Wednesday, October 19, 2011

New Research Continues to Point to a Super Progenitor

Everyone knows biology is full of complicated designs, but evolutionists think it arose spontaneously, as a result of the play of natural laws. In other words, it happened to happen. First there was nothing, then there was something, then that something became very complicated. All this just happened to happen.

There are many problems with this evolutionary narrative. One is that we can’t explain how such complexity could have arisen on its own. Another is that if evolution is true, then complexity must have somehow formed early in evolutionary history. In fact, evolutionists sometimes use this fact to dodge the failure of their idea. They say that immense complexities, such as molecular machines and codes, are not really a problem because they occurred so early in evolutionary history. That early history, these evolutionists say, falls under the origin of life (OOL) phase, not evolution proper. So with a wave of the hand, they dismiss major failures of their idea.

But the failure of the evolutionary expectation of simple beginnings will not go away so easily. One such example in the news is the last universal common ancestor (LUCA) to all life. If evolution is true, then this ancient progenitor of all life must have been extremely complex. Here is what I wrote ten years ago in my book Darwin’s God:

[T]he next step was to piece together what the progenitor would have looked like by comparing the genetic differences and similarities of the three lineages. But the task became confusing due to the wide variety of genes between and amongst the three lineages. No clear picture of a simple progenitor emerged. Instead the only solution seemed to be a super progenitor that already had most of the highly complex traits found in each of the three lineages. The super progenitor would have been as complex as modern cells yet would have somehow arisen in a short time.

This story has not changed and recent research continues to point to a mythical “super progenitor.”

Last Universal Common Ancestor More Complex Than Previously Thought

New evidence suggests that LUCA was a sophisticated organism
after all
, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct.

The study builds on several years of research into a once-overlooked feature of microbial cells, a region with a high concentration of polyphosphate, a type of energy currency in cells. Researchers report that this polyphosphate storage site actually represents the first known universal organelle, a structure once thought to be absent from bacteria and their distantly related microbial cousins, the archaea. This organelle, the evidence indicates, is present in the three domains of life: bacteria, archaea and eukaryotes (plants, animals, fungi, algae and everything else).

The existence of an organelle in bacteria goes against the traditional definition of these organisms, said University of Illinois crop sciences professor Manfredo Seufferheld, who led the study.

"It was a dogma of microbiology that organelles weren't present in bacteria," he said. But in 2003 in a paper in the Journal of Biological Chemistry, Seufferheld and colleagues showed that the polyphosphate storage structure in bacteria (they analyzed an agrobacterium) was physically, chemically and functionally the same as an organelle called an acidocalcisome (uh-SID-oh-KAL-sih-zohm) found in many single-celled eukaryotes.

Their findings, the authors wrote, "suggest that acidocalcisomes arose before the prokaryotic (bacterial) and eukaryotic lineages diverged." The new study suggests that the origins of the organelle are even more ancient.

So even given evolutionary assumptions, this evidence indicates an early organelle and with it, early complexity.


"There are many possible scenarios that could explain this, but the best, the most parsimonious, the most likely would be that you had already the enzyme even before diversification started on Earth," said study co-author Gustavo Caetano-Anollés, a professor of crop sciences and an affiliate of the Institute for Genomic Biology at Illinois. "The protein was there to begin with and was then inherited into all emerging lineages."


But the evolution of even a single protein is astronomically unlikely, even according to evolutionist’s unrealistically optimistic assumptions.

The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.

"You can't assume that the whole story of life is just building and assembling things," Whitfield said. "Some have argued that the reason that bacteria are so simple is because they have to live in extreme environments and they have to reproduce extremely quickly. So they may actually be reduced versions of what was there originally. According to this view, they've become streamlined genetically and structurally from what they originally were like. We may have underestimated how complex this common ancestor actually was."

Early complexity is yet another example of evolutionary expectations gone wrong. Religion drives science, and it matters.

62 comments:

  1. Ummm, are you confusing the LUCA with the first life? It certainly sounds that way. They are not the same thing. The most recent common ancestors of myself and my cousins are the grandparents we share - yet they themselves had ancestors.

    The LUCA was not the first life. So why should that undermine ToE if it was (relatively) complex?

    Also, what exactly about this points to a 'super progenitor' (whatever that might be)? Is this merely yet more God-of-the-Gaps logic?

    More to the point, why are you uncritically accepting the findings of these 'evolutionists'? Isn't their work flawed by the religiously-motivated science they do? Or do you not object to scientific studies when you can misrepresent them to fit your own conclusions?

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  2. "There are many possible scenarios that could explain this, but the best, the most parsimonious, the most likely would be that you had already the enzyme even before diversification started on Earth," said study co-author Gustavo Caetano-Anollés, a professor of crop sciences and an affiliate of the Institute for Genomic Biology at Illinois. "

    Before the diversification that led to extant life, but more than likely the LUCA was only one of a great diversity of organisms present at that time.

    Complexity is not a linear measure, but multifaceted. The earliest life was probably loosely integrated, but still complex in many respects. The LUCA was tightly integrated, which is what most people mean by complexity.

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  3. Dr. Hunter's point, as always, is that Evolutionary Predictions are Continually Proven Wrong. Here the theory predicted simplicity for the LUCA (or--splitting hairs to accommodate the first two comments above--the speculative first life or the many speculative lives). Instead, research points to vast complexity. But does the theory suffer? No, because evolution is based on religious faith: there cannot be anything wrong with the theory of evolution because the only other theory, Creation, cannot be right--God would not have created life as we actually find it, a supremely arrogant assumption.

