Saturday, August 14, 2010

Of Mice and Men: Unconserved Transcription Factors Binding

You probably learned in high school biology class that the new DNA data has powerfully confirmed evolution. Take any gene and it reveals differences between the species exactly as we would expect. And this sentiment is not limited to high school textbooks. As the Chair of a university Biology department once wrote to me, “DNA sequences provide an absolute and irrefutable record” that evolution is a fact. “Virtually every single gene sequence we examine,” he explained, “can be seen to be represented in closely related species and in more distantly related species with increasing numbers of nucleotide changes as we look at more distant species.” It was, he concluded, “absolute proof, in hard copy, reiterated in every single gene of every single organism.” That is an unfortunately common misrepresentation of the data but the story doesn’t end there. The DNA evidence has falsified several other evolutionary predictions.

Vast stretches of identical DNA segments are found in distant species. Multitudes of differences are found in the DNA of cousin species. Retroviruses that were so often considered to be junk now must be viewed crucial to evolutionary history if Darwin was right. These are some obvious surprises that DNA offered up to evolutionists, but there are more subtle contradictions. One of them, which shows up repeatedly, is the way DNA interacts with proteins.

Consider a recent study of how transcription factor binding is not conserved between mice and men. Transcription factors are proteins that bind to DNA and influence which genes are expressed (transcribed). You may recall that proteins are created by first transcribing genes. So in this complex regulatory network, genes are transcribed to create transcription factor which then return to regulate gene expression.

Evolutionists believe their theory is crucial to biology. Nothing in biology makes sense, they say, except in the light of evolution. We know what questions to ask and where to look only because we have Darwin’s powerful ideas guiding and motivating our research. But transcription factors in the mouse and human do not follow the evolutionary pattern.

Not only do these transcription factors often bind to retrovirus sections of DNA—which evolutionists so often considered to be nothing more than worthless junk—they also usually do not bind in the same DNA locations in spite of their importance. As one commentary explained:

Remarkably, they find that the genomic locations of binding sites for two key regulatory proteins (OCT4 and NANOG) are poorly conserved across species, despite their functional importance in mammalian embryonic stem cell biology. […]

Unexpectedly, only ~5% of binding sites for the two transcription factors OCT4 and NANOG were found in orthologous positions in human and mouse ES cells, suggesting major differences in genome-wide binding profiles between species.

And the story becomes even more contradictory with many of the binding sites were found in non conserved junk DNA:

Remarkably, many of these RABS [repeat-associated binding sites] were found in lineage-specific repeat elements that are absent in the comparison species, suggesting that large numbers of binding sites arose more recently in evolution and may have rewired the regulatory architecture in embryonic stem cells on a substantial scale.

Furthermore, even those genes with conserved transcription factor binding often revealed more detailed differences in the particular binding location:

However, among genes whose OCT4 dependence was conserved between human and mouse, most of the OCT4 binding sites identified were not directly conserved. Instead, the disappearance of a binding site in one species was compensated for by the emergence of a new binding site for the same transcription factor nearby.

The commentary concludes that these findings are consistent with other recent lineage-specific findings:

The notion that some regulatory networks have substantially changed in evolution is also supported by recent independent observations of lineage-specific network rewiring in vertebrate preimplantation embryos and adult liver tissue.

Of course there have been no observations of "network rewiring," lineage-specific or otherwise. This is yet another unfortunate misrepresentation of science. Yes, the new findings are consistent with other recent findings that species differ in subtle yet dramatic ways. But none of this was expected by evolutionary theory. As the paper explains:

Together, these results suggest that many genes have been rewired into the core regulatory network of human embryonic stem cells following the insertion of transposable elements.

So species-specific studies are required:

In contrast, OCT4 and NANOG have very different binding profiles in human and mouse embryonic stem cells, with only ~5% of their sites being homologously occupied. The fact that there is also a limited concordance between regions experimentally observed to be bound and conserved elements, as determined from multispecies sequence alignments, implies that in vivo maps in the relevant species will be important in the study of many mammalian systems. Moreover, to help explain the vast occupancy differences, we showed that species-specific transposable elements have been an important source of new sites in both species.

