Sunday, July 10, 2011

Surprise, Human Genome Didn’t Solve All the Mysteries: Life is Complicated and Evolution Fails Yet Again

Here is a Nature News Feature that speaks volumes about the state of evolutionary theory. It explains how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of. It is yet another monumental failure of evolutionary theory, even though we all know evolution is a fact.

Not that long ago, biology was considered by many to be a simple science, a pursuit of expedition, observation and experimentation. At the dawn of the twentieth century, while Albert Einstein and Max Planck were writing mathematical equations that distilled the fundamental physics of the Universe, a biologist was winning the Nobel prize for describing how to make dogs drool on command.

And yet life scientists such as Joseph LeConte were absolutely certain evolution was true. They did not have the foggiest notion of how the biological world could have arisen on its own. In fact they didn’t understand much about the biological world period. But that never got in the way of their certainty.

The molecular revolution that dawned with the discovery of the structure of DNA in 1953 changed all that, making biology more quantitative and respectable, and promising to unravel the mysteries behind everything from evolution to disease origins. The human genome sequence, drafted ten years ago, promised to go even further, helping scientists trace ancestry, decipher the marks of evolution and find the molecular underpinnings of disease, guiding the way to more accurate diagnosis and targeted, personalized treatments. The genome promised to lay bare the blueprint of human biology.

Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements — sequences that make RNA or have a regulatory role without coding for proteins. Non-coding DNA is crucial to biology, yet knowing that it is there hasn't made it any easier to understand what it does. "We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not," says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK.

Translation: Evolution’s simplistic, gene-centric, just-add-water view of biology led researchers to believe that sequencing the entire genome would lead to great breakthroughs. That naïve view became yet another failed evolutionary expectation.

Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary.

With the ability to access or assay almost any bit of information, biologists are now struggling with a very big question: can one ever truly know an organism — or even a cell, an organelle or a molecular pathway — down to the finest level of detail?

I once debated an evolutionist who said the purpose of science is to explain, and that evolution explains biology. False. As usual it is the exact opposite. Evolution does not explain biology. Evolution is constantly surprised by scientific findings.

"It seems like we're climbing a mountain that keeps getting higher and higher," says Jennifer Doudna, a biochemist at the University of California, Berkeley. "The more we know, the more we realize there is to know."

Isn’t evolution amazing?

"The crux of regulation," says the 1997 genetics textbook Genes VI (Oxford Univ. Press), "is that a regulator gene codes for a regulator protein that controls transcription by binding to particular site(s) on DNA."

Just one decade of post-genome biology has exploded that view. Biology's new glimpse at a universe of non-coding DNA — what used to be called 'junk' DNA — has been fascinating and befuddling.

In the past few years the story of regulation has become profoundly more complex than evolutionists ever imagined. Needless to say, there is no credible, scientific, explanation for how it all evolved.

Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Indeed. It is also “incredibly naïve” to insist we know how such complexity arose.

Even for a single molecule, vast swathes of messy complexity arise. The protein p53, for example, was first discovered in 1979, and despite initially being misjudged as a cancer promoter, it soon gained notoriety as a tumour suppressor — a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53, and it even commands its own meetings. Yet the p53 story has turned out to be immensely more complex than it seemed at first.

In 1990, several labs found that p53 binds directly to DNA to control transcription, supporting the traditional Jacob–Monod model of gene regulation. But as researchers broadened their understanding of gene regulation, they found more facets to p53. Just last year, Japanese researchers reported3 that p53 helps to process several varieties of small RNA that keep cell growth in check, revealing a mechanism by which the protein exerts its tumour-suppressing power.

Even before that, it was clear that p53 sat at the centre of a dynamic network of protein, chemical and genetic interactions. Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems wilfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions.

Of course beyond just-so stories, evolutionists have no idea how such complexity evolved. And yet p53 is just one example of biology’s complexity that defies evolution.

And reading further it is good to see a point of agreement:

The p53 story is just one example of how biologists' understanding has been reshaped, thanks to genomic-era technologies. Knowing the sequence of p53 allows computational biologists to search the genome for sequences where the protein might bind, or to predict positions where other proteins or chemical modifications might attach to the protein. That has expanded the universe of known protein interactions — and has dismantled old ideas about signalling 'pathways', in which proteins such as p53 would trigger a defined set of downstream consequences.

"When we started out, the idea was that signalling pathways were fairly simple and linear," says Tony Pawson, a cell biologist at the University of Toronto in Ontario. "Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It's infinitely more complex."

Indeed, those networks of information are “infinitely more complex” than expectations. That is hardly surprising given that those expectations came from evolutionary theory. What the data are revealing is nothing like what evolution expected.

But even with the deluge of data being provided by high-throughput technologies and the power of super computers will not easily solve biology’s infinite complexity:

In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the 'virtual human'. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.

In many cases, the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions that are simply exercises in cataloguing.

In retrospect, it was probably unrealistic to expect that charting out the biological interactions at a systems level would reveal systems-level properties, when many of the mechanisms and principles governing inter-and intracellular behaviour are still a mystery, says Leonid Kruglyak, a geneticist at Princeton University in New Jersey. He draws a comparison to physics: imagine building a particle accelerator such as the Large Hadron Collider without knowing anything about the underlying theories of quantum mechanics, quantum chromodynamics or relativity. "You would have all this stuff in your detector, and you would have no idea how to think about it, because it would involve processes that you didn't understand at all," says Kruglyak. "There is a certain amount of naivety to the idea that for any process — be it biology or weather prediction or anything else — you can simply take very large amounts of data and run a data-mining program and understand what is going on in a generic way."

A certain amount of naivety? But if all of biology arose from those random mutations and the like, shouldn’t biology be easy to understand?

Some, such as Hiroaki Kitano, a systems biologist at the Systems Biology Institute in Tokyo, point out that systems seem to grow more complex only because we continue to learn about them. "Biology is a defined system," he says, "and in time, we will have a fairly good understanding of what the system is about."

So biology’s complexity is just an illusion of too much knowledge. Once we figure all this out we’ll see how simple it actually is. Sounds like another prediction of evolution. Will it follow the trend of its failed predecessors?

Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. "Famous people would get up and say, 'We will understand everything after this'," she says. "Biology is complex, and that is part of its beauty." She need not worry, however; the beautiful patterns of biology's Mandelbrot-like intricacy show few signs of resolving.

Yet another failed prediction.

The notion that all of this evolved into existence is outrageous. It violates both simple common sense and detailed analysis, and makes mockery of science. When will taxpayers stop funding this religious drivel?

124 comments:

  1. Hunter: "What the data are revealing is nothing like what evolution expected."

    A point of order here. All of these examples go back to Crick and the Central Dogma rather than evolutionary theories. The faults here lie on the heads of molecular biologists being either uncreative and/or simply unaware of systems theories. Or simply human arrogance.

    Various evolutionists may compound that or not, but it seems rather cheeky to blame them for the faults of others.

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  2. Speaking of religious drivel, what alternative theory and specific research do you propose, Cornelius, that will find better answers than current and ongoing evolutionary theory and research?

    Oh, and the IDiots on UD say that ID accepts evolution. Are they wrong?

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  3. Hey Cornelius, why don't you list for us all the positive supporting evidence for ID that came out of the Human Genome Project.

    Shouldn't take you too long.

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  4. Incredible.

    Was I the only one to notice that in all Cornelius' above quotes not a single one actually supports his conclusion that ToE falls short?

    It's all just 'Biology is complicated. More so than we thought.'

    That's like saying a sudden realisation that the universe is bigger than we though invalidates our theory of gravity. Or the realisation that there were more strains of bacteria than we realised invalidates germ theory.

    FAIL.

    Must try harder next time, Cornelius.

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  5. This post makes the repeated mistake of taking scientists' prognostications about the theory of evolution and treating them as scientific predictions of the theory of evolution.

    Let me tell you a little secret. Scientists in every field have been prognosticating the moment when "all the mysteries would be solved" since the beginning of science itself. They've been wrong every time before, and there is no reason to believe that they'll be right now or in the foreseeable future.

    Does that therefore mean that all of science has been falsified? I suspect that you actually believe that to be true, though you'd only ever admit it about evolution.

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  6. Excellent examples. Once again real science mocks the Darwinian preconceptions. I almost feel sorry for these scientists. Every day they go to work and find out more about how wrong their assumptions are. Must be depressing.

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  7. Venture Free: "This post makes the repeated mistake of taking scientists' prognostications about the theory of evolution and treating them as scientific predictions of the theory of evolution."

    True enough. To help out Cornelius and others here distinguish between the two, would you be so kind as to list the scientific predictions? Just the fundamentals is fine.

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  8. Actually, I'd suggest that Cornelius has confused predictions of scientific theories with prophecy.

    Predictions of scientific theories are a function of the underlying explanation of the phenomena that theory encompasses. They represent potential outcomes that cannot stand alone from the underlying explanation and are subject to cause and effect. This includes causes which are outside and not necessarily related to the theory itself. As such, predictions of scientific theories do not take into account an infinite number of un-conceived and unrelated, yet parallel possibles that could effect actual observations.

    On the other hand, prophecy supposedly isn't derived from putting together piece after piece after piece to eventually conclude what should occur. It's an empirical mandate about reality. In many cases, this is based on claims of supernatural foreknowledge of what eventually did occur or inside information about the will of a omnipotent being. As such, prophecy represents the claim of an empirically observable outcome which supposedly takes into account an infinite number of un-conceived and unrelated, yet parallel possibilities.

    So, in the case of prophecy, if an empirical mandate is not observed it must be false. However, evaluating the predictions of scientific theories as if they were empirical mandates fails to take into account the underlying explanation they were derived from.

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  9. Heh. And Galileo thought the Sun was the center of the Universe.

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  10. The complexity of biology does nothing to discredit ToE. How could it? Nothing can discredit it. It is an inevitable truth, an article of faith. Any challenge is certain to be overcome by yet-undiscovered evidence. Anyone who disputes it should be mocked.
    What if ID isn't a credible alternative? Even if the only alternative is 'we have no idea whatsoever,' the theory is nonsense for weak-minded crowd followers. It's easy to stand in a crowd and point your finger and mock. It's also cowardly.

