half since the publication of On the Origin of Species biologists have all too often reinforced this objection by actually so defining fitness. For example, C.H. Waddington writes, in Towards a Theoretical Biology, the fittest individuals are those that are “most effective in leaving gametes to the next generation.” It appears therefore that evolutionary theory requires a definition of fitness that will protect it from the charges of tautology, triviality, unfalsifiabilty, and consequent explanatory infirmity. If no such definition is in fact forthcoming, then what is required by the theory's adherents is an alternative account of its structure and content or its role in the research program of biology.



    Okay so far?

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  69. Zachriel: If we expose these two strains to antibiotics, we note that one strain dies and one strains lives. We will call the strain that lives "antibiotic resistant." Okay so far?

    Joe G: That is what I have already said.

    Good! That's a "yes," then. So the term "antibiotic resistance" is not meaningless as you said previously, but refers to observed differences in individual bacteria. By the way, we call these sorts of distinctions "traits."

    Now, it can be shown that the presence of antibiotic resistance is a heritable trait. That is, the offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant. Are we okay with this then?

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  70. Zachriel:
    So the term "antibiotic resistance" is not meaningless as you said previously...

    That is not what I said.

    I take it you still have difficulty understanding English.

    Zachriel:
    ...but refers to observed differences in individual bacteria. By the way, we call these sorts of distinctions "traits."

    In the absence of teh artificial selection pressure how do you know which is which?

    Zachriel:
    Now, it can be shown that the presence of antibiotic resistance is a heritable trait. That is, the offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant.

    Umm no.

    Ya see the resistant strain most likely evolved from a non-resistant strain.

    It can also go the other way- the non-resistant evolved from the resistant.

    But again all this is irrelevant and just a distraction to hide the fact that you don't know what you are talking about.

    And it is also very telling that you are ignoring my posts.

    But more to the point-

    If variation leads to survival, which leads to reproduction, ie fitness, then variation is not random with respect to it.

    It is very simple actually.


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  71. Joe G: That is not what I said.

    Regardless, we agree that "antibiotic resistance" refers to observable differences in individual bacteria.

    Zachriel: Now, it can be shown that the presence of antibiotic resistance is a heritable trait. That is, the offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant.

    Joe G: Umm no.

    Really? You're actually saying that antibiotic resistance is not a heritable trait?

    The average mutation rate in E. coli is about one mutation per 1000 cell divisions. And most of those mutations will have no effect on antibiotic resistance. Hence, the majority of offspring are exact clones, and the vast majority share the state of the resistance trait.

    Tago et al., Escherichia coli mutator Delta polA is defective in base mismatch correction: The nature of in vivo DNA replication errors. Journal of Molecular Biology 2005.

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  72. Drake et al. Rates of spontaneous mutation, Genetics 1998.

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  73. Zachriel:
    Regardless, we agree that "antibiotic resistance" refers to observable differences in individual bacteria.

    Observable under specific artificial circumstances.

    It is not observable in the wild.

    You wouldn't know an anti-biotic resistant bacteria from a non-resistant bacteria outside of a control.

    Zachriel:
    You're actually saying that antibiotic resistance is not a heritable trait?

    No I am saying there isn't any guarantee the offspring will be the same as the parent.

    That is the whole thing behind the theory- descent with modification.

    Descent without modification isn't evolution.

    I was under the impression we were discussing evolution, not stasis.

    Zachriel:
    Hence, the majority of offspring are exact clones, and the vast majority share the state of the resistance trait.

    So much for the theory of evolution...

    With something like that it is no wonder the bacterial flagellum is out of the reach of accumulating genetic accidents.

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  74. If variation leads to survival, which leads to reproduction, ie fitness, then variation is not random with respect to it.

    It is very simple actually.


    What part opf that don't you understand?

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  75. Joe G: Observable under specific artificial circumstances.

    No, but irrelevant. There are differences in individual bacteria such that some are resistant to antibiotics and some aren't. Do you disagree?

    Joe G: No I am saying there isn't any guarantee the offspring will be the same as the parent.

    But that wasn't the statement you disagreed with:

    Now, it can be shown that the presence of antibiotic resistance is a heritable trait. That is, the offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant.

    Joe B: I was under the impression we were discussing evolution, not stasis.