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  4. Zachriel:"Before the diversification that led to extant life, but more than likely the LUCA was only one of a great diversity of organisms present at that time. "

    Any evidence for this?

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  5. Blas: Any evidence for this?

    Each surviving branch on the phylogenetic tree is only one of many branches. More specifically, "The new study suggests that the origins of the organelle are even more ancient."

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  6. Zachriel:"Each surviving branch on the phylogenetic tree is only one of many branches. More specifically, "The new study suggests that the origins of the organelle are even more ancient."

    Any evidence of not surviving branches?

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  7. Red Reader -

    "Dr. Hunter's point, as always, is that Evolutionary Predictions are Continually Proven Wrong."

    No. He'd LOVE that to be true. But it just isn't the case. Cornelius has never once presented a whiff of evidence which falsifies ToE, including this.

    "Here the theory predicted simplicity for the LUCA (or--splitting hairs to accommodate the first two comments above--the speculative first life or the many speculative lives)"

    Umm, how did you manage to read my post and not grasp my point? I thought I made it rather simple - the first life was not the LUCA. Life might have existed for many, many years before the LUCA arrived. This is not splitting hairs, it illustrates a categorical failure to understand on the part of yourself and possibly Cornelius too.

    "evolution is based on religious faith: there cannot be anything wrong with the theory of evolution because the only other theory, Creation, cannot be right"

    This is indeed the picture Cornelius paints, but it is simply utterly wrong. ToE is NOT based on the assumption that ID/Creationism is wrong. It is based on objective, empirical evidence. It is ID/Creationism which is based on the religiously-motivated assumption that ToE must be wrong. ToE, like ALL scientific theories, says nothing at all about what God would or would not do. It does, however, assume methodological naturalism. But that isn't the same thing.

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  8. Ritchie:"Umm, how did you manage to read my post and not grasp my point? I thought I made it rather simple - the first life was not the LUCA. Life might have existed for many, many years before the LUCA arrived."

    So, according to ToE a self replicative molecule started a darwinian selection process and formed one and only one common ancestor of all life?
    Can you bring any evidence?

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  9. Blas: Any evidence of not surviving branches?

    If you are referring to branches from before the posited LUCA, then the evidence is found in analysis of the structure and genetics of extant organisms. The evidence suggests that there was substantial horizontal evolution in the pre-LUCA epoch.

    Blas: So, according to ToE a self replicative molecule started a darwinian selection process and formed one and only one common ancestor of all life?

    There's still a lot unknown about early life, but the evidence suggests that primordial life was a community of disparate proto-organisms. Out of this, one branch survived to diversify into all other organisms.

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  10. Zachriel:"the evidence is found in analysis of the structure and genetics of extant organisms"

    What do you found that suggest that?

    " but the evidence suggests that primordial life was a community of disparate proto-organisms"

    Which evidence suggest it? Suggest means maybe no?
    And so, according to your evidence evolution made a myriad of protoorganisms selected only one that diverged in a myriad of organisms. In an only branch of the tree that really is a bush because LGT.

    The pre UCLA organisms had LGT?

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  11. Blas: What do you found that suggest that?

    Let's make sure we have a common language. You do understand that organisms, both extant and extinct, form objective nested hierarchies, which along with the fossil succession supports common descent? In other words, we have diverging trees appearing to go back to common ancestor(s)?

    Blas: And so, according to your evidence evolution made a myriad of protoorganisms selected only one that diverged in a myriad of organisms.

    Not a single organism, but a population that was highly diverse and sharing components horizontally.

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  12. Zachriel:"we have diverging trees appearing to go back to common ancestor(s)?"

    Let assume yes.

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  13. Blas: Let assume yes.

    Assume that the hypothesis is supported, or assume that you understand it?

    In any case, the bifurcating tree is largely supported across a great many taxa. (That doesn't mean it is without anomalies. For instance, hybridization is a violation of bifurcation, as is convergence in certain characteristics, but the overall pattern is clear.) From the evidence, they converge very closely, within standard resolutions, to a single root. Do you understand this?

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  14. Zachriel said: "Do you understand this?"

    Yes.

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  15. Ritchie:

    "Dr. Hunter's point, as always, is that Evolutionary Predictions are Continually Proven Wrong."

    No. He'd LOVE that to be true. But it just isn't the case. Cornelius has never once presented a whiff of evidence which falsifies ToE


    You are conflating two different things.

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  16. CH -

    "You are conflating two different things."

    True. But you haven't ever shown up an evolutionary prediction proven wrong either.

    You routinely turn up new and surprising biological discoveries and CLAIM they falsify evolutionary predictions, but this is far from the same thing.

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  17. Blas said...
    Zachriel said: "Do you understand this?"

    Yes.

    So Zachriel, the observed nested hierarchies of traits is the evidence that "primordial life was a community of disparate proto-organisms" and "there was substantial horizontal evolution in the pre-LUCA epoc" and that a LUCA was "a population that was highly diverse and sharing components horizontally."

    That is an amazing extrapolation!

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  18. Blas: Yes.

    So you accept Common Descent of mammals, vertebrates, eukaryotes?

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  19. Zachriel said...

    So you accept Common Descent of mammals, vertebrates, eukaryotes?

    I accept that a Common Descent is the easiest way to explain the nested hierarchy of traits.

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  20. Blas: I accept that a Common Descent is the easiest way to explain the nested hierarchy of traits.

    Why don't you accept it in fact? (This is clearly relevant as understanding the history of the earliest life requires untangling the threads of descent.)