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  11. If mankind were to create a robot that could physically do just 75% of what the human body could do, what would the technology look like
    (not to mention conciousness or reproduction)?

    What would it take?

    That is why I have always believed that biologists were just scratching the surface of understanding the working of the cell and human body.

    Complex, working systems, need a myraid of finely tuned, integrated and networked components. "Components" like in a wrist watch does not appear to do the living system justice. Living systems are more akin to a tightly networked computer server farm. Yet, the integration and networking and communication among the "components" in a living cell and body is far more thorough. Saying that it's technology is far more advanced does not do it justice. It's in a whole different league.

    Biologists are beginning to step out of the kiddy pond and seeing the lake. They are getting a glimpse of the bigger picture as CH describes. Yet for the human body to do what it does, there is a mind blowing ocean of technology awaiting discovery that makes Einstein's physics look like Math 101.

    The evolutionist awaits a myraid of "chicken and egg" issues as these fully integrated and complex network systems are understood. The evolutionary position will become more and more an unreasonable fantasy. The working of the cell has to be understood as a whole... a whole network of interdependent components.

    As King David said 3000 years ago, we are fearfully and wonderfully made. "Fearfully" as in reverence and mind blowing awe. That is exactly right. Score one for King David of Bible fame. Score zero for Uncle Charlie Darwin and his warm little pond goo. That's just one reason why I have confidence in the Bible. Uncle Charlie's bad science is not dependable.

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  12. Apparently we have none around here that can put forth any variant of a prediction of Evolution. So here's the most common notions of it in predictive form:

    "At some unknowable point in our future all life will become descended from some unknowable organism that existed at some unknowable point in our past."[1]

    This is the reason why Evolution should not hang by the failures of Biology; as they have no relation to one another. One is a disciple of science and the other is an episode of Futurama.

    [1] Scott, feel free to exchange 'all life' with 'some life' if it suits you.

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  13. badwiring -

    "The complexity of biology does nothing to discredit ToE. How could it? Nothing can discredit it. It is an inevitable truth, an article of faith."

    No, the quotes in the OP don't discredit ToE because they don't discredit ToE. They might as well be talking about physics, or the opera, or Jerry Seinfeld.

    "What if ID isn't a credible alternative? Even if the only alternative is 'we have no idea whatsoever,' the theory is nonsense for weak-minded crowd followers. It's easy to stand in a crowd and point your finger and mock. It's also cowardly."

    Another statement dripping with irony.

    It is true that 'We don't know' is a perfectly legitimate scientific position, and also true that one theory is not confirmed by disroving it's rivals. Theories have to account for the evidence on their own.

    However it is ID which is playing this 'discredit the rivals' game. Look at this very blog. Cornelius does nothing but (try to) pick at ToE for no other reason than to make ID seem credible by comparison.

    As far as EVIDENCE goes ToE is the ONLY theory bringing home the bacon.

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  14. Jquip -

    Just a passing comment:

    "At some unknowable point in our future all life will become descended from some unknowable organism that existed at some unknowable point in our past."

    Why should this be a prediction of evolution? Imagine if life on Earth began independantly not once, but twice. And all life was descended from either one of these first two organisms.

    It's possible.

    What you are referring to is common descent, which is a seperate (though closely related)theory. Now it's true that modern biologists accept common descent, but it is not a cornerstone element of evolutionary theory. If we find out life started not once, but twice, the principles of evolution via natural selection would not at all be overturned.

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  15. Neal -

    "Complex, working systems, need a myraid of finely tuned, integrated and networked components."

    True. Biology is complex. Very complex. But you seem to be fixated on this idea that it is TOO complex to have evolved. Which NO scientist is saying. I'm sure the more closely you look at a snowflake the more you find to marvel and awe at, but that doesn't mean some divine being must have SCULPTED it, does it?

    Life is complex NOW. But that doesn't mean it started out complex. It's changed. That's the point.

    "Score one for King David of Bible fame. Score zero for Uncle Charlie Darwin and his warm little pond goo. That's just one reason why I have confidence in the Bible."

    That is exactly why you will never be a scientist. You put all your faith in your RELIGION. And then you have the nerve to mock science, CALLING it religion, when in fact you just don't really understand the difference.

    The arrogance and hypocrisy is almost tangible.

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  16. badwiring said...

    The complexity of biology does nothing to discredit ToE. How could it?


    Then tell us why should it? Be specific. We already know that an iterative, adaptive feedback processes with variation filtered by selection can and does produce amazingly complex things. We have ample evidence that just such a process, one we call evolution, has been at work for over 3 billion years,

    Nothing can discredit it.

    ToE is quite falsifiable. It just hasn't been falsified. You really should learn the difference, it's important.

    It is an inevitable truth, an article of faith. Any challenge is certain to be overcome by yet-undiscovered evidence.

    Nope, not certain. But based on the existing evidence that's sure the way to bet.

    Anyone who disputes it should be mocked.

    Anyone with such a dirt poor understanding of the actual science who posts strawman nonsense on a public BB deserves to be mocked.

    What if ID isn't a credible alternative? Even if the only alternative is 'we have no idea whatsoever,' the theory is nonsense for weak-minded crowd followers.

    Yes, ID as currently offered is nonsense for weak-minded crowd followers.

    It's easy to stand in a crowd and point your finger and mock. It's also cowardly.

    You mean like CH and you and Gary and Tedford and Eocene and every last one of you Intelligent Design Creationists have been doing non-stop towards the scientific community's findings since this this blog began.

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  17. Jquip said...

    Apparently we have none around here that can put forth any variant of a prediction of Evolution. So here's the most common notions of it in predictive form:


    Wow armchair philosopher clown, you put forth your 'challenge' and waited an entire 3 1/2 hours to declare victory.

    I guess you missed this example from the other day. The Center for Disease Control (CDC) uses evolutionary models to predict the evolutionary pathways of disease vectors so it can best allocate resources to fight expected problems. This is critically important in preventing / halting pandemics like HIV/AIDS.

    Epidemiology, Evolution, and Future of the HIV/AIDS Pandemic

    Tell us APC, what have ID and Creationism done in the way of predictions, especially useful ones?

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  18. Ritchie: "Why should this be a prediction of evolution?"

    As I said that's just based on common notions. Perhaps you could provide a proper example of a scientific prediction of evolution.

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  19. Thorton: "I guess you missed this example from the other day."

    Now that's a good attempt; though I assume you haven't read the thing either. Or perhaps you would have noted some of the following:

    "In this section, we describe simple models for ..." -- They are simply modelling allele frequencies using bog standard population models. Nothing of interest or contention here.

    "We argue that it will take thousands of years before evolution in the human population ..." -- Would you accept a scientific prediction that Christ will return in thousands of years? That until then we just have to hold our breath?

    "The implications of this are straightforward if not optimistic: we cannot count on evolution in our population to save us from the AIDS epidemic, at least not in our lifetimes or that of many generations to come." -- But don't worry if He doesn't show up. He'll get here eventually.

    "Not so clear, however, is whether natural selection will favor changes in the virulence of this retrovirus or, if so, in what the direction that change would be." -- The CDC swings both ways.

    "Nonetheless, one should interpret these results cautiously because the evidence that no relationship exists between the virulence of HIV and its transmissibility remains largely circumstantial, albeit more compelling than that for a positive relationship. Until the results of studies addressing this issue become unequivocal, we cannot rule on the plausibility of the different scenarios for evolution of increasing or decreasing virulence of this retrovirus." -- eg. It was a pure modelling exercise absent any evidence, presuming far too much, and otherwise untestable.

    Not least of which the modelling over a steady state population of 10,000. Which, I assume you agree, would not be tested even though we are certainly capable of doing so.

    The far larger problem is that they aren't even discussing the mechanisms; just assumptions of what might happen at differing levels of tinkering within standard population models. This is such a joke that it doesn't even rise to the level of a scientific prediction under the well established notions of microevolution that, I presume, no one here has a disagreement with.

    "Tell us APC, what have ID and Creationism done in the way of predictions, especially useful ones?"

    The same as the Evolutionary theories so far: Bupkus. That said, the ID folks have been a nice fitness gradient to force the evolution of Evolutionists. They've now started showing their work. Or, ya know, doing science. It's a refreshing change.

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  20. Hi all, sorry had to post.

    'The notion that all of this evolved into existence is outrageous. It violates both simple common sense and detailed analysis'


    Well, one could predict that if TP53 is involved in so many systems / pathways that are fundamental to a host of cellular processes including (but probably not limited to) cell cycle regulation, apoptosis and senesence, then it had to have originated around the time that the simplest forms of multi-cellular life emerged and therefore would be present in the simplest of life forms as well as the most complex. One could also predict that the seperate genetic changes that may have affected this gene as different lineages diversified would allow scientists to generate some sort of phylogeny maybe? Perhaps, TP53 may even be part of a larger 'super-family' of genes that have homologs and orthologs throughout multi-cellular lifeforms that also, through genetic analyses, appear to form some sort of hierarchy... If only scientists could find such a thing huh.

    Oh yeah, the p53/p63/p73 superfamily. Highly conserved genes found all the way up from C.elegans to H.sapiens.

    http://cshperspectives.cshlp.org/content/2/7/a001131.full

    I'd post more links but don't see the point. The info is out there for those who wish to see it. No amount of linking to primary data or peer-reviewed journal articles will help those that don't want to.

    CH, p53 is not a good example if you want to poke a stick at the ToE.

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  21. Jquip said...

    Thorton: "I guess you missed this example from the other day."

    Now that's a good attempt; though I assume you haven't read the thing either. Or perhaps you would have noted some of the following:


    LOL! The armchair philosopher clown is shown up, resorts to quote mining to soothe his damaged ego.

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  22. Thorton: "LOL! The armchair philosopher clown is shown up, resorts to quote mining to soothe his damaged ego."

    Yes, I'm aware you've no valid counterarguments. For future reference you should dig up the study on antibacterial resistance and population models that showed completely counter-intuitive but valid results consistent with the Modern Syntheses. (Spread and vector for in and out patients.) It's still only microevolution, but at least it's a good link to throw at people in debate. The CDC bit? Not so much.

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  23. Jquip said...

    Thorton: "LOL! The armchair philosopher clown is shown up, resorts to quote mining to soothe his damaged ego."