    No, we were discussing the claim that mutations are random with respect to fitness. That conversation obviously requires an understanding of fitness, and that requires a minimal understanding of traits, heredity, and the correlation between traits and reproductive success.

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  76. Zachriel:
    There are differences in individual bacteria such that some are resistant to antibiotics and some aren't.

    What differences?

    Just saying "differences" isn't very scientific.

    Zachriel:
    That is, the offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant.

    If that is the case then where is the evolution?

    Fitness and evolution are directly correlated.

    And as Stanford pointed out fitness is a nonsensical concept.

    And as pointed out by Berlinski it is very difficult to quantify.

    Also fitness and variation are directly correlated.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?

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  77. Joe G: If that is the case then where is the evolution?

    We were discussing the claim that mutations are random with respect to fitness. That conversation obviously requires an understanding of fitness, and that requires a minimal understanding of traits, heredity, and the correlation between traits and reproductive success. At this point, as our readers can see, you are still stuck on "trait."

    Zachriel: There are differences in individual bacteria such that some are resistant to antibiotics and some aren't.

    Joe G: What differences?

    Some bacteria are resistant to antibiotics and some are not (as was specified in the sentence you responded to).

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  78. Just wanted to say that it is quite funny to watch these discussions between Zachriel (or any other educated person fot that matter) and Joe G. Keep it going!

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  79. Zachriel:
    We were discussing the claim that mutations are random with respect to fitness.

    Your example says fitness and variation are directly correlated.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?

    And when I ask "what differences?" it means be specific.

    When you just say "anti-biotic resistance" it is a sure thing that you don't know what you are talking about.

    But all readers already knew that.

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  80. Joe G: Your example says fitness and variation are directly correlated.

    You had suggested that "fitness" was a nonsensical concept, while "variation" refers to variations in heritable traits, so we certainly have to define traits first.

    If we expose these two strains to antibiotics, we note that one strain dies and one strains lives. We will call the strain that lives "antibiotic resistant," a trait of that strain. Are we okay with this?

    Then we had a problem with heredity. The offspring of antibiotic resistant bacteria will normally be antibiotic resistant, and the offspring of non-antibiotic resistant bacteria will normally be non-antibiotic resistant. Are we okay with this?

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  81. Your example says fitness and variation are directly correlated. That is given YOUR definition of fitness.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?



    Answer the question Zachriel.

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  82. Zachriel:
    You had suggested that "fitness" was a nonsensical concept,...

    And I supported that claim.

    You choose to ignore that support and prattle on anyway.

    I take it that you don't care that everyone laughs at you.

    That must be why you choose to remain anonymous.

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  83. Zachriel: You had suggested that "fitness" was a nonsensical concept

    Joe G: And I supported that claim.

    You went on to use the term as if it had a meaning.

    Joe G: If variation is key to fitness then how can it be random with respect to it?

    You demand an answer to a question where one of the terms you insist is nonsensical. In order to answer your question, we have to agree to what those terms means. Variation refers to differences in traits *between* organisms.

    Joe G: And as Stanford pointed out fitness is a nonsensical concept.

    Stanford is not a person. The essay was by Alexander Rosenberg, and does not represent a consensus in his field of philosophy, much less biology. In order to resolve this issue, we need to examine the definition carefully to make sure we have a scientifically unambiguous measure. To do that, we have to build our definition from fundamental concepts.

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  84. Your example says fitness and variation are directly correlated.

    That is given YOUR definition of fitness.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?



    Answer the question Zachriel.


    We are using YOUR definition. And it does not matter that I and many people think it is nonsensical.

    Answer the question.

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  85. Joe G: That is given YOUR definition of fitness.

    You claimed that fitness was a "nonsensical concept." We need to resolve that issue first or your question is rendered nonsensical. And that means having a clear understanding of traits and heredity. These are not difficult concepts.


    TRAITS and VARIATION: We can show that all bacteria are not alike. That is they exhibit "variation." In particular, we can show that some bacteria are resistant to antibiotics and some are not. We call this trait "antibiotic resistance." Are we okay so far?

    HERITABLE: We can show that antibiotic resistance is a heritable trait. That is, most offspring will express the same trait as their parent. Do you disagree?