In other words, evolution doesn’t help explain the findings. What is remarkable is how evolutionists are able to fit even contradictory evidence into their thinking:

we were also able to identify a group of human-specific target genes that show evidence of having been added to the core regulatory network of human embryonic stem cells via the insertion of transposable elements. Although we do not expect all binding events to directly influence gene expression, this data adds important support to a seminal hypothesis on the impact of repeats on the evolution of transcription regulation.

A seminal hypothesis? That is how evolutionists describe unfounded speculation that invokes serendipity to explain unexpected findings.

Genes added to the core regulatory network via the insertion of transposable elements? This is a remarkable example of how evolution has compromised both science and the peer review process. They conclude:

Our results reveal the striking plasticity of the core regulatory network of mammalian embryonic stem cells and the importance that transposable elements have had in facilitating this functional turnover.

This is what happens when evolution is mandated as true. Religion drives science and it matters.

47 comments:

  1. Hmmmmmmmm , you know, Monsanto prides itself as being able to cross species barriers by inserting a fish gene for cold water tolerance into a plant for cold weather crop harvesting. Is it possible for Evolutionists to cross Information Truth barriers and insert evolution into the data ???

    As usual, good article, for which I have every confidence it will infuriate the blind faithful. Time and again various articles openly expose and shed light on brilliantly constructed machinery and mechanisms, then hijack those clearly designed systems for specific goal driven purposes and attached evolutionary word/terms giving "Emperor Charlie" full credit, yet never once attempting to show and prove how such how such machinery evolves in the first place. It just did.

    Quite simply the flavourite response is, "They Just Did".

    ReplyDelete
  2. Another interesting topic. But it may not be as outlandish as Dr Hunter would have us perceive it.

    For example:

    A seminal hypothesis? That is how evolutionists describe unfounded speculation that invokes serendipity to explain unexpected findings.

    The “unfounded speculations” can be found in the following references provided by the authors of the quoted paper:

    20. Davidson, E.H. & Britten, R.J. Regulation of gene expression: possible role of repetitive sequences. Science 204, 1052–1059 (1979).

    21. McClintock, B. The significance of responses of the genome to challenge. Science 226, 792–801 (1984).

    22. Brosius, J. Retroposons—seeds of evolution. Science 251, 753 (1991).

    ReplyDelete
  3. Cornelius Hunter: Vast stretches of identical DNA segments are found in distant species. Multitudes of differences are found in the DNA of cousin species.

    Yes. That's what makes it a nested hierarchy; common traits across an entire class, and differences between smaller groupings.

    Our results reveal the striking plasticity of the core regulatory network of mammalian embryonic stem cells and the importance that transposable elements have had in facilitating this functional turnover.

    Yes, regulatory structures are evolutionarily pliable. So?

    ReplyDelete
  4. Ah, more 50s nostalgia from Cornelius Hunter. In the last post he presented an 1850s understanding of evolution (once you recognize that there are these things called genes that outlive their owners, altruistic suicide to benefit kin, including offspring, is immediately understandable).

    Today we get a more "up to date" 1950s version. We have an understanding that there is this thing called DNA that gets passed down like Grandma's potato salad recipe. A good start. Unfortunately, there have been numerous advances since then, and this post even touches on some of these (maybe taking us into the 80s), but seems to describe them in such a way as to suggest an unfamiliarity with recent scientific understanding, as David noted above.

    "False friends" are words in two languages that look identical but have different meanings (similar to homographs, or sometimes homonyms, in a single language); "pain" in English or French is one example. Now imagine if there were only four letters in our languages, and we continued to use short words in each language. We would get many, many more false friends. Take it one step further, and say that our short words have variable spellings, so that in (a,b,e,l), "bale" and "ball" have the same meaning. Now we get even more false friends.