    Yes, I'm aware you've no valid counterarguments.


    LOL! That's a good little clown. Go LA LA LA! and declare victory. VICTORY!. Works every time for the rest of the IDCers around here

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  24. As far as EVIDENCE goes ToE is the ONLY theory bringing home the bacon.

    ToE is like a man who swears that he once saw an island full of unicorn-riding monkeys. Anyone who disputes it is ignorant and arguing from ignorance. He brings home the EVIDENCE.

    But when you scratch the surface of that evidence, what do you find? Hoof prints and other evidence of horse-like creatures. And monkeys are real, aren't they? And so are islands. And a monkey could fall out of a tree and land on a unicorn. And the rhinoceros has something that looks like a horn. See, this EVIDENCE is piling up. I can go on all day like this!

    The trouble is that all of EVIDENCE doesn't even add up to unicorn droppings. The only real, substantial reason to believe it that you choose to.

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  25. Jquip -

    "As I said that's just based on common notions. Perhaps you could provide a proper example of a scientific prediction of evolution."

    Well off the top of my head there's the Tiktaalik. Neil SSubin et al purposefully set off in search of a creature using the already drawn up tree of life. They estimated that the first terrestrial vertibrate (the first of our ancestors to set foot (or whatever) on land) was to be found 350 million years ago, and this is the rock strata they set out to search in the Canadian Arctic. Tiktaalik was a huge vindication. It fitted the description perfectly - a fish-like creature wonderfully 'designed' for out-of-water life with all the features of the first terrestrial.

    This might not be quite what you meant. After all, had they found nothing we would merely have concluded that the creature had lived, but we just hadn't found it. ToE would not have been toppled.

    So let me give you another. When the human genome was found to consist of 23 pairs of chromosomes while all the other apes have 24 pairs, it was a major apparent problem for ToE. No doubt if Cornelius was blogging at the time he would have written about it being another major falsification for ToE and insist that we drop the silly theory immediately.

    But could ToE be salvaged? Yes. IF one of the pairs of human chromosomes had signs of fusing, this would be evidence that we, like all other apes, once had 24 pairs.

    This was a solid test with a solid prediction - for ToE to stand, one human chromosome pair had to have fused. Otherwise something was MAJORLY wrong. Human common ancestry with apes - and thus the whole tree of life, was at stake. And it was not a difficult test, after all, there are only 23 pairs of chromosomes to search. ToE was throwing up a solid, falsifiable, surprising prediction.

    And we looked and what did we find? Chromosome pair 2 does indeed bare the telltale marks of having once been two pairs which then fused. A huge vindication for ToE.

    Just for fun, let's compare this with ID. Well, first of all ID would not have led us to make such a prediction. ID could explain humans having only 23 pairs much like it can explain ANY possible discovery in biology. It would have explained humans having 22 pairs, or 7, or 1,000. We would have just said 'the Designer made it that way' and gone nowhere from there, predicting nothing, discovering nothing, explaining nothing. Just saying...

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  26. badwiring -

    "But when you scratch the surface of that evidence, what do you find? Hoof prints and other evidence of horse-like creatures. And monkeys are real, aren't they? And so are islands. And a monkey could fall out of a tree and land on a unicorn. And the rhinoceros has something that looks like a horn. See, this EVIDENCE is piling up. I can go on all day like this!"

    Much as I enjoy your colourful ranting, it is only so much nonsense. You are simply wrong. You are criticising a theory you clearly do not understand with barely coherent rantings. If you have a LEGITIMATE criticism, let me know. No, publish in a scientific journal and let EVERYONE know. I promise you fame and riches await if you do.

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  27. Tiktaalik was a huge vindication.
    Yes, and then it was discarded. That's how the EVIDENCE works. It's not like real science where one hypothesis is supplanted with a better one. No, they just dig up a skeleton, rant and rave that it's the critical piece of evidence they've been missing, and then quietly abandon it.
    Some of us are smart enough to be skeptical when the next crucial piece of evidence appears. Some swallow everything hook, line and sinker because they have such strong faith, and they don't even notice when the evidence is discredited a year later. They keep posting about it on blogs.

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  28. Ritchie,

    Let's move on to your next overwhelming piece of evidence: Apes have 24 chromosomes, and apparently humans used to have 24 chromosomes.
    What exactly does that prove? My last two computers each had 4 USB ports. Did one produce the other?
    Yes, I realize that living things reproduce and computers don't. The point is that it's possible and likely for two things to have the same components. Clever engineers re-use components. The chromosomes aren't evidence of descent. They don't mean anything unless you assume your conclusion.
    ID predicts that a designer would re-use components, just like we do. So you see, the evidence you cite could support entirely separate explanations. How can it be convincing evidence for one or the other?
    You people go on and on about your evidence, but when you scratch the surface there's nothing there. And then you go to your fallback approach, mocking anyone who disagrees. That's a sign of weakness.

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  29. Once again the Darwhiners reveal their fathomless naivety and gullibility.

    Evolution did it because there is no god and he wouldn't have done it that way.

    Profoundly scientific that.

    The whole central point of this blog, "Religion drives science", is thus demonstrated every single time CH posts and we look at the "rebuttals", if I may abuse the term!

    The same old frantic and apoplectic ire, spewed forth at ever more vehement, in direct proportion the weight of the argument presented by CH. It's a wonder their brains don't come issuing forth along with the codswallop, so soft are they!!

    Argument from incredulity is a major substance of the outrageously foolish ToE.

    Sadly, none of the Darwinistas ever get it, because their minds are on HOLD.

    Even when demonstrated mathematically, - math doesn't count for them, mechanics doesn't count, engineering doesn't count, combinatorial dependencies don't count, entropy doesn't count, ... and on and on they go

    We know thus that logic doesn't count either, (for evolution has no explanation for its existence).

    Gee what does count?! Nothing but the very trivial gratuitously extrapolated into the monumental!!

    So they pull the opaque garbage bags over their heads and scramble, squealing like little piggies, "There is no God and I am his prophet so SHUT UP Dr. Hunter!"

    No intelligent rebuttals of any kind.

    Just the ubiquitous just-so-story and the equally ubiquitous denial of reality, denial of the math, denial of all evidence.

    No wonder they and their predictions are failing over and over again.
    But still :
    "the BEAT GOES ON, the beat goes on
    Drums keep pounding a rhythm to the brain
    La de da de de, la de da de da

    That's Darwinian fundamentalist "science" all over - La de da de de, la de da de da

    ReplyDelete
  30. badwiring said...

    "Tiktaalik was a huge vindication."

    Yes, and then it was discarded.


    Tiktaalik was discarded? When did that happen? Do you have any references from the scientific literature? AFAIK Tiktaalik is still regarded as a wonderful illustrative example of a fish to tetrapod transitional form. No one is claiming it was the first species to transition, or the only one.

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  31. Gary the yappy little puppy said...

    Even when demonstrated mathematically, - math doesn't count for them, mechanics doesn't count, engineering doesn't count, combinatorial dependencies don't count, entropy doesn't count, ... and on and on they go


    All you demonstrated moron is that you don't have the faintest clue how evolutionary processes actually work.

    Here's a test for you yappy puppy. You walk into a room full of people playing cards and you see one person holding the A K Q J 10 of spades. What is the probability of those cards being there for:

    1) straight 5 card poker, no draw
    2) draw poker, rules allow a single 3-card discard and redraw
    3) 'alternate' draw poker, rules allow up to five 3-card discard and redraws
    4) 'alternate' draw poker, rules allow an unlimited number of discard and redraws

    Go on puppy, show us how to accurately compute the probability when you don't know the rules or the history of the game.

    ReplyDelete
  32. Yes, AFAYK.
    http://news.nationalgeographic.com/news/2008/09/080924-fish-fingers.html

    There's never much of an admission, just they now they found another fish which they claim was the real transition from fish to tetrapods and came along much earlier.

    That's the way it's always done. Find a fossil and claim that it fills in some gap. Then find another fossil and claim that this one fills in that gap. But what about the first one? That's not scientific correction. It's an ideologically driven quest to find evidence after the conclusion has already been made.

    And supposedly Tiktaalik was well suited for terrestrial life? It had fins, not legs. People with something meaningful to show don't resort to hyperbole.

    Never mind the fact that there are living fish that can leave water and support themselves on their limbs, and no one calls them "transitional." They are just fish.

    ReplyDelete
  33. Badwiring said..
    'ID predicts that a designer would re-use components'
    Does it really? Why? On what basis do you make that prediction. Why wouldn't a designer come up with novel components? Or does ID predict that too?

    ReplyDelete
  34. Thornton,

    Forget about science - you need to learn how to communicate with adults. If you were a child I wouldn't even want you to play with my son. He's five years old and would never speak to anyone as you do.

    ReplyDelete
  35. Lmao. I love the quote at the end of that article Badwing.

    "Nothing comes from nothing in evolution," he said.

    ReplyDelete
  36. MrT

    ID predicts the reuse of components because it's an efficient pattern known to be used by those who design. Anyone who builds a house uses wood cut to standard sizes and they don't reinvent electrical wiring.
    By itself, I don't think that makes a convincing case for anything. But it demolishes the notion that homology is evidence of descent. How can a thing be evidence of one theory when it can also be evidence of a contradictory theory.
    Check out this study and tell me if homology is evidence of descent.
    http://www.edmunds.com/toyota/camry/history.html

    ReplyDelete
  37. But there is nothing to stop a person going out and completly redefining housebuilding. Using completely novel components, materials and plans a person could build something unique that was habitable could they not, indeed I'm sure a lot of architects do, or at least try, this quite often. It could totally break with house 'homology' and be truly novel, you can't predict that that would never happen can you? But if I understand it right that is what ToE predicts with regards common descent which is why, if such a thing was discovered, it would have the potential to falsify the theory. I hope I explained myself ok there. For example, if you or I had a child tommorrow and that child had the gene for vitamin-C bio-synthesis reintroduced, completely intact and it was exactly the same as is found in all the rest of the animal kingdom that never lost it then that would pretty much throw ToE out the window and would be very much akin to your designer re-using an efficient design. Sorry, think I may have rambled a bit there lol.

    ReplyDelete
  38. I kinda see your point about homology alone as evidence for descent, although something is niggling me about it lol. But it isn't the only evidence of descent. In fact the more compelling evidence comes from genetics doesn't it?