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  21. Zachriel said...
    Why don't you accept it in fact?

    How can accept it in fact if it is not observable or reproducible?

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  22. Blas, how can you accept ID, a god, and any of the stories in the bible, as fact, since they're not observable or reproducible?

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  23. The whole truth said...
    Blas, how can you accept ID, a god, and any of the stories in the bible, as fact, since they're not observable or reproducible?

    God it is not a scientific concept,as it is not material you reach the concept of God with the reason not with sicence. Do you think that the concept of common descent is not scientific as the concept of God? Religion drive science?

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  24. Zachriel, you really didn't answer the question as to WHY paleontologists Niles Eldredge and Stephen Jay Gould proposed the theory of punctuated equilibrium.

    Stop evading WHY these well known paleontologists proposed it. You need to ask yourself why this makes you uncomfortable about directly answering this simple question.

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  25. The Whole Truth,

    It seems like evolutionists and young earth creationists both have a problem that neither have adequately resolved.

    Evolutionists simply don't have ENOUGH time using their proposed mechanisms for change to do what they say evolution did even using their own time scales.

    Young earth creationists have not countered evidence for an old earth sufficiently.

    --

    Personally I am highly skeptical of rubbing stamping age claims by anybody. Yes, I know how confident so and so is about their claims (and the reasons they give), but I take it all with a grain of salt. With that said, my position on creation by an intelligent God is not based on the age of the earth.

    --

    Regarding macro change, rather than give you the standard definition which you can look up, I'd say that it is difficult for me to define because no one has every observed it happening in recorded history.

    My reason is simply that it's hard to seriously define a fairy tale.

    Small changes that are bounded are observed, but nothing beyond that is ever observed. Macro change would require unbounded, directional change, and we don't see it in the real world.

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  26. Blas: How can accept it in fact if it is not observable or reproducible?

    You do understand the scientific method? For instance, it is quite possible to determine the physical existence of molecules without directly observing them.
    http://www.aip.org/history/einstein/brownian.htm

    Neal Tedford: Zachriel, you really didn't answer the question as to WHY paleontologists Niles Eldredge and Stephen Jay Gould proposed the theory of punctuated equilibrium.

    Of course we didn't. YOU introduced punctuated equilibrium, and we asked you to give us a brief explanation of the theory so that we could better understand your point of view.

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  27. Zachriel said...
    "You do understand the scientific method? For instance, it is quite possible to determine the physical existence of molecules without directly observing them.
    http://www.aip.org/history/einstein/brownian.htm"

    Molecules are a concept that explains facts
    But, at least, for molecules, I can perform reproducible experiments (actuals) that are explained by that concept and discard almost any other explanation..

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  28. Zachriel, you're being evasive. I don't really care to argue over who introduced or whatever. Okay, I introduced it. Happy? My definition? Just Google it and use the standard definition and explanation.

    WHY did paleontologists Niles Eldredge and Stephen Jay Gould propose the theory of punctuated equilibrium? As paleontologists they were familar with the fossil record. What was it about the fossil record that directly led to the theory of punctuated equilibrium?

    Is punctuated equilibrium a problem for you, Zachriel?

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  29. Blas: Molecules are a concept that explains facts But, at least, for molecules, I can perform reproducible experiments (actuals) that are explained by that concept and discard almost any other explanation..

    Well, you can do the same with Common Descent. You can make observations that support the hypothesis.

    Let's consider a historical examples, continental drift. Do you reject continental drift? What about Lincoln's assassination? You have to rely upon other people's written reports, having presumably not seen the event yourself. What about yesterday? You have to rely on your own unreliable memories. Not sure how far you want to carry this.

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  30. Neal Tedford: Zachriel, you're being evasive. I don't really care to argue over who introduced or whatever.

    You introduced punctuated equilibrium in order to make a point. When questioned, you refused to clarify what you meant. Yet, you say others are being evasive. It seems doubtful you could fairly represent any aspect of the Theory of Evolution.

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  31. Zachriel said...
    "Well, you can do the same with Common Descent. You can make observations that support the hypothesis."

    Yes if there are actual observation that discard other alternatives yes.

    "Let's consider a historical examples, continental drift. Do you reject continental drift? What about Lincoln's assassination? You have to rely upon other people's written reports, having presumably not seen the event yourself. What about yesterday? You have to rely on your own unreliable memories. Not sure how far you want to carry this."

    Well for historical examples we have to use the historical method. That is we have to relay in witnesses, documents and plausibility of the historical fact, and always you are going to have some degree incertaynity because of the number and credibility of witnesses, interpratation of documents etc. Then events in the past are always a probability to be a fact.

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  32. Blas: Well for historical examples we have to use the historical method. That is we have to relay in witnesses, documents and plausibility of the historical fact, and always you are going to have some degree incertaynity because of the number and credibility of witnesses, interpratation of documents etc.

    All scientific findings are tentative, and have to be judged based on the totality of the available evidence, so you haven't drawn a distinction. A geologist might determine that a volcano erupted 70 thousand years ago, or an astronomer that a nova exploded forming the Crab Nebula, or a forensic scientist that someone was murdered even though there are no known witnesses.

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  33. Zachriel said...
    "All scientific findings are tentative,"

    Not all findings, you can experience the force of gravity whatever explanation you give for that force, you can demostrate the haredity laws, you can prove that DNA is trancripted in RNA that is traduced in proteins.
    But if you think that all findingd are tentative, why are you asking to accpet common descent as a fact?