    FITNESS: We can then show that this trait can be correlated with differential reproduction in environments that include the presence of antibiotics. We call a differential reproductive advantage "fitness." Are we okay with this?

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  86. Zachriel:
    You claimed that fitness was a "nonsensical concept."

    That is irrelevant.

    As I said if we take your definition and use it as if it were useful we still come out with the fact that variation provided the fitness and therefor is not random with respect to it.

    Zachriel:
    We can show that all bacteria are not alike.

    Right there is variation.

    Zachriel:
    In particular, we can show that some bacteria are resistant to antibiotics and some are not.

    Only by artificially introducing the anti-biotic.

    And even then it all depends on that anti-biotic.

    There are more than one.

    IOW we cannot tell which are anti-biotic resistant BEFORE the anti-biotic is applied.

    And even then all we can do is assume that all survivors are anti-biotic resistant.

    IOW it is all after-the-fact, ie meaningless.

    Zachriel:
    We can show that antibiotic resistance is a heritable trait.

    So there were bacteria that were originally designed with this resistance.

    They had to be because according to you it is doubtful that mutations accumulated to allow such a thing.

    Zachriel:
    We can then show that this trait can be correlated with differential reproduction in environments that include the presence of antibiotics.

    Yes I understand that if we control who lives and dies that we can also control who reproduces.

    As I said given what you are saying at face-value what I said is confirmed.

    Your example says fitness and variation are directly correlated.

    That is given YOUR definition of fitness.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?



    Answer the question Zachriel.

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  87. Joe G: Right there is variation.

    Good. There is variation in traits, in particular, some bacteria have antibiotic resistance and some don't.

    Joe G: Only by artificially introducing the anti-biotic.

    So we have a valid scientific test!

    By the way, antibiotics exist in nature, and they are not always lethal. We might also trace the resistance to a particular gene and be able to tell that way. But as long as there is a test, that's all that matters.

    Joe G: IOW it is all after-the-fact, ie meaningless.

    Meaningless? Please. It can be a matter of life-or-death in the struggle between bacteria and their human hosts. In any case, there is a valid scientific test that can determine whether a strain of bacteria have antibiotic resistance or not.

    Zachriel: We can show that antibiotic resistance is a heritable trait.

    Joe G: So there were bacteria that were originally designed with this resistance.

    What is so difficult about simply saying that antibiotic resistance is a heritable trait?

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  88. As I said given what you are saying at face-value what I said is confirmed.

    Your example says fitness and variation are directly correlated.

    That is given YOUR definition of fitness.

    Your very example says that variation is key to fitness.

    If variation is key to fitness then how can it be random with respect to it?



    Answer the question Zachriel.

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  89. Joe G: Your very example says that variation is key to fitness.

    Does your use of the word "key" have a clear meaning? I note that you have refused to clarify the terms in your question.

    Based on the ordinary readings of the definitions provided, mutation can be random with respect to fitness as fitness is defined as a differential reproductive advantage due to hertiable traits. Consequently, some members of a population may be more or less fit than that other members of the population.

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  90. Your very example says that variation is key to fitness.

    Zachriel:
    Does your use of the word "key" have a clear meaning?

    "Serving as an essential component".

    Zachriel:
    Based on the ordinary readings of the definitions provided, mutation can be random with respect to fitness as fitness is defined as a differential reproductive advantage due to hertiable traits.

    Yet based on your example variation is essential to fitness, not random with respect to it.

    What would happen to the bacteria in an anti-biotic environment if the variation for anti-biotic resistance did not exist?

    Perhaps you should choose an example that actually demonstrates what it is you are trying to say.

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  91. Zachriel:
    Consequently, some members of a population may be more or less fit than that other members of the population.

    And then again maybe not. It all depends.

    This fitness concept is such a powerful and unambiguous thing is making me all shivery and stuff...

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  92. Joe G: Yet based on your example variation is essential to fitness, not random with respect to it.

    If the population is comprised of exact clones, then they have equal fitness. If a mutation causes a decrease in reproductive potential in a given environment, that individual has lower fitness in that environment. This is true regardless of the cause or distribution of the mutations. That's because fitness, as defined, is a differential between members of a population.

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  93. Zachriel:
    If the population is comprised of exact clones, then they have equal fitness.