    ReplyDelete
  39. I understand your point. But nonetheless, every point homology scores for descent is also a point scored for design. Not that I deny any type of descent. Descent isn't really the issue. It's the causative power of random mutations and selection.

    ReplyDelete
  40. Genetics have been a problem as well. If we compare one set of genes we're closely related to a chimpanzee. Compare another and we're right next to the sea cucumber. So how do we pick the set of genes to use? We use the ones that confirm what we expect.

    ReplyDelete
  41. badwiring said...

    Yes, AFAYK.
    http://news.nationalgeographic.com/news/2008/09/080924-fish-fingers.html

    There's never much of an admission, just they now they found another fish which they claim was the real transition from fish to tetrapods and came along much earlier


    Just as a I thought - nothing in there about Tiktaalik being discarded. Just evidence of different other intermediate forms in different lineages. Like I already pointed out, no one claimed Tiktaalik was the was the first species to transition from water to land, or the only one.

    So you didn't understand the article, or you are just doing the usual Creationist dishonest spin. I'll give you the benefit of the doubt and assume woeful ignorance.

    BTW, if you want to speak with Dr. Per Alhberg, one of the one of the world's leading expert on Devonian tetrapods and who actually discovered Tiktaalik, he hangs out at Talkrational.org Unlike Gary's bogus claim with Sanford, Per actually does post there under his real name. He enjoys making Creationists who misrepresent his work look like fools.

    You up for making these claims to him in person?

    ReplyDelete
  42. badwiring said...

    Thornton,

    Forget about science - you need to learn how to communicate with adults.


    When I meet a Creationist who behaves like an adult and wants to honestly discuss the evidence I treat him like an adult. Rare, but it does happen. When I get scientifically illiterate boobs like you screaming (not arguing) from personal ignorance I don't. It's totally up to you.

    ReplyDelete
  43. Ritchie: Since you ask for the comparison, allow me here to play Devil's Advocate with an ID position.

    "Well off the top of my head there's the Tiktaalik."

    Tiktaalik was a great find. As you say they used two assumptions. 1. To look for where current Evolutionary theories stated it should be. 2. To look for amphibious creatures where one should find amphibious creatures. Both statements came from Neil (IIRC) in an interview.

    If we're going Occam then all we need is the second statement as the first is entirely superfluous. But for attempting vindication we do need that first one. And so we've Tiktaalik. (Though I'm really distressed that looking for amphibians in places other than deep oceans was considered, by itself, such a step forward for Paleontology.)

    Now for Satan's Sidebar. In the reasonably common ID notion of Frontloading one would then state that we would expect to find evidence of proper tetrapods pre-existing Tiktallik. Last year they found tetrapod tracks that clear that goal by 25 million years. This is the same sort of happening as with the exquisite eye a few days back which introduced you to me.

    If we're to consider Tiktaalik a vindication of Evolution then certainly the tracks are a refutation of it. And a vindication of Frontloading within ID. If we consider it anything else then we're going afield after cherished dogma rather than weighing the evidence. Enough of that Sidebar.

    The problem here is that predictions are future tense items. Because X, then we predict that Y follows. But in both cases for Tiktaalik we have inverterted this to: Because Y, therefore X is the cause. Or classic Post Hoc Ergo Propter Hoc.

    "ToE would not have been toppled."

    Which should make your skin crawl. This is just Dice in the Gaps. Something to consider. Back to it:

    "Otherwise something was MAJORLY wrong."

    This again is Because Y, therefore X is the cause. If Evolution is correct then it would be correct whether or not #2 underwent fusion. I seem to remember that it used to be a fad to claim that Evolution was wrong because a loss would be fatal; and so the need for a fusion. But by the same token Mules have no such problem. So no matter what outcome was found we would still be able to bolt on a Propter Hoc to get the deed done. But the fusion v. fatality argument is one of biology proper rather than Evolution.[1]

    Satan's Sidebar again: Given empirical testing we know fusions occur. So finding a fusion event in humans does not rule out a designer. We just haven't found the evidence yet. And so ID is not toppled. End Sidebar.

    What both theories are lacking is a proper prediction. And while you fear that ID may lead to stagnation, I'm thrilled with them being about as they cured the stagnation under Darwin.

    Though I'm sure I misrepresented something in the ID position that I'm bound to catch flak for.

    [1] Memory serves that I read a paper earlier this year that mentioned the theoretical fusion site evidence is found all over the place rather than just in the 2q (IIRC) region. If you have a handy link to refresh the noggin' it would be appreciated.

    ReplyDelete
  44. badwiring said...

    I understand your point. But nonetheless, every point homology scores for descent is also a point scored for design.


    What would be a point not scored for design look like? There are plenty of things that if found would falsify ToE. How do you falsify Intelligent Design?

    Not that I deny any type of descent. Descent isn't really the issue. It's the causative power of random mutations and selection.

    Then offer another mechanism (along with supporting positive evidence) for the empirically observed matching patterns in the fossil and genetic records. Merely claiming 'it was designed that way' is not a mechanism.

    ReplyDelete
  45. Badwiring,
    I'm not sure what genes we have that are closely homologous to sea cucumbers, I certainly can't name any right now, but I'll accept for this point that there are some (maybe many), however, I can and will make predictions about those genes that rely on common descent. 1) Chimpanzees will also have those genes. 2) Any variations between the sea cucumber's gene and ours will also be shared by the chimp (with some possible additional changes 3) Genes that are highly conserved between us, chimps and sea cucumbers will have highly conserved and very important roles, such as the p53/p63/p73 superfamily ie, they don't get much variation because they are lethal if changed much and will therefore be highly conserved between almost all species. 3) Genes that are conserved between humans and chimps but are not found in sea cucumbers will be related to phenotypes/proteins that are specific to 'higher' lifeforms, maybe the HOX genes would be a good example of that?
    It is not that we use ones that confirm what we expect, it is just that we should expect different things of different genes depending upon the nature of that gene and the protein/s it codes for. (that is taking a narrow view of the genome/proteome/exome etc but the point is the same). You follow me?

    ReplyDelete
  46. But again the problem arises that ToE as I understand it could be falsified at almost any point, I'm not talking about 'failed predictions', but actual stone cold falsifications like a croco-duck or whatever. ID could never be falsified, could it? I just don't see how...

    ReplyDelete
  47. Jquip,

    Now for Satan's Sidebar. In the reasonably common ID notion of Frontloading one would then state that we would expect to find evidence of proper tetrapods pre-existing Tiktallik

    Evidence? Why would the frontloading manifest itself earlier than in common descent? A popular form of frontloading ( mike gene) views the front loading as a " bias " towards a ultimate goal . If so it seems it might well proceed at any pace it desired.

    ReplyDelete
  48. Rather than common descent,perhaps evolutionary theory

    ReplyDelete
  49. vlikovskys: "A popular form of frontloading ( mike gene) ..."

    Well, I'm not an ID guy or terribly versed on it's particulars so I'm probably mixing things around. Roughly the idea that the information pre-existed, and can only be lost over time. Behe's riff whatever name it goes under.

    ReplyDelete
  50. Thornton,

    I assume that this forum is unmoderated, and I assume that's why you're here. You lack the ability to discuss matters as a well-raised adult. Note that I say so in response to your snarling, rabid, irrational attacks, not because I disagree with you. I disagree with many people, but the vast majority conduct themselves in a manner that you should learn from if you can rise above whatever atrocious childhood you suffered.
    We all run across trolls, but I seem to have entered your cave. I'll leave you to it. Enjoy the darkness.

    ReplyDelete
  51. Ritchie said, "Which NO scientist is saying"

    That's incorrect unless you define a scientist as only those that are evolutionists. That's the usual route.

    Recenty "after watching their pro-LSEA scientific peers testify about scientific problems with evolution, one anti-LSEA LSU biologist still had the audacity to testify before the House Education Committee that "there is no controversy among professional biologists about fact of evolution". When one representative asked him, "Did you hear the testimony of the other professors we had here that were speaking before this committee?," he fumbled in response. So please let me state plainly to you what is going on here: Some Darwinian activists have an agenda to impose censorship on students by bluffing that there is no scientific controversy over neo-Darwinian evolution."

    http://www.evolutionnews.org/2011/05/science_law_and_economics_come046871.html

    Yes, life is not only too complex to have evolved but it displays immense specified complexity. A snowflake? No An ice sculpture of Mickey Moose in front of a 4 star hotel? Yes, designed. That's the difference.


    Regarding first life. Yes it was immensely complex too. Evolutionists have to dumb down life in order to entertain their fantasy as realistic. Evolutionists thrive in the shadows of half truths and ignorance. Increasing knowledge of living organisms is not on the evolutionists side.

    You said, "I'm sure the more closely you look at a snowflake the more you find to marvel and awe at, but that doesn't mean some divine being must have SCULPTED it, does it?"

    Seriously? Your question is very telling about your view of life. That you would even make the comparison is an absolute hoot. Other evolutionists bring up water and the carving of the Grand Canyon. Could acceptance of evolution by you and these others really be that silly simple or is your bias just making you blind to the obvious?

    ReplyDelete
  52. MrT said, "But again the problem arises that ToE as I understand it could be falsified at almost any point, I'm not talking about 'failed predictions', but actual stone cold falsifications like a croco-duck or whatever. ID could never be falsified, could it? I just don't see how..."

    ---

    or whatever? How about a platypus? See evolution is not allowed to fail.

    ReplyDelete
  53. Jquip,
    Roughly the idea that the information pre-existed, and can only be lost over time

    Neal might know better but that is kinda a young earth creationist's argument ,things could't be old cause they are degrading. Frontloading does have pre- existing info but it can be indistinguishable from evo.





    I don't think either really helps you refute Richie's Tiktallik example. Perhaps you might try " it might be an example of common descent but that doesn't prove Darwinism"

    Or you could go Neal's route Your question is very telling about your view of life. That you would even make the comparison is an absolute hoot. Other evolutionists bring up water and the carving of the Grand Canyon. Could acceptance of evolution by you and these others really be that silly simple or is your bias just making you blind to the obvious?

    It doesn't make sense but impossible to deconstruct.