    "and have to be judged based on the totality of the available evidence, so you haven't drawn a distinction. A geologist might determine that a volcano erupted 70 thousand years ago, or an astronomer that a nova exploded forming the Crab Nebula, or a forensic scientist that someone was murdered even though there are no known witnesses."

    Without witnesses or documents it will depend of the plausibility of the fact, as we know what happen when a vulcano explode, how look a man murdered and a nova exploded it easy to accept that in the past that things happened. The time when happened it will be relative to the assumption we make to calculate that time.

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  34. Zachriel, just copy and paste the explanation of punctuated equilibrium from wikipedia or a evolutionist website if you like and that would be fine with me. It's the evolutionists baby.

    My question is very simple, "WHY did paleontologists Niles Eldredge and Stephen Jay Gould propose the theory of punctuated equilibrium? As paleontologists they were familar with the fossil record. What was it about the fossil record that directly led to the theory of punctuated equilibrium?"

    This is a problem for you isn't?

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  35. Blas: you can demostrate the haredity laws,

    Which is why genetics (the study of heredity) is a dead science; there's nothing more to learn.

    In fact, we've only scratched the surface in the understanding of heredity. Hereditary laws are subject to revision, and have been revised many times.

    Blas: But if you think that all findingd are tentative, why are you asking to accpet common descent as a fact?

    "In science, fact can only mean confirmed to such a degree that it would be perverse to withhold provisional assent."

    Blas: Without witnesses or documents it will depend of the plausibility of the fact,

    Let's start with a simple historical claim, one without witnesses or documents. Dinosaurs roamed the Earth.

    Neal Tedford: My question is very simple, "WHY did paleontologists Niles Eldredge and Stephen Jay Gould propose the theory of punctuated equilibrium? As paleontologists they were familar with the fossil record. What was it about the fossil record that directly led to the theory of punctuated equilibrium?"

    You made a claim. We asked a question. Instead of answering the question, you threw it back at us. Are you withdrawing your previous claim?

    To answer your question, you have to understand the theory first. Can you briefly describe the theory?

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  36. Zachriel said..

    "In science, fact can only mean confirmed to such a degree that it would be perverse to withhold provisional assent."

    According to your definition then would be preverse to withhold provisional assent to the existence of Flogisto.

    "Let's start with a simple historical claim, one without witnesses or documents. Dinosaurs roamed the Earth."

    Agree

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  37. Blas: According to your definition then would be preverse to withhold provisional assent to the existence of Flogisto.

    Well, no. It was a working hypothesis, but had only vague supporting evidence, such as the loss of weight of most burnt materials.

    In any case, such is the nature of science. Findings can change, even those once accepted as fact.

    Zachriel: Let's start with a simple historical claim, one without witnesses or documents. Dinosaurs roamed the Earth.

    Blas: Agree

    Which undercuts your suggestion about not accepting historical findings because they are "not observable or reproducible."

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  38. Zachriel said...
    Well, no. It was a working hypothesis, but had only vague supporting evidence, such as the loss of weight of most burnt materials.

    In any case, such is the nature of science. Findings can change, even those once accepted as fact.

    Then I will wait before accept the findings of Common Descent.

    "Zachriel: Let's start with a simple historical claim, one without witnesses or documents. Dinosaurs roamed the Earth.

    Blas: Agree

    Zachriel:Which undercuts your suggestion about not accepting historical findings because they are "not observable or reproducible."


    I can observe the bones of an animal, that it is not of a living animal. This bones corresponds to a reptil animal. Today animals go extint. Applying the historical method it is plausible that in the past existed an animal we call dinosaurs.

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  39. Blas: I can observe the bones of an animal, that it is not of a living animal. This bones corresponds to a reptil animal. Today animals go extint. Applying the historical method it is plausible that in the past existed an animal we call dinosaurs.

    Right. Furthermore, we can study those bones to make many determinations about what they ate, how they reproduced, and so on. We do this by proposing and testing hypotheses. Similarly with the Theory of Common Descent.

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  40. Zachriel said...
    "Right. Furthermore, we can study those bones to make many determinations about what they ate, how they reproduced, and so on. We do this by proposing and testing hypotheses. Similarly with the Theory of Common Descent."

    Yes, as we do not see transformation of one specie in other, on the contrary we witnesses conservation of traits, the hypotheses of Common Descent lacks the attribute of plausibility to be an "historical fact".

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  41. Blas: we do not see transformation of one specie in other,

    In fact, we observe speciation, and the process of speciation.

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  42. "Blas: we do not see transformation of one specie in other,

    Zachriel:In fact, we observe speciation, and the process of speciation."

    To say we observe something that can make plausible the Common Descent we have to observe a fish becaming an air breathing fish, a land mammal becaming a sea swimming mammal or similar things.

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  43. Blas: To say we observe something that can make plausible the Common Descent we have to observe a fish becaming an air breathing fish, a land mammal becaming a sea swimming mammal or similar things.

    Apparently, you don't understand the scientific method. The Theory of Evolution proposes that it takes thousands or millions of years for such transformations. As we can't make observations over such long time spans, instead, we use the hypothesis to deduce empirical predictions, then we test those empirical predictions. How did you think science worked?

    Consider continental drift. There was circumstantial evidence in geology that continents once fitted together. The discovery of mechanisms involving the currents in the Earth's interior supports this theory. The posited origin of the Earth as a condensate from the primordial nebula supports the theory. The direct measurements of continental drift add additional support. Nothing "proves" that the continents have drifted for millions of years, but all the observations are consistent with continental drift over long eons of time.