    Even if one gives birth to a mutant?

    Zachriel:
    If a mutation causes a decrease in reproductive potential in a given environment, that individual has lower fitness in that environment.

    If? If not then what happens?

    What if we have a population with many variations yet not one variation confers an advantage over any others?

    Add to that a varying environment.

    Kind of shoots your control all to heck.

    But that is what nature is really like.

    However all that is moot because variation provides fitness- in your example- and therefor is not random with respect to it.

    Again this all relates to the Lederberg experiment.

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  94. Joe G: Even if one gives birth to a mutant?

    Then it's not an exact clone.

    Joe G: What if we have a population with many variations yet not one variation confers an advantage over any others?

    If the variations do not result in differential reproductive potential, then there is no change in fitness.

    Joe G: However all that is moot because variation provides fitness- in your example- and therefor is not random with respect to it.

    That is incorrect. Some variation is beneficial. Some is detrimental. And some makes no difference in fitness. The mere existence of variation is not sufficient to determine fitness. Which shows that fitness and variation are not directly dependent.

    Joe G: Again this all relates to the Lederberg experiment.

    Amazing how the Lederbergs can be so wrong and you so right.

    Joe G: This fitness concept is such a powerful and unambiguous thing is making me all shivery and stuff...

    That's why the conversation should be grounded in specifics: We can show that there are differences in bacteria such that, depending on the environment, they may have differential reproductive potential. In particular, we have bacteria with and without the heritable trait of antibiotic resistance. Are we okay so far?

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  95. Even if one gives birth to a mutant?

    Zachriel:
    Then it's not an exact clone.

    The parent or offspring?

    Which brings up something else- say the parent also mutated during reproduction.

    IOW after the split neither resembles the original.

    Zachriel:
    If the variations do not result in differential reproductive potential, then there is no change in fitness.

    What if something other than variation results in differential reproduction?

    Or what if the variation is not heritable?

    However all that is moot because variation provides fitness- in your example- and therefor is not random with respect to it.

    Zachriel:
    That is incorrect.

    Not according to you.

    Zachriel:
    Some variation is beneficial.

    EXACTLY!!!! Winnah, winnah, chicken dinnah!

    Zachriel:
    Some is detrimental. And some makes no difference in fitness.

    So you don't understand what I said- IOW you don't have any clue as what I have been telling you for days.

    Good planning means to be ready for everything you- the population- possibly can.

    Soldiers have died protecting their population- you can't always save everyone from every eventuality.

    But with bacteria how many have to be saved in order for that species to survive?

    Zachriel:
    The mere existence of variation is not sufficient to determine fitness.

    And yet the mere existence of no variation is.

    Also fitness is "determined" AFTER the fact, so I don't think the word fits.

    Zachriel:
    Which shows that fitness and variation are not directly dependent.

    And yet you can't have fitness without it.

    Zachriel:
    Amazing how the Lederbergs can be so wrong and you so right.

    Knowledge is a wonderful thing.

    Ya see they did not know about the communications networks that scientists now study.

    I have the knowledge that they didn't.

    Zachriel:
    We can show that there are differences in bacteria such that, depending on the environment, they may have differential reproductive potential.

    Yes I know- if we kill some bacteria the surviving bacteria may out reproduce them.

    Then again if there isn't any food around the survivors ain't going to be very much of anything.

    So when a concept depends on many just-so factors, it probably doesn't translate very well to the real world.

    And as a matter of fact I linked to an essay about a paper that demonstrates that very thing.

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  96. Joe G: What if something other than variation results in differential reproduction?

    All sorts of things can affect reproduction. Fitness is defined by those traits that lead to a reproductive advantage. An advantage is not a certainty of success, though.

    Joe G: Or what if the variation is not heritable?

    Phenotypic and genotypic fitness are distinct. They are correlated, but not identical.

    Joe G: Good planning means to be ready for everything you- the population- possibly can.

    But fitness doesn't apply to the population, but to organisms. If a bacteria doesn't have antibiotic resistance, and finds itself in an antibiotic environment, then it has low fitness compared to those that do.

    Joe G: Also fitness is "determined" AFTER the fact, so I don't think the word fits.

    If it helps, we'll make them different colors.