    Genes are thousands of letters long, so although we see convergent changes in nucleotides, we don't see false friends (complete convergence from widely separate origins) at the nucleotide sequence level for genes.

    However, the targeted binding sites for transcription factors that influence gene regulation are short strings (sometimes less than ten nucleotide letters) in this four letter alphabet, and often these transcription factors tolerate substantial sequence variablity.

    Two examples (Sean Carroll, Endless Forms Most Beautiful):

    tinman binding site = TCAAGTG
    dorsal binding site = GGGXXXXCCY, where X = A or T and Y = A or C

    With many hundreds to a few thousands of regulatory genes and binding sites on hand, there are many, many short strings that can influence regulation. A picked up piece of salvage sequence from a retroposon might be treasure, or might yield treasure upon mutation, or might lead to fatal error.

    Again we have a confirmation bias in the living world that needs to be recognized. We only see descendants of ancestors that successfully reproduced through an unbroken chain over billions of years. We know there must have been a viable great^1,000 grandmother; we forget about the weird great^1,000 uncle who failed to leave any offspring.

    This is the explanation for the substantial morphological differences we find in animals like chimps and humans that are very closely related (~97% nucleotide identity; 30% identical proteins).

    ReplyDelete
  5. John ,you seem to know a lot - how and why did first gene arise?

    ReplyDelete
  6. Thank God we are now learning the truth. I can see how biologists want to remove divine action from their studies. Physicists did this and have gained considerable credibility. However, physicists study mundane physical interactions. All these interactions were set by God when He created the universe and have not changed. It is possible therefore to devise simple mathematical formula. However, the biologists are fundamentally mistaken in thinking that they could explain all of life with its explosions of rapid diversity by static natural laws. We now have the evidence to with the only reasonable conclusion that God did it.

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

    ReplyDelete
  8. Peter, on the contrary, Quantum Mechanics seems to provide as good a proof of God’s existence as there is. I'm not saying that there's absolute proof but it is so weird that each physicist have their own opinion. My humble opinion is to keep an open mind.

    ReplyDelete
  9. Peter and Espagnat -

    Exactly how did you arrive at the conclusion that biology or quantum mechanics contain evidence for God? Is it indeed just God of the Gaps logic - "look, there's a mystery we haven't solved yet, it must be God." Because that has never turned out to be true yet!

    I wonder if you are so ready to 'keep an open mind' to magic or fairies or invisible pixies as explanations for observed phenomena. You know what they say about having a mind so open your brain falls out.

    ReplyDelete
  10. Ritchie

    "I wonder if you are so ready to 'keep an open mind' to magic or fairies or invisible pixies as explanations for observed phenomena. You know what they say about having a mind so open your brain falls out."
    =======================

    Wow Ritchie, stay out of the Arizona heat and take that glove off. You know, that Beatles "Blue Meanie Flying Glove" with the accusative pointing index finger and three pointing fingers back at you ???

    ReplyDelete
  11. Peter said:

    "I can see how biologists want to remove divine action from their studies. Physicists did this and have gained considerable credibility. However, physicists study mundane physical interactions. All these interactions were set by God when He created the universe and have not changed. It is possible therefore to devise simple mathematical formula. However, the biologists are fundamentally mistaken in thinking that they could explain all of life with its explosions of rapid diversity by static natural laws."
    ======================

    That's why there is a difference between hard sciences like astronomy, geology, physics, etc and the soft sciences like biology, anthropolgy, psychology , etc.

    Never underestimate the power of an Evolutionary Biologist's ability to keep things muddled, grey, fuzzy or blurred and demand that these are nothing more than the HARD FACTS as espoused and Sermoned by them from a grand standing soap box of an Academic Pulpit.

    Religious fogma and blind faith are powerful drivers for keeping the faithful in line.

    ReplyDelete
  12. Eugen: how and why did first gene arise?

    If I knew that, I'd be on a platform in Stockholm. Looking around, this is definitely not Stockholm.