    Hope that helps

    ReplyDelete
  54. Jquip -

    "In the reasonably common ID notion of Frontloading one would then state that we would expect to find evidence of proper tetrapods pre-existing Tiktallik. Last year they found tetrapod tracks that clear that goal by 25 million years."

    I get where you are coming from, but you're still slightly off. To invalidate the intermediary step Tiktaalik represents, what we need to find are tetrapods which MASSIVELY predate Tiktaalik. If we found tetrapods predating it by hundreds of millions of years, then ToE would be in trouble.

    But this is not the case. The footprints to which you refer, I believe, predate Tiktaalik by only 10 million years (correct me if I'm wrong). Now this sounds a lot, but this is still a relatively brief window in paleontological terms. What we are discovering is the emergence of quadrupedalism - the first tetrapods. There is wiggle room to adust dates by the odd 10 million years here and there. This is not a huge, theory-undermining discovery, no matter how the Creationists paint it. All the footprints really show is that Titaalik was not the absolute first species to walk - which is a perfectly reasonable observation. Considering speciation and the nature of the tree of life to branch, Titaalik may not even be a direct ancestor of all tetrapods, but a very closely-related cousin of that ancestor.

    Also, ID would not predict such a thing anyway. It accounts for the presence of footprints just as it accounts for their absense. As a theory in it's own right, ID provokes no such prediction. Unless of course you are simply going by the 'ID position' that 'ToE is wrong', and that is precisely the point. ID advocates do no actual science themselves, they simply try to undermine ToE. But, as we've already established, you do not validate your theory by attacking alternative theories. You theory has to stand on its own.

    ""ToE would not have been toppled."

    Which should make your skin crawl. This is just Dice in the Gaps. Something to consider."

    But it didn't topple. And what do you mean by Dice in the Gaps, btw?

    ReplyDelete
  55. (cont)

    "This again is Because Y, therefore X is the cause. If Evolution is correct then it would be correct whether or not #2 underwent fusion."

    I'm not sure I follow. If no human chromosomes showed any sign of fusion, then how could we explain the disappearance of a chromosome pair? It would, at the very least, have been an incredibly awkward, 'inconvenient' fact which potentially belied everything we thought we understood about common ancestry.

    But it was not. It led us to make a specific, surprising prediction, which was then validated.

    "Given empirical testing we know fusions occur. So finding a fusion event in humans does not rule out a designer. We just haven't found the evidence yet. And so ID is not toppled."

    True. This discovery does not topple ID. But nothing topples ID. ID can account for any data at all. This is ID's flaw - it can account for anything, therefore it predicts nothing. It is scientifically barren. 'Humans and apes have different numbers of chromosomes? The designer made them that way. Humans have a fused chromosome pair? The designer made them that way.' This is not a productive, explanatory scientific theory, it is a catch-all, retrospective explanation. An excuse. Unfalsifiable, untouchable, useless.

    "What both theories are lacking is a proper prediction. And while you fear that ID may lead to stagnation, I'm thrilled with them being about as they cured the stagnation under Darwin."

    Cured the stagnation under Darwin? I have no idea what you are referring to here. The Theory of Evolution via Natural Selection has been a productive, predictive scientific theory for 150 years. It has revolutionised our understanding of biology.

    a) When was there ever a time when it stagnated?
    b) What do you imagine ID has done to combat this stagnation?

    I will concede that ID (and it's endless quarrel with ToE) has helped to thrust the 'debate' into the public consciousness. But that is not the same thing. In the halls of academia - to the people who actually DO science, ToE has never failed to be productive.

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  56. Neal -

    "That's incorrect unless you define a scientist as only those that are evolutionists. That's the usual route."

    That's because practically all of them are. Only the crackpot religious fundies who've managed to swindle themselves a degree somehow are not.

    "Some Darwinian activists have an agenda to impose censorship on students by bluffing that there is no scientific controversy over neo-Darwinian evolution."

    No, Neal, there really ISN'T a debate between scientists about the fact of evolution. You can give a Creationist a degree and dress him in a lab coat, but if what he is advocating is not science, then he is no scientist.

    "Yes, life is not only too complex to have evolved but it displays immense specified complexity."

    SHOW us that life is TOO COMPLEX to have evolved.

    "A snowflake? No An ice sculpture of Mickey Moose in front of a 4 star hotel? Yes, designed. That's the difference."

    Lol at Mickey Moose...

    But why is an ice sculpture a more apt metaphor? Looking closer at the minute intricacies of the cell is akin to looking closer at the minute intricacies of a snowflake.

    "That you would even make the comparison is an absolute hoot. Other evolutionists bring up water and the carving of the Grand Canyon. Could acceptance of evolution by you and these others really be that silly simple or is your bias just making you blind to the obvious?"

    Bluster and rhetoric. If I'm so wrong, then explain why. Don't just talk yourself us with this verbal chest-drumming. Put your evidence where your mouth is.

    ReplyDelete
  57. I'm wondering where I can see the ID/creation literature that specifically predicts the discovery of p53, and that it would turn out to be more complex than originally thought.

    Anyone?

    ReplyDelete
  58. badwiring said...

    Thornton,

    I assume that this forum is unmoderated, and I assume that's why you're here. You lack the ability to discuss matters as a well-raised adult.

    (snip the rest of the puerile excuse making)



    LOL! Another ignorant Creationist who got called on his bluster, then whines and makes excuses as he heads for the exit.

    Pity you couldn't be bothered to learn even the least thing about the solid science you are criticizing. Oh well, almost no Creationists will. The people who do take the time to study and learn, they're called scientists.

    ReplyDelete
  59. "I'm wondering where I can see the ID/creation literature that specifically predicts the discovery of p53, and that it would turn out to be more complex than originally thought."

    That's not how it works. You have to tell them what the data is, and then they'll tell you why ID predicted it. I mean what good is a prediction if it might turn out to be wrong?

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  60. "That's not how it works. You have to tell them what the data is, and then they'll tell you why ID predicted it. I mean what good is a prediction if it might turn out to be wrong?"

    It gets even better - they know ID would have predicted it NO MATTER WHAT THE DATA IS.

    After all, we can't have 'scientific' theories making falsifiable claims or anything, now can we?

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  61. "Regarding first life. Yes it was immensely complex too."

    Neal, how do you know that?

    ReplyDelete
  62. Venture Free and Ritchie, of course you're right about ID predictions but I thought I'd give the IDiots a chance. :)

    ReplyDelete
  63. Ritchie said, "Looking closer at the minute intricacies of the cell is akin to looking closer at the minute intricacies of a snowflake."

    Seriously?

    "The term "specified complexity" was originally coined by origin of life researcher Leslie Orgel to denote what distinguishes living things from non-living things:

    In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity." - wiki

    ReplyDelete
  64. But I'm not claiming crystals are alive, am I? I'm claiming they are complex.

    And the closer you look, the more complex you find out they are.

    Just like the cell.

    ReplyDelete
  65. Ritchie, Are you saying a crystal or snowflake is as complex as a cell? Do they impress you as much as a cell does?

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  66. Ritchie:

    The snowflake is different than a cell because a snowflake does not have lot of different stuff in it. A cell has lots of different molecules. And the shape of a snowfalke can be explained by looking at the shape of the molecules. Nothing in chemistry or physics can account for a cell.

    ReplyDelete
  67. The whole truth said...
    "Regarding first life. Yes it was immensely complex too."

    Neal, how do you know that? "

    --

    What is the minimum number of genes essential for cellular growth? What is the minimum cellular structure necessary for a living, reproducing organism? What is the minimum number of proteins in this cell?

    Immensely complex.

    Blue-green bacteria utilizes quantum mechanics to achieve extremely efficient energy transfer. How far back in the fossil record does blue-green bacteria go?

    http://discovermagazine.com/2009/feb/13-is-quantum-mechanics-controlling-your-thoughts

    http://www.nature.com/nphys/journal/v6/n6/full/nphys1652.html

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  68. Fil -

    "Ritchie, Are you saying a crystal or snowflake is as complex as a cell? Do they impress you as much as a cell does?"

    No, not necessarily. My point was the more closely you look at a snokflake the more complex you realise it it - much like a cell.

    Yet no matter how complex you discover the snowflake to be, you wouldn't attribute it to being crafted by the hands of magical beings.

    So why apply that argument to the cell?

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  69. Functionality is irrelevant?

    ReplyDelete
  70. nat -

    "The snowflake is different than a cell because a snowflake does not have lot of different stuff in it."

    That is true. But I think you may have missed my point. See above post to Fil.

    "A cell has lots of different molecules. And the shape of a snowfalke can be explained by looking at the shape of the molecules."

    But can it? Maybe those explanations are all insufficient!! After all, they are based on the assumption that crystals are NOT physically arranged by a designer! This is a metaphysical assumption! A religious premise! The established theories about how crystals are formed are religiously biased rubbish! Religion drives science, and it matters!

    *sarcasm mode off*

    Now, have a really good read through that last paragraph and see if you can work out exactly why I'm wrong. And then consider Cornelius' arguments by the same measure.

    ReplyDelete
  71. Fil -

    It is only another dimension of complexity. I don't see why it should change the principles at all.

    ReplyDelete
  72. Ritchie said, "No, Neal, there really ISN'T a debate between scientists about the fact of evolution. You can give a Creationist a degree and dress him in a lab coat, but if what he is advocating is not science, then he is no scientist."

    --

    Recenty "after watching their pro-LSEA scientific peers testify about scientific problems with evolution, one anti-LSEA LSU biologist still had the audacity to testify before the House Education Committee that "there is no controversy among professional biologists about fact of evolution". When one representative asked him, "Did you hear the testimony of the other professors we had here that were speaking before this committee?," he fumbled in response. So please let me state plainly to you what is going on here: Some Darwinian activists have an agenda to impose censorship on students by bluffing that there is no scientific controversy over neo-Darwinian evolution."

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  73. Ritchie, we see snowflakes form, we can duplicate the process, we can clearly explain the process. If evolutionists could do the same, there would be no debate.

    Furthermore, there is a clear difference between complex structures and specified complexity.