    Similarly, we can observe organisms evolve at rates consistent with the transformations seen in the fossil record. We have the nested hierarchy generally supporting bifurcating descent. The Theory of Common Descent guides research in non-trivial ways, including in the discovery of heretofore unknown fossil forms. All available evidence supports the Theory of Common Descent.

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  44. Zachriel said...
    "Apparently, you don't understand the scientific method. The Theory of Evolution proposes that it takes thousands or millions of years for such transformations. As we can't make observations over such long time spans, instead, we use the hypothesis to deduce empirical predictions, then we test those empirical predictions. How did you think science worked?

    Consider continental drift. There was circumstantial evidence in geology that continents once fitted together. The discovery of mechanisms involving the currents in the Earth's interior supports this theory. The posited origin of the Earth as a condensate from the primordial nebula supports the theory. The direct measurements of continental drift add additional support. Nothing "proves" that the continents have drifted for millions of years, but all the observations are consistent with continental drift over long eons of time."

    All that observations are provisional as were the observations supporting flogisto theory.

    "Similarly, we can observe organisms evolve at rates consistent with the transformations seen in the fossil record. We have the nested hierarchy generally supporting bifurcating descent. The Theory of Common Descent guides research in non-trivial ways, including in the discovery of heretofore unknown fossil forms. All available evidence supports the Theory of Common Descent."

    We do not see organism evolving.
    This discussion can go ahead for a very long time because for the events in the past, no matter the use of the historical method, there is always room for subjectivity. The confidence on witnesses, the interpretation of the documents, the grade of plausibility is never objective. So historical are never as facts as scientificfacts. Think in recent events, there is people that do not believe the man was on the moon or people that beleive the 911 was an conspiracy of US goverment.

    The only evidence avaiable for common descent is the nested hierarchy of traits(with exceptions) All the other evidence is based on this and assuming Common descent. No one of the evidence rule out an orchard model of evolution without common descent.

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  45. "We do not see organism evolving.
    This discussion can go ahead for a very long time because for the events in the past, no matter the use of the historical method, there is always room for subjectivity. The confidence on witnesses, the interpretation of the documents, the grade of plausibility is never objective. So historical are never as facts as scientificfacts. Think in recent events, there is people that do not believe the man was on the moon or people that beleive the 911 was an conspiracy of US goverment."

    But of course religious fairy tales should not be subjected to the same scrutiny of subjectivity and lack of direct observation, right?

    Maybe one of you ID pushers can show that you were actually there when your chosen god designed and created the universe, the Earth, life, man and woman, animals, bacteria, minerals, chemicals, plants, angels, demons, the devil, everlasting life, consciousness, heaven, hell, rainbows, death, morality, the words in the bible, miracles, and all the other stuff you give him credit for?

    And no, I'm not agreeing that we do not see organisms evolving.

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  46. Blas: All that observations are provisional as were the observations supporting flogisto theory.

    Say scientific findings are provisional doesn't add anything, as all scientific findings are provisional.

    Blas: We do not see organism evolving.

    Of course we do. And we can measure it quantitatively, just as we do the movement of continents.

    Blas: This discussion can go ahead for a very long time because for the events in the past, no matter the use of the historical method, there is always room for subjectivity.

    The testing of scientific hypotheses is not a subjective process, but the heart of the scientific method.

    Blas: So historical are never as facts as scientific facts.

    Dinosaurs roamed the Earth.

    Blas: The only evidence avaiable for common descent is the nested hierarchy of traits(with exceptions)

    Well, no. We also have the observation of mechanisms sufficient to account for the historical record.

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  47. Zachriel said...
    "Say scientific findings are provisional doesn't add anything, as all scientific findings are provisional."

    Why bother you bring an example?

    Zachriel said...
    "Of course we do. And we can measure it quantitatively, just as we do the movement of continents."

    Well tell me when will an actual fish will start to breath air.

    Zachriel said...
    "The testing of scientific hypotheses is not a subjective process, but the heart of the scientific method."

    How do you test objectively test a past event?

    Zachriel said...
    "Dinosaurs roamed the Earth."

    I bet we can find a dinosaurs denier.

    Zachriel said...
    "Well, no. We also have the observation of mechanisms sufficient to account for the historical record."

    Wich mechanism? Chance?

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  48. Blas: Why bother you bring an example?

    Because most everyone understands that "Dinosaurs roamed the Earth" is a strongly supported scientific finding. Hence, we CAN make factual statements about history absent human witnesses or records.

    Blas: Well tell me when will an actual fish will start to breath air.

    Some fish do breathe air.
    http://en.wikipedia.org/wiki/Lungfish

    Blas: How do you test objectively test a past event?

    By proposing and testing hypotheses. So, if you posit there was a global flood a few thousand years ago, you not only have to account for the quantity of water, but the hypothesis should entail specific empirical consequences, such as deposits across the Earth's surface. Turns out that those predictions are inconsistent with the evidence.

    Blas: I bet we can find a dinosaurs denier.

    Of course you can. Some people think they are Napoléon Bonaparte. And maybe he is, but we're talking about what can be shown to have scientific validity.

    Blas: Wich mechanism? Chance?

    Mechanisms of variation and selection, as well as historical contingency.

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  49. Zachriel said: "Because most everyone understands that "Dinosaurs roamed the Earth" is a strongly supported scientific finding."

    findings that as you said "All scientific findings are tentative"

    Zachriel said:"Hence, we CAN make factual statements about history absent human witnesses or records."

    In the same way scientist could make factual claims about flogisto. Why you do not want I give the example?