    Zachriel: Which shows that fitness and variation are not directly dependent.

    Joe G: And yet you can't have fitness without it.

    Of course you can. For instance, if all the organisms are exact clones, they have the same fitness.

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  97. Zachriel:
    All sorts of things can affect reproduction.

    Yes, I know.

    Zachriel:
    Fitness is defined by those traits that lead to a reproductive advantage.

    Even if that individual doesn't take advantage of that advantage?

    Zachriel:
    An advantage is not a certainty of success, though.

    Then how do you know an advantage existed?

    Or what if the variation is not heritable?

    Zachriel:
    Phenotypic and genotypic fitness are distinct. They are correlated, but not identical.

    That doesn't answer the question.

    Good planning means to be ready for everything you- the population- possibly can.

    Zachriel:
    But fitness doesn't apply to the population, but to organisms.

    Good planning so that the population survives is all the population cares about.

    And that good planning includes organisms.

    It is that good planning that tells the organisms what is present in the environment so they can figure out what they- the organisms- need.

    Zachriel:
    For instance, if all the organisms are exact clones, they have the same fitness.

    Or no fitness at all.

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  98. fitness:

    (1) (biology) A biological condition in which a competing variant is increasing in frequency relative to other competing variants in a population.

    (2) A relative measure of reproductive success of an organism in passing its genes to the next generation.

    (3) The relative ability of an individual (or population) to survive, reproduce and propagate genes in an environment.


    Nothing about mere capability in that.

    I told you using wikipedia was a bad idea.

    I cannot find any (other) reference that sez fitness is related to mere capability.

    Always and without fail- save for wikipedia- fitness is related to reproductive success.

    And more specifically the passing on of your genes- which is where sexual reproduction can mess with things a little.

    Ya see even though a person can have many offspring, and those offspring have many more, and so on, the original person may not have any genes left in the family after a few generations.

    But anyway...

    -

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  99. Just a passing thought -

    Thought this link might be relevant here

    http://www.stephenjaygould.org/library/gould_tautology.html

    Stephen Jay Gould waxing lyrical on exactly what is meant by fitness in biology and how we define it - and especially the repreceussion for the theory of evolution and those who misunderstand it.

    It's a little old, but seems relevant here. It's short and well worth the read.

    The key passage, is think, is this:

    "But let me first admit that Bethell's criticism applies to much of the technical literature in evolutionary theory, especially to the abstract mathematical treatments that consider evolution only as an alteration in numbers, not as a change in quality. These studies do assess fitness only in terms of differential survival. What else can be done with abstract models that traced the relative successes of hypothetical genes A and B in populations that exist only on computer tape? Nature, however, is not limited by the calculations of theoretical geneticists. In nature, A's "superiority" over B will be expressed as differential survival, but it is not defined by it."

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  100. Joe G: Then how do you know an advantage existed?

    In the case of antibiotic resistance in bacteria, by repeated experimentation.

    Joe G: Or what if the variation is not heritable?

    This is your answer: Phenotypic and genotypic fitness are distinct. They are correlated, but not identical. A correlation is a statistical relationship and allows us to make probabilistic predictions. Because we are concerned with heritable variation (see above), this discussion concerns genotypic fitness.

    Zachriel: But fitness doesn't apply to the population, but to organisms.

    Joe G: Good planning so that the population survives is all the population cares about.

    A population is not the unit of measure for fitness per the definition you agreed to use, but the differential reproductive potential due to inherited traits compared to others in the population and in a particular environment.

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  101. Joe G: Nothing about mere capability in that.

    Definition #3 refers to ability.

    We had agreed to a definition. Our readers can understand why you had avoided being explicit in your use of terminology.

    Joe G: fitness is related to reproductive success.

    Of course fitness is related to reproductive success. We have defined it as a differential reproductive potential due to inherited traits compared to others in the population in a given environment.

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  102. These studies do assess fitness only in terms of differential survival.

    There's been a lot of philosophical discussion about this common definition in genetics. Once we establish that traits can lead to differential reproductive success, then we can turn that around and hypothesize that differential reproductive success is due to traits—even if we do not know what those traits are. It's a very strong relationship, so the correlation does imply causation. This is something we can experimentally verify, but it should be remembered that the population genetic definition is derived from this correlation.

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