    "The term "specified complexity" was originally coined by origin of life researcher Leslie Orgel to denote what distinguishes living things from non-living things:

    In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity." - wiki

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  74. Neal Tedford: "Ritchie, we see snowflakes form, we can duplicate the process, we can clearly explain the process. If evolutionists could do the same, there would be no debate. "

    Neal, we see snowflakes form, we can duplicate the process, we can clearly explain the process. If geologists could do the same with canyons, there would be no debate. No one has ever seen a grand canyon form, no one has made one in a lab. The best they can do is demonstrate microerosion.

    Religion drives geology, and it matters.

    Neal, Did you ever find the names of those two theologians who had an old-earth interpretation of Genesis prior to 1659? Or do you care to retract that claim?

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  75. Neal -

    "Recenty "after watching their pro-LSEA scientific peers testify about scientific problems with evolution, one anti-LSEA LSU biologist still had the audacity to testify before the House Education Committee that "there is no controversy among professional biologists about fact of evolution". When one representative asked him, "Did you hear the testimony of the other professors we had here that were speaking before this committee?," he fumbled in response. So please let me state plainly to you what is going on here: Some Darwinian activists have an agenda to impose censorship on students by bluffing that there is no scientific controversy over neo-Darwinian evolution."

    I have no idea what you are referencing here. Is this a quote? Who from? Is it your own testimony? In which case you'll need to be a bit more specific.

    In either case: 'There is a legitimate scientific controversy because I heard one guy brow-beaten for a minute' isn't really cutting the mustard, is it? The only challenge to ToE comes from religious quarters - people who champion Creationism and ID because they cannot deal with letting go of their cherished belief that God somehow made the world, or at least had a hand in it. This is not science. This is religion. And it needs to stay out of science.

    "Ritchie, we see snowflakes form, we can duplicate the process, we can clearly explain the process. If evolutionists could do the same, there would be no debate."

    We CAN replicate the process. I refer you to Lenski and his E.Coli studies.

    The trouble is that whenever we do, Creationists and ID-ers start insisting that this is only an observation of MICROevolution, not MACROevolution, as if there is some great fundamental difference between the two.

    But there isn't. The only difference is that of scale. An expample of microevolution in action IS an example of macroevolution in action. And we have lots of them!

    If you don't accept this then refer to DC's 'microerosion vs macroerosion' point above.

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  76. Ritchie, Lenski's E. Coli is still very much E. Coli, dogs are still dogs, fruit flies are still fruit flies, and tomatoes are still tomatoes. There are barriers of exponentially increasing improbabilities of change that evolutionists are not dealing with in an open and scientifically critical manner.

    Also I quoted the Louisiana House Education Committee meeting twice for you. The first time included the link to the article.

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  77. "Lenski's E. Coli is still very much E. Coli, dogs are still dogs, fruit flies are still fruit flies, and tomatoes are still tomatoes."

    God I wish I had a penny for every time I heard this one. And it's still as lame as ever.

    Of course it's still E.Coli. What else do you expect it to be? But now they are twelve different strains of E.Coli. This is speciation!

    "There are barriers of exponentially increasing improbabilities of change that evolutionists are not dealing with in an open and scientifically critical manner."

    What are these barriers? I believe I've asked you this before. Why do the improbabilities of change exponentially increase? Where are these barriers drawn? Please, please attempt to answer. I really want you to address this. This is somethnig you've been smacking your head against again and again. Please, please, answer this in as much detail as you can. What are these barriers? EXACTLY how do they limit the amount a genepool can change, and, if possible, why?

    "Also I quoted the Louisiana House Education Committee meeting twice for you. The first time included the link to the article."

    I beg your pardon, you did indeed.

    And it's the personal testimony of an ID advocate.

    Rock solid evidence there then. You're essentially taking an ID advocate's word for it.

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  78. Jquip: What both theories are lacking is a proper prediction. And while you fear that ID may lead to stagnation, I'm thrilled with them being about as they cured the stagnation under Darwin.

    Theories are explanations for observed phenomena. A theory's predictions represent assumptions of what we should observe if a theory's prediction is true, in reality. However, this means that predictions can be no better than our current day best explanations for other phenomena that might impact these observations.

    As such, a theory's predictions are vulnerable to things we have yet to discover. As such, we cannot evaluate a theory's predictions in isolation from it's underlying explanation.

    To elaborate, explanations are not all encompassing. They represent a link in a chain of hard to vary assertions about reality. Our current version of a theory may posit it's "link" fits at a particular location and spans a particular distance. However, this is based on current assumptions about the links before and after it. As such, our lack of knowledge about these surrounding links doesn't necessarily falsify the theory's underlying explanation for the phenomena in question. Nor does science claim to know these things with the certainty being implied.

    So, again, it's unclear how one can interpret a theory's prediction in isolation from its explanation.

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  79. Scott said, "...our lack of knowledge about these surrounding links doesn't necessarily falsify the theory's underlying explanation for the phenomena in question. Nor does science claim to know these things with the certainty being implied.

    --

    Yet evolutionists consider evolution a settled fact. It is not allowed to be falsified. It must have happened because it is the only explanation allowed. Yes, I know the silly difference evolutionist make between the fact and the theory. LOL. The evolutionist see's a botanist grow bigger tomatoes and sees in that rock solid and settled evidence that man evolved from a warm little pond. Twelve strains of E. Coli settles it. And they wonder why after 150 years of such quack science hardly a quarter of the population actually buys it.

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  80. Tedford the idiot said...

    Yet evolutionists consider evolution a settled fact. It is not allowed to be falsified.


    Sure it can be falsified idiot, we've even listed for you ways to do it. It just hasn't. Feel free to try.

    It must have happened because it is the only explanation allowed.

    Wrong again idiot. If you have a better explanation for all the empirical observations, one that's more parsimonious, more consilient across all scientific disciplines, more logically consistent, and makes better predictions than the current theory then let's hear it.

    Yes, I know the silly difference evolutionist make between the fact and the theory.

    It's obvious you don't.

    The evolutionist see's a botanist grow bigger tomatoes and sees in that rock solid and settled evidence that man evolved from a warm little pond. Twelve strains of E. Coli settles it.

    We see again the fat-headed pastor's total "understanding" of evolutionary theory.

    And they wonder why after 150 years of such quack science hardly a quarter of the population actually buys it.

    That's only true in the US where religious fundamentalism still adversely affects science education. The rest of the educated world overwhelmingly accepts ToE.

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  81. Neal, you didn't really answer my question about first life:

    "Neal, how do you know that?"

    There are two possible answers. You were there, or you learned it from discoveries made by science. The same science you dismiss when it's convenient.

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  82. Neal -

    Please, please get back to me on the issue of these barriers to genetic drift...

    I REALLY want to know.

    Unless you're quietly coming to the realisation that THERE AREN'T ANY of course...?

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  83. Ritchie:

    We don't need a designer to explain a snowflake. The laws of chemistry are enough. The laws of chemistry are not enough to explain a car, or a piece of flint with a sharp edge, or a some rocks inside a cave arrainged in a circle. Same thing with a cell.

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  84. Ritchie:

    When there is a series of mutations that provide a benefit for an organism, there are often side effects that accumulate and counteract the benefits. Why wouldn't this same thing happen with genetic drift? Negative side effect accumulate.

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  85. nat -

    "We don't need a designer to explain a snowflake. The laws of chemistry are enough. The laws of chemistry are not enough to explain a car, or a piece of flint with a sharp edge, or a some rocks inside a cave arrainged in a circle. Same thing with a cell."

    How is it the same thing with a cell?

    "When there is a series of mutations that provide a benefit for an organism, there are often side effects that accumulate and counteract the benefits. Why wouldn't this same thing happen with genetic drift? Negative side effect accumulate."

    What do you mean 'side effects'? If a 'beneficial' mutation has negative side effects which counteract the benefits, then on average it is not a beneficial mutation, is it?

    If a mutation is beneficial it helps the organism's chances of survival and reproduction, and is likely to be passed on and spread throughout the gene pool. If it hinders it, it will likely die out with it. I don't see why this is a difficult concept to grasp at all.

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  86. squid ink schuster said...

    When there is a series of mutations that provide a benefit for an organism, there are often side effects that accumulate and counteract the benefits. Why wouldn't this same thing happen with genetic drift? Negative side effect accumulate.


    Squiddy, a beneficial mutation by definition means the overall combined effects provide an increase in the animal's evolutionary fitness.

    Once again, you go out of your way to butcher a simple concept.

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  87. Ritchie:

    We can't explain the complexity of a cell with just the laws of chemistry. Its has to oome from someplace.


    Thorton and Richie:

    We are talking about genetic drift, which, in my understanding does not involve a benefit. In a series of mutations, whether there is a benefit or not, there may be side effects that are harmful. Eventually, the side effects accumulate, and the harmfull effects cancel any benefit.

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  88. squid ink schuster said...

    We are talking about genetic drift, which, in my understanding does not involve a benefit. In a series of mutations, whether there is a benefit or not, there may be side effects that are harmful. Eventually, the side effects accumulate, and the harmfull effects cancel any benefit.


    Congratulations squiddy. You've managed to produce an understanding of genetic drift that is almost, but not quite, entirely unlike the scientific one.

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  89. nat -

    "We can't explain the complexity of a cell with just the laws of chemistry."

    Of course there is always more to discover. That is what science is all about. If we had all the answers wrapped up we wouldn't need to do any more investigating, would we?

    As such the 'laws of chemistry' are always being tweaked and modified in accordance with new evidence. As such, science grows and gets progressively more accurate.

    Yes, there are mysteries in science. There are, and probably always will be. But this is not evidence that our existing theories are wrong. That's Cornelius' little curveball.

    A scientific theory is a framework for future research.

    "Its has to come from someplace."

    This is a seperate point. And while true, notice we are not talking about ToE anymore. We are talking about abiogenesis. Which is a seperate, yet related, theory. You could prove without a shadow of a doubt that the first replicating cell appeared at the snap of God's almighty fingers and that would still say nothing about the veracity of ToE. Evolution only kicks in once the first self-replicator exists. It does not speak to its origins.

    "We are talking about genetic drift, which, in my understanding does not involve a benefit."

    Take two samples of a same species. Keep them apart (that is, allow no gene flow between them) and they will eventually drift apart genetically. Each sample is evolving, that is, in each gene pool, only beneficial (and neutral) mutations are being added, but in different ways. Different beneficial (and neutral) mutations are being added to the mix, and the two gene pools become less and less alike. They drift further apart from each other.