    Zachriel said: "Some fish do breathe air.
    http://en.wikipedia.org/wiki/Lungfish"

    Yes, off course 400Mya ago, more or less the same period when according to ToE other fish started to breath air got legs and became an amphibian. I was asking for the NEXT fish that will start to breath air again. We have been waiting for 400Mya. What can you predict as you "can measure it quantitatively"?

    Zachriel said: "By proposing and testing hypotheses. So, if you posit there was a global flood a few thousand years ago, you not only have to account for the quantity of water, but the hypothesis should entail specific empirical consequences, such as deposits across the Earth's surface. Turns out that those predictions are inconsistent with the evidence."

    So you are testing hypothesis in the actual enviroment, that is not testing past events. That tested hypotesys may make plausible the past events not tested.

    Blas said: Wich mechanism? Chance?

    Zachriel said: "Mechanisms of variation and selection, as well as historical contingency."

    So chance accounts for all the living world we see?

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  50. Blas: findings that as you said "All scientific findings are tentative"

    That's right, but some claims are so well established that it is reasonable to give provisional assent.

    Blas: In the same way scientist could make factual claims about flogisto.

    The problem with philostogen is that it didn't produce clear entailments. Consequently, it was appropriate to consider it tentatively, but not to consider it demonstrated.

    Blas: I was asking for the NEXT fish that will start to breath air again.

    It possible, but not likely as the niche is already filled. In any case, such transformations can take millions of years, so we wouldn't expect to see such a sudden transformation.

    Blas: What can you predict as you "can measure it quantitatively"?

    From the evidence he compiled for macroevolutionary changes, Darwin posited, but could not directly observe, microevolution. We can now observe microevolution—and not just in the lab. Indeed, very patient researchers have now been able to observe and measure rates of evolutionary adaptation in the wild.

    Blas: So you are testing hypothesis in the actual enviroment, that is not testing past events.

    You are observing evidence of past events. Remember? Dinosaurs roamed the Earth.

    Blas: So chance accounts for all the living world we see?

    Mechanisms of variation and selection, as well as historical contingency.

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  51.  Zachriel said...
    “That's right, but some claims are so well established that it is reasonable to give provisional assent.”

    Scientifically speaking what does "reasonable" means?

     Zachriel said...“The problem with philostogen is that it didn't produce clear entailments. Consequently, it was appropriate to consider it tentatively, but not to consider it demonstrated.”

    You are saying this now. If you have lived in that time you would taked it as a scientific fact.

     Zachriel said...“It possible, but not likely as the niche is already filled. In any case, such transformations can take millions of years, so we wouldn't expect to see such a sudden transformation.”

    Also were filled the sea, but a pakicetus become a whale in less than 50?Mya. We are waiting for a breathing fish for 400Mya. And I´m not asking for a population of breathing air fishes, I´m just looking for the intermediates sort of mutant fishes? Intermediates forms? Transitional forms? Any kind that could fit to evolution. 

     Zachriel said...“You are observing evidence of past events. Remember? Dinosaurs roamed the Earth.”
    Observing dinosaurs bones is testing bones not testing dinosaurs. You test the bones and give plausibility to the dinosaurs roaming the Earth in the past.

     Zachriel said...”Mechanisms of variation and selection, as well as historical contingency.”

    Variation by chance, selection by chance and historical contingency (chance) accounts for all the living world we see.

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  52. Blas: Scientifically speaking what does "reasonable" means? c

    In science, it means the hypothesis has specific, confirmed entailments.

    Blas: You are saying this now. If you have lived in that time you would taked it as a scientific fact.

    No, but perhaps as a working assumption. A better example would be Galileo's claim that the Sun was the center of the Universe. A good working hypothesis, consistent with the available evidence, but not completely accurate.

    Blas: Also were filled the sea, but a pakicetus become a whale in less than 50?Mya.

    Mammals fill a different niche than fishes. They are warm-blooded, large brained and highly active organisms due to larger amounts of oxygen they can utilize.

    Blas: I´m just looking for the intermediates sort of mutant fishes? Intermediates forms? Transitional forms? Any kind that could fit to evolution.

    Lungfish.

    Blas: Observing dinosaurs bones is testing bones not testing dinosaurs.

    Quite the contrary. Observing dinosaur bones is not observing dinosaurs, but it is testing dinosaurs. If the fossils are the remains of actual organisms, then we can look for additional evidence, such as additional fossils, partially digested food, coprolites, eggs, immature members of the species, entire ecosystems!

    Blas: Variation by chance, selection by chance and historical contingency (chance) accounts for all the living world we see.

    Adding "by chance" misconstrues the terms. Variation is hardly random, but observed in all natural populations. Selection is no more random than a planet orbiting its star.

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  53. Zachriel said “In science, it means the hypothesis has specific, confirmed entailments.”

    And common descent has more confirmed entailments than an orchard model of evolution? Has more confirmed antailments than flogisto had?

    Zachriel said “Lungfish. “

    Lungfish” evolved 400Mya, I was asking when your “quantitativly measured observation of evolution” predicts the NEXT attempt of fishes to breath air, following the “non ramdom variation·



    Zachriel said “Adding "by chance" misconstrues the terms. Variation is hardly random, but observed in all natural populations. Selection is no more random than a planet orbiting its star.”

    So if variation is not ramdom is fixed. Them we have to predict which and when will be the future variations. Can you do that?

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  54. Blas: And common descent has more confirmed entailments than an orchard model of evolution?

    Yes. In particular, the nested hierarchy is strongly supported for most taxa except the most primitive.

    Blas: Lungfish” evolved 400Mya, I was asking when your “quantitativly measured observation of evolution” predicts the NEXT attempt of fishes to breath air, following the “non ramdom variation·

    As the niche is filled, it is unlikely fish could invade it. Not sure your point. Perhaps you are trying to say that it is difficult to predict the future course of evolution? If so, it's difficult to predict the future course of weather, but that doesn't mean weather isn't due to air pressure, evaporation, and such mechanisms.

    Blas: Them we have to predict which and when will be the future variations.

    No more than we can always predict the color of a baby's eyes with certainty. That doesn't mean there aren't laws of heredity involved. There is an interplay of normal variation within a population, mechanisms of novel variation, and chance.

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  55. Zachriel said...
    "Yes. In particular, the nested hierarchy is strongly supported for most taxa except the most primitive."

    Again, the only evidence in favour of the common descent and that do not rule out the orchar model is the nested hierarchy of traits with exceptions. That was my first question in this discussion, this is the evidence that "Before the diversification that led to extant life, but more than likely the LUCA was only one of a great diversity of organisms present at that time. "

    "As the niche is filled, it is unlikely fish could invade it. Not sure your point. Perhaps you are trying to say that it is difficult to predict the future course of evolution?"

    No, the point is that evolution do not know the niche is filled (neither you) and if it is ramdom in 400 Mya should be more attempts
    to breath air that is big advantage .

    "If so, it's difficult to predict the future course of weather, but that doesn't mean weather isn't due to air pressure, evaporation, and such mechanisms."

    But ToE is the theory that explain the weather not only his mechanisms. ToE says he can explain step by step the changes of the weather.

    "No more than we can always predict the color of a baby's eyes with certainty. That doesn't mean there aren't laws of heredity involved. There is an interplay of normal variation within a population, mechanisms of novel variation, and chance."

    That examples can be predicted by every theory of the origin of the species. If your affirmation that .

    "Of course we do (see organism evolving). And we can measure it quantitatively, just as we do the movement of continents."

    You have to be able to predict where, better to what, the organism are evolving now.

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  56. Blas: Again, the only evidence in favour of the common descent and that do not rule out the orchar model is the nested hierarchy of traits with exceptions.

    There's more than just the nested hierarchy. There's also the succession of fossils. And the nested hierarchy applies not just to morphological characters, but molecules traits, as well.

    In any case, you agree that many fundamental taxa have a common ancestor. Metazoa? Plants? Just dogs? How many trees? Which trees?

    Blas: That was my first question in this discussion, this is the evidence that "Before the diversification that led to extant life, but more than likely the LUCA was only one of a great diversity of organisms present at that time.

    Yes, we'll consider that once we have some common ground.

    Blas: But ToE is the theory that explain the weather not only his mechanisms. ToE says he can explain step by step the changes of the weather.

    Yes, so can weather science, but because weather is a complex phenomena, long term predictions are only statistical in nature.

    Blas: You have to be able to predict where, better to what, the organism are evolving now.

    Short term predictions are easy. Long term predictions can be nigh impossible. That's normal for any complex system. Consider something as simple as turbulent flow. You can't predict where a molecule of water will be in a river, even though you can watch the river's flow to the sea.

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  57. Zachriel said:“There's also the succession of fossils”.

    Why this is evidence of common ancestor?

    Zachriel said:“ And the nested hierarchy applies not just to morphological characters, but molecules traits, as well”.

    If you have nested morphological characters is expected nested molecular traits, unless the morphological can be not related to molecular. You are counting twice the same evidence nested hierarchy of traits, one of that traits is molecular traits, always with exceptions.

    Zachriel said: "In any case, you agree that many fundamental taxa have a common ancestor. Metazoa? Plants? Just dogs? How many trees? Which trees?” 

    Well I can´t rule out any hypotesis, maybe each animal is just a branch that goes directly to “one of a great diversity of organisms present at that time(LUCA´s time)".

    Zachriel said: "Yes, we'll consider that once we have some common ground." 

    Big extrapolation!

    Zachriel said:”Yes, so can weather science, but because weather is a complex phenomena, long term predictions are only statistical in nature.” 

    “Short term predictions are easy. Long term predictions can be nigh impossible. That's normal for any complex system. Consider something as simple as turbulent flow. You can't predict where a molecule of water will be in a river, even though you can watch the river's flow to the sea.”

    So looking at short term events, you cannot predict the future, but based on that short term events can describe past events in a way that “it would be perverse to withhold provisional assent.”

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  58. Blas: Why this is evidence of common ancestor?

    Because it is empirical confirmation of an entailment from the Theory of Common Descent.

    Blas: If you have nested morphological characters is expected nested molecular traits, unless the morphological can be not related to molecular.

    Broken genes drift in accordance with neutral evolution, and exhibit a nested hierarchy—even though they are not connected to phylogenetic traits.

    Blas: Well I can´t rule out any hypotesis, maybe each animal is just a branch that goes directly to “one of a great diversity of organisms present at that time(LUCA´s time)".

    You suggested an orchard. When pressed, you can't provide any specifics. Please point to two organisms that you do not think are related.

    Blas: So looking at short term events, you cannot predict the future, but based on that short term events can describe past events in a way that “it would be perverse to withhold provisional assent.”

    Even accounting for language differences, your position just doesn't seem coherent. Let's try this again. We can have knowledge of all the relevant mechanisms, yet not be able to make long term predictions of complex systems such as weather. That doesn't mean the long term predictions are influenced by magic. It's just the nature of complex systems that individual trajectories exhibit chaos. Similarly, even if we have complete understanding of all the mechanisms of evolution doesn't mean we can make long term predictions with any certainty.