    "In a series of mutations, whether there is a benefit or not, there may be side effects that are harmful. Eventually, the side effects accumulate, and the harmfull effects cancel any benefit."

    I have to agree with Thornton here. You are making this far more complicated than it is with some rather twisted reasoning.

    Take a species sample. Add a mutation to the gene pool. This mutation is, on balance, beneficial. It might also include limitations or 'side effects' (and I'm only guessing what you mean by this), but if the 'side effects' outweigh the benefits, then it isn't a beneficial mutation. It is a harmful mutation. So the gain must outweigh the cost.

    Then add another beneficial mutation. Again, the benefit has to outweigh the 'side effects'. What happens to the gene pool? It improves. Even though the 'side effects' accumulate.

    If the 'side effects' ever accumulated in a way that cancelled out the benefits, then that would add up to an non-beneficial feature overall and it would be selected against.

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  90. I understand that the research shows that even in a series of beneficial mutations, there are side effects that are harmful. These can accumulate to the extent that the increase in fitness diminishes. Eventually the increase in benefit will beomce zero. This is due to the increasingly harmful side effects. If the mutations provide no benefit, then the negative effects wil be even more pronounced. This may very well means that there is a limit to how many mutations, beneficial or otherwise, an organism can tolerate, which means there is a limit to how far evolution can go.

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  91. Nat -

    Isn't your objection is entirely hypothetical?

    Hats off to you for trying - Neal won't even GUESS at a possible limit to genetic drift.

    But I really don't think your hypothesis holds. For one thing, why would the negative 'side effects' of new mutations acculumate while benefits did not?

    Again remember - natural selection weeds out the harmful mutations from the beneficial ones. So only advantageous (or, at least, neutral) mutations survive to be spread throughtout the gene pool...

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  92. To Natchuster.
    With regards to chemistry and physics explaining the cell.
    As was mentioned in the OP, p53 mainly acts as a transcription factor and initiates transcription of hundreds of genes.
    Do you think chemistry/physics can explain this?

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  93. squid ink schuster said...

    I understand that the research shows that even in a series of beneficial mutations, there are side effects that are harmful. These can accumulate to the extent that the increase in fitness diminishes. Eventually the increase in benefit will beomce zero. This is due to the increasingly harmful side effects. If the mutations provide no benefit, then the negative effects wil be even more pronounced. This may very well means that there is a limit to how many mutations, beneficial or otherwise, an organism can tolerate, which means there is a limit to how far evolution can go.


    Didn't you make this same stupid argument just a few weeks ago? And wasn't it explained to you that the above condition, asymptotically approaching a limit to maximum fitness, only applies in a fixed, unchanging environment, something you never get in the real world?

    Is there a reason you keep repeating this stupidity? Are you hoping everyone will get tired of responding to the same nonsense and you can declare victory by default?

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  94. Are you sure that we won't get an accumulation of negative side effects even in a changing environment? If you make random changes to any complex system, eventually you will cause serious damage. And I seem to recall that whether evolution can proceed beyond a certain limit because NS had limits. Was unresolved. Maybe I'm wrong.

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  95. In other words, the negative sides effects might have a cumulative negative effect no mattere what direction evolution moves in.

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  96. MrT:

    I understand that the function of P53 is not well known, so it is hard to tell. And I'm talking about the origin of the complexity of the cell, not the current function.

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  97. Ritchie: Looking closer at the minute intricacies of the cell is akin to looking closer at the minute intricacies of a snowflake.

    So looking at the intricacies of a human body is like looking at the intricacies of a snowman. Got it.

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  98. squid ink schuster said...

    Are you sure that we won't get an accumulation of negative side effects even in a changing environment?


    Yes. Selection weeds them out.

    If you make random changes to any complex system, eventually you will cause serious damage.

    No, not if the system has an adaptive feedback mechanism. Evolution is an adaptive feedback mechanism.

    And I seem to recall that whether evolution can proceed beyond a certain limit because NS had limits. Was unresolved.

    It was resolved, no such limit was identified. You 'remember' a lot of things that are flat out false. Funny about that.

    Maybe I'm wrong.

    You're wrong.

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  99. Fil -

    "So looking at the intricacies of a human body is like looking at the intricacies of a snowman. Got it."

    Ha. If you like.

    Would you conclude that a snowman has to have been intelligently designed because the exact shape and arrangement of every single crystal in every single snowflake that went into making the snowman is too improbable to make come about by mere chance?

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  100. Ritchie,

    I would say that the odds of finding a snowman that was there without being created would validate evolution.

    I would also say that the snowflakes that make up a snowman could be randomly chosen and the end result of a snowman would be the same, or close enough to make no difference. Try that with a human body.

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  101. But whenever you have a series of mutation beneficial or not a bunch of side effects accumulate, changing emvironment or not. The effect of these side effects might accumulte, and eventually prevent any further evolution. The negatve feedback mechanism will eventually kick in, and prevent any more evolution.

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  102. Although, I must admit my claim is unverifiable, never having examing every snowflake....ever...in detail.

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  103. squid ink schuster said...

    But whenever you have a series of mutation beneficial or not a bunch of side effects accumulate, changing emvironment or not.


    No squiddy. Whether the cumulative effects are positive, neutral, or negative depends entirely on the environment.

    The effect of these side effects might accumulte, and eventually prevent any further evolution.

    No squiddy. Negative mutations don't accumulate because if they are negative (WRT fitness) in their particular environment, selection will tend to eliminate them.

    The negatve feedback mechanism will eventually kick in, and prevent any more evolution.

    What negative feedback mechanism is that squiddy? Describe it to me. You don't even understand what the term means.

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  104. Are you sure that negative side effects are only negative in one environment? The whole point of negative epistasis is that even beneficial mutations have negative side effects in the very same environment that they have a benefit in. These accumulate, and the negative effect increases. And the negative side effects will still be there even if the environment changes. The mutation might be one that effects the baic functioning of the organism. Too many of these, and it may prove fatal.

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  105. Neal: Yet evolutionists consider evolution a settled fact. It is not allowed to be falsified. It must have happened because it is the only explanation allowed.

    Let's break these claims down, shall we?

    01. Yet evolutionists consider evolution a settled fact.

    Again, I'd suggest that this is equivocation. Should some armchair scientist claim that evolution is True, with a capital 'T', they do not understand science, the problem of induction, etc.

    I think you'd agree that the existence of Christians who think abortionist should be shot and killed doesn't necessitate that Christianity mandates such behavior.

    Furthermore, this would be a "problem" for all fields of science, not just biology as Cornelius has yet to disclosed how we can actually know anything is True with a capital 'T'.

    Without a solution to the problem of induction, this is mere hand waving, by finding "fault" in evolutionary because it cannot meet some impossible criteria, which cannot be met by all other fields either.

    The funny thing is, Cornelius keeps dogging direct questions designed to clarify these very issues.

    02. It is not allowed to be falsified.

    Apparently, you can't tell the difference between a prediction of a scientific theory and the empirical mandate of prophecy. These are two different things, which you're either unwilling or unable to differentiate between. I've addressed this <a href="http://darwins-god.blogspot.com/2011/07/different-door-more-of-evolutions.html?showComment=1310587407332#c362496017475017838>elsewhere</a> in more detail.

    03. It must have happened because it is the only explanation allowed.

    First, see above. Unlike prophecy, "must have happened" isn't part of the scientific repertoire as you're implying. Second, the supernatural is implicitly anti-explanation. If "God did it", then no explanation is possible in principle, not just practice.

    That is, unless you're suggesting that God can be explained? Of course, this seems unlikely as God would become part of nature and no longer deemed worthy of worship.

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  106. squid ink schuster said...

    Are you sure that negative side effects are only negative in one environment? The whole point of negative epistasis is that even beneficial mutations have negative side effects in the very same environment that they have a benefit in.


    That's not even close to what the term negative epistasis means. Some of the things that come out of your mouth are just astounding, in a 'it's hard not to point and laugh' way.

    These accumulate, and the negative effect increases. And the negative side effects will still be there even if the environment changes. The mutation might be one that effects the baic functioning of the organism. Too many of these, and it may prove fatal.

    That's right squiddy. The more deleterious mutations the greater the chance the animal dies before it reproduces. The net effect is that the bad genes keep getting removed from the population. Keep trying. You've *almost* got your Creationist brain around how selection works.

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  107. So what does negative epistasis mean? My understanding is that it means there are negative side effects to even good mutations that confer a benefit. These side effects accumulate, and eventually cancel the benefits. Evolution stops. The only way to start it again is to change the environment and evolve in a different direction. But the negative side effects are still there. More mutations that will drive evolution in a different direction may continue to have negative side effects. Thses will accumulate no matter what dirction evolution proceeds in, eventually stopping evolution.

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  108. box of rocks schuster said...

    So what does negative epistasis mean? My understanding is that it means there are negative side effects to even good mutations that confer a benefit. These side effects accumulate, and eventually cancel the benefits. Evolution stops.


    Wrong, and once again I see you're too lazy to do a 10 second Google search to try and educate yourself.

    Epistasis is when the effect of one gene is modified by its interaction with one or more other genes. Negative epistasis is when two or more genes which are by themselves are not harmful WRT to evolutionary fitness combine to produce a negative (reduced) overall effect on fitness.

    From Wiki on epistasis

    "Negative epistasis and sex are thought to be intimately correlated. Experimentally, this idea has been tested in using digital simulations of asexual and sexual populations. Over time, sexual populations move towards more negative epistasis, or the lowering of fitness by two interacting alleles. It is thought that negative epistasis allows individuals carrying the interacting deleterious mutations to be removed from the populations efficiently. This removes those alleles from the population, resulting in an overall more fit population."

    Selection tends to remove the bad genes, just as I told you earlier.

    The only way to start it again is to change the environment and evolve in a different direction. But the negative side effects are still there. More mutations that will drive evolution in a different direction may continue to have negative side effects. Thses will accumulate no matter what dirction evolution proceeds in, eventually stopping evolution

    Er...no. So wrong and dumb I don't even know where to start.

    Do you enjoy being such a willfully ignorant tool? I assume you must.