    In order to untangle the historical patterns, and the mechanisms involved, we have to look at the evidence, propose and test hypotheses. Turns out that the Theory of Evolution fits the evidence very well, and makes all sorts of verifiable predictions.

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  59. Zachriel said: “Because it is empirical confirmation of an entailment from the Theory of Common Descent.” 

    Please can you explain which is the entailment that implies a Common Descent?

    Zachriel said: “Broken genes drift in accordance with neutral evolution, and exhibit a nested hierarchy—even though they are not connected to phylogenetic traits.”

    Is another trait “broken genes” and the nested hierarchy of broken genes do not fit the nested hierarchy of traits, you have to claim exceptions in both.
     
    Zachriel said: “You suggested an orchard. When pressed, you can't provide any specifics. Please point to two organisms that you do not think are related”.

    Too be precise I think is not a fact that are related, if you want an example: Man and chimpanzee.

    Zachriel said:“That doesn't mean the long term predictions are influenced by magic.”

    I do not understand why you are bringing magic here

    Zachriel said:“It's just the nature of complex systems that individual trajectories exhibit chaos.”

    Well as you said you cannot predict the position of a molecule of water but can predict the the flow of the river, can you predict the flow of evolution? Maybe I was too specific in my question before. Can you predict flow of the evolution of the actual fishes? There will be another try to breath air in the future? What can ToE predict about the evolution of actual species?

    Zachriel said:“Similarly, even if we have complete understanding of all the mechanisms of evolution doesn't mean we can make long term predictions with any certainty.”

    Why? If you can go back to one LUCA, and also as you said “ Turns out that the Theory of Evolution fits the evidence very well, and makes all sorts of verifiable predictions.”

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  60. Zachriel: There's also the succession of fossils.

    Blas: Please can you explain which is the entailment that implies a Common Descent?

    The fossil record provides snapshots in time of the transitions that are entailed in descent with modification, a key component of the Theory of Common Descent.

    Zachriel: Is another trait “broken genes” and the nested hierarchy of broken genes do not fit the nested hierarchy of traits, you have to claim exceptions in both.

    In fact, the pattern of sequences in broken genes fit the same nested hierarchy, even though they are not tied to phylogenetic traits.

    Zachriel: Too be precise I think is not a fact that are related, if you want an example: Man and chimpanzee.

    If humans are related to chimpanzees, then we would expect that there once existed more primitive human-like organisms that more closely resemble primitive apes. For instance, we would predict a transition in brain sizes. And that is what we see.

    Zachriel: That doesn't mean the long term predictions are influenced by magic.

    Blas: I do not understand why you are bringing magic here

    We have ready explanations for why the long term trajectory of complex systems are unpredictable without having to invoke mysterious causes.

    Blas: What can ToE predict about the evolution of actual species?

    That they will continue to adapt to the changing environment or go extinct.

    Zachriel: Similarly, even if we have complete understanding of all the mechanisms of evolution doesn't mean we can make long term predictions with any certainty.

    Blas: Why?

    Because the trajectory of complex systems can be inherently unpredictable, i.e. chaotic, over the long term.

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  61. Zachriel said...
    "The fossil record provides snapshots in time of the transitions that are entailed in descent with modification, a key component of the Theory of Common Descent."

    "If humans are related to chimpanzees, then we would expect that there once existed more primitive human-like organisms that more closely resemble primitive apes. For instance, we would predict a transition in brain sizes. And that is what we see."


    You can find both evidence in an orchard model. And when you find that Australopithecus sediba and Homo ergaster do not fit the sequence of growing brains is evidence against common descent?


    Zachriel:In fact, the pattern of sequences in broken genes fit the same nested hierarchy, even though they are not tied to phylogenetic traits.

    But the nested hierarchy of broken genes make as related with guinea pigs. That is evidence against common descent?

    Zachriel:"That they will continue to adapt to the changing environment or go extinct."


    No Zachriel, Common descent means that actual species will change independant of the changing enviroment. They are going to select the best fitted mutants. Which mutants the theory is especting to see?

    Zachriel: "Similarly, even if we have complete understanding of all the mechanisms of evolution doesn't mean we can make long term predictions with any certainty.

    Because the trajectory of complex systems can be inherently unpredictable, i.e. chaotic, over the long term."

    That is why evrithing we find in the past fit the ToE. But really seems to me we do not have complete understanding of all the mechanisms of evolution.

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  62. Blas: You can find both evidence in an orchard model.

    No. In an orchard, you don't expect branches from different trees to converge.

    Blas: But the nested hierarchy of broken genes make as related with guinea pigs. That is evidence against common descent?

    No they don't. The broken GULOP gene in apes is broken in the same way, but the broken gene in guinea pigs is broken in a different way. When examining the sequences, the guinea pig is clearly in the out-group, with the sequence of the broken gene supporting the familiar nested hierarchy.

    Blas: Common descent means that actual species will change independant of the changing enviroment.

    You had asked about prediction of the Theory of Evolution. Descent with modification is intrinsic to the Theory of Common Descent. Not all changes are going to be adaptive, and lineages may split without adaptation, but the environment is still important for most such divergences by isolating the subpopulations.

    Blas: They are going to select the best fitted mutants. Which mutants the theory is especting to see?

    Mutation can be shown to be largely random with respect to fitness. In large populations, you may see every possible mutation occurring. If small populations, more contingency is involved. However, it's important to understand that all natural populations are diverse, some organisms will be taller, or have a slower metabolism, or narrower leaves. It's among this diversity that natural selection works.

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