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  109. Sometimes there are negative side effects, even if there is a benefit. Evolution is a trade off.
    The increase in fitness is bigger than the negative side effect. But the side effects accumulate. So, due to negative epistasis, evolution eventually comes to a halt, because the negatives outweigh the benefits. The only conceivable way to get evolution going again is to change the environment. But the negative side effects are still there, and maybe continue to accumulate. So, even sooner than before they will overcome the benefits of the new mutations.
    If the negative side effects dammage the basic functioning of the organism, then I would expect to see negative effects in whatever direction evolution proceeds.

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  110. Have we reached the point in our discussion where just call me ignorant, stupid, disingenuous, without telling me why? Then I guess it's time to stop.

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  111. natschuster: "Have we reached the point in our discussion where just call me ignorant, stupid, disingenuous, without telling me why?"

    Thorton has been telling you WHY you're wrong on this particular issue for weeks. The reason you get called stupid, disingenuous, and other things is because you keep saying things like "Have we reached the point in our discussion where just call me ignorant, stupid, disingenuous, without telling me why?

    For what it's worth, I think you're either stupid or disingenuous, not necessarily both. (although I can't completely rule out that you're both)

    It is truly amazing to see a fellow human being, especially one who claims to be a teacher, struggle with such a simple concept.

    If an organism was born with a mutation that gave it the ability to shoot lasers out of its eyes, paralyze its pray by thought alone, and to become completely invisible to it's predators but caused it to drop dead five minutes before it reached reproductive age, this would be a negative trait overall, and obviously would be selected against.

    If a trait conveys an advantage overall, it is selected for, no matter what negative aspects it has. If a trait conveys a disadvantage overall, it is selected against, no matter what positive aspects it has.

    This is the important part; pay attention:

    The instant that a trait (or group of traits) convey a disadvantage, no matter how slight, they will be selected against and removed from the population.

    Mutations that have an overall disadvantage do not accumulate over time.

    Could we possibly say this any more simply?

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  112. squid ink schuster said...

    Sometimes there are negative side effects, even if there is a benefit. Evolution is a trade off.
    The increase in fitness is bigger than the negative side effect. But the side effects accumulate. So, due to negative epistasis, evolution eventually comes to a halt, because the negatives outweigh the benefits. The only conceivable way to get evolution going again is to change the environment. But the negative side effects are still there, and maybe continue to accumulate. So, even sooner than before they will overcome the benefits of the new mutations.
    If the negative side effects dammage the basic functioning of the organism, then I would expect to see negative effects in whatever direction evolution proceeds.


    OK, so you refuse to read about or learn what negative epistasis actually means, then just mindlessly repeat the same unadulterated bullcrap.

    Have we reached the point in our discussion where just call me ignorant, stupid, disingenuous, without telling me why? Then I guess it's time to stop.

    I've been telling you WHY for months with virtually every post, as others have too. You've ignored every post trying to correct your misunderstandings.

    When you continually act willfully ignorant, stupid, and disingenuous, why are you surprised when you get called on the behavior?

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  113. I read up on negative epistasis. As best as can figure, it means that there are negative side effects that accumulate. The research shows that fitness benefits of mutations decrease with each beneficial mutation becuase of the accumulation of the negative side effects. The negative effects do not lead to extinction, because the positive effects outweigh them. But the negatve effect, increase, acumulate, and become more pronounced. This eventually cancels out the fitness benefits, and evolution stops.

    Sickle cell disease is caused by a mutation that has a benefit, resistance to malaria. But it has a side effect, it is often fatal. But it didn't lead to extinction because he benefit outweighs the negative effect. But add another mutation with a negative side effect, and yuo m ight get really big problems.

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  114. DC:

    A mutation can have an overall advantage, with a negative side effect, so it will be selected for. The next mutation has a benefit, but a negative side effect as well. Since the negative effect is amplified the overall benefit is less, and the oncrease in fitness is less. With the third mutation, for example, the negative effect is so great that it cancels out the benefit. Evolution stops. The overall negative effect of any one mutation is not enough to stop evolution. Its the cumulative effect.

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  115. DC:

    I'm not talking about mutations that have an overall disadvantage accumulating. I'm talking abut how each individual mutation is selcted fro because there is an overall advantage, until the negative side effects acumulate, and out weigh the advantages. This is, as best as I can figure, what negative epistasis means, and why t puts a limit on evolution.

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  116. nat -

    I'm still confused. If each single mutation is, on balance beneficial, then why do you imagine these negative 'side effects' accumulating and not the benefits?

    If you picture a string of single mutations, and the benefits of each outweigh the side effects, then the side effects will never outweigh the benefits no matter how many mutations you add.

    Imagine each beneficial mutation has a benefit (+3) and a negative side effect (-1). Overall score = +2. A positive number. Add another (+3 and -1) and you get 4. Add another, 6. Another, 8. You will ever get a negative number. Infact the overall score will never decline, or even level off. It will keep growing - despite the fact that the 'negative side effect' score accumulates, because it is more than compensated for by the positive score (the benefits) accumulating too.

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  117. natschuster said...

    I read up on negative epistasis. As best as can figure, it means that there are negative side effects that accumulate.


    Bullcrap. Where specifically did you read that?

    The research shows that fitness benefits of mutations decrease with each beneficial mutation becuase of the accumulation of the negative side effects.

    Bullcrap again. What research said that? If you're talking about the recent Cooper paper that showed the diminishing returns effect of combined beneficial mutations, it said nothing about the accumulation of negative side effects. You're pulling that straight out of your rectum.

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  118. This is from the scienc daily review.

    "It was found that the beneficial mutations allowing the bacteria to increase in fitness didn't have a constant effect. The effect of their interactions depended on the presence of other mutations, which turned out to be overwhelmingly negative."

    What does this mean? The mutations interfer with each other. This is a negative side effect. This might still happen venif yuo change the environment.

    Ritchie:

    The paper sighted above show that the negative effects do increase. The whole art of engineering is balancing costs versus benefits. Wehn you add a feature to anything, there always a cost. Y'know, "no free lunch." As you add features to anything, the costs increase and multiply. Why should organisms be different?

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  119. http://www.nature.com/ng/journal/v37/n11/abs/ng1660.html

    This is an example of what I mean.

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  120. nat -

    "The whole art of engineering is balancing costs versus benefits. Wehn you add a feature to anything, there always a cost. Y'know, "no free lunch." As you add features to anything, the costs increase and multiply. Why should organisms be different?"

    They are not different. Every feature will have a cost. A tortoise's mutation to develop a thicker shell means they must acquire the extra minerals, calcium, etc., that go into producing the extra-thick shell. It will also need to be slightly stronger to carry such extra weight, and so on.

    But what you are imagining specifically is a build-up of 'costs' which then prohibits further genetic diversification in any way - a build up of 'side effects' which renders ANY future evolution impossible. It is this which I do not accept, and do not understand why you do.

    In the case you reference above, what we have are two conditions each evolved to combat the same problem - malaria. However, when both occur in the same individual, they cancel each other out and leave the individual susceptible to malaria again.

    What does this mean in terms of natural selection? Well, it means that if malaria is a strong enough selection pressure then eventually, in the long run, we will see everyone in this population with either of the conditions - not neither and not both. If one of the conditions is, for some reason I can only guess at, more successful then the other, then that may become more commonly held and eventually drive the other extinct too. Or, perhaps more likely, we my end up with a divide in the population.

    But in no case I can conceive of will we end up with an end to genetic diversification.

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  121. squid ink schuster said...

    This is from the scienc daily review.

    "It was found that the beneficial mutations allowing the bacteria to increase in fitness didn't have a constant effect. The effect of their interactions depended on the presence of other mutations, which turned out to be overwhelmingly negative."

    What does this mean? The mutations interfer with each other. This is a negative side effect. This might still happen venif yuo change the environment.


    It is 'negative' only in that it made the beneficial ones taken together be less beneficial than each one applied separately. They were all still beneficial, just to a lesser degree. They were not negative AT ALL with respect to overall evolutionary fitness.

    An analogy would be you driving your car off the road and hitting a tree. Just wearing a seatbelt may improve your chances of surviving by 20%. Having an air bag may improve your chances of surviving by 20%. But having an airbag and wearing a seat belt may increase your chances of surviving by only 30%, not 40%. The effects are still beneficial but not directly cumulative.

    There's nothing in the paper or even the SD review at all about an accumulation of negative effects over generations. That's your pure BS spin.

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  122. They where beneficial, but they interfered with eacg other. That's a side effect.


    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002056

    And what about the case I linked above, about sickle cell disease and thalasemia?

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  123. natschuster said...

    They where beneficial, but they interfered with eacg other. That's a side effect.


    But it's not a side effect that reduces overall fitness, only makes it less beneficial.

    There are no accumulated negative effects, no matter how much you try and dishonestly misrepresent the results.

    And what about the case I linked above, about sickle cell disease and thalasemia?

    What about it? Each mutation by itself was beneficial, but epistasis reduced the effectiveness of having both mutations together to be effectively neutral.

    Still nothing about accumulated negative effects that lower fitness over generations.

    It's amazing how you latch on to a dumb idea that's completely opposite to what the research shows and just ride it into the ground. That's exactly why you come across as willfully ignorant, stupid, and disingenuous.

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  124. nat -

    re the malaria case, far from being a problem for evolution, this is an example of evolution.

    We have a selection pressure - malaria. Two solutions have arisen to defend against it. As it happens, the two solutions are also incompatible. If this was a strong selection pressure we would end up with a population that had one or other condition, but not neither and not both.

    This could potentially be the start of speciation - a gene pool splitting into two. A polulation divided by which of the two conditions it uses to combat malaria. These conditions could mutate, be added to and grow. In time these could become rather significant differences - significant enough to lead to speciation.

    In practice, of course, this is extremely unlikely to happen. Many tiny variances and divisions do not grow important enough to split species, genera and so on - but a few do. And besides, we humans travel so much that there is a lot of gene flow throughout the whole human race. There seems to be no genetic isolation to allow for a seperate human species. And besides, we usually combat malaria using medicines and treatments, so the disease is unlikely to become such a powerful selection pressure.

    But follow the principle. Imagine this is occurring in an animal population very much at the mercy of natural selection. Could it be the start of a species divinding into two? It just might.

    This is not a problem for evolution - this is evolution in action!

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