    One focus of current origins of life research that certainly is promising is the RNA world hypothesis.
    If we think of genes as DNA sequences rather than associated RNA transcripts, I think we could say that reverse transcription to form DNA likely preceded transcription. RNA purines have been produced under realistic early Earth conditions, and it is possible that another nucleic acid (such as PNA) may have preceded RNA.

    That said, origins is a chemistry problem, and is largely outside of my knowledge base and literature focus. I think RobertC would know much more than I do on this subject.

    One comment, you asked "how" and "why;" to the scientist, these are really the same question. To get at the bigger picture why, you may need to reach outside of science.

    ReplyDelete
  13. Ritchie:

    IMHO the Gaps have gotten bigger, not smaller. They used to say that the Universe was infinitely old, so there was no need to invoke a creator. Now we know that the Universe had a beginning that requires an causal explanation. That' a Gap. They looked at the equations that describe the function of the Universe and discovered apparent exquisite fine tuning. And they used to believe in spontaneous generation of life from inanimate matter. Now we know that this can't happen. The origin of life is another Gap. And in Darwin's Day they though that cell where simple blobs of jelly, and heredity was controlled by highly malleable thingies called Gemules. Now we know the simplest cell is at least as complicated as a city. And the heredity is controlled by a phenomenal information processing system we call the genome. More gaps.

    And evolution relies a great deal on the argument that "God wouldn't do it that way," or "God didn't have to do it that way." So there is a lot "Evolution of the Gaps."

    ReplyDelete
  14. Eocene -

    Do you actually have a POINT to go along with your mindless childish simile?

    ReplyDelete
  15. natschuster -

    "In my opinion the gaps have gotten bigger, not smaller."

    I think I know what you mean. Back in the day we used to wonder at pregnancy and the seasons. Now it's black holes and abiogenesis. But the fallacy of God of the Gaps remains - just because you don't understand something, it does not justify concluding that your prefered guess is the explanation. This is true no matter the scale of the mystery.

    Also, you assert that we now know the universe had a beginning and requires a cause, that life cannot spontaneously arise, and that we have identified 'fine tuning'. In fact we do not know any of this. Do not take them as established scientific facts because they are not.

    And contrary to the claims of our blog host, evolution does NOT rely on any assumption of what God would or would not have done/created. It is a fallacy Cornelius cannot seem to free his thinking from and it is disappointing to see others picking it up.

    ReplyDelete
  16. Ritchie:

    I guess I shouldn't have said "we know." I should have said "the evidence indicates that things happened for which there is no good naturalistic explanation now."

    And I didn't say all evidence for evolution depends on the argument that "God wouldn't do it that way" but some does, e.g. junk DNA. Or the argument runs, "God didn't have to do it that way."

    ReplyDelete
  17. natshuster:

    And I didn't say all evidence for evolution depends on the argument that "God wouldn't do it that way" but some does, e.g. junk DNA.

    I think you have it backwards: Creationists have argued that noncoding DNA can’t be junk, because God wouldn’t have created junk. See, for example:

    ‘Junk’ DNA: evolutionary discards or God’s tools?

    http://www.answersingenesis.org/tj/v14/i2/junk_dna.asp

    ReplyDelete
  18. natschuster: And I didn't say all evidence for evolution depends on the argument that "God wouldn't do it that way" but some does, e.g. junk DNA. Or the argument runs, "God didn't have to do it that way."

    God only comes up when scientists talk informally (or in a few instances where the scientist in question has very strong religious convictions and cannot control himself or herself).

    The giraffe (like other mammals, including ourselves) has laryngeal nerve wiring that is better explained by evolution from a fish ancestor than it is by giraffes and fishes having separate origins (whether those origins are god-guided or naturalistic, it doesn't matter).

    The same is true for junk DNA; whether it is truly functionless or has weak function that is not critically dependent on sequence stability, all it proves is that natural selection does not have tight control over the entire genome. We've known that for a while now.

    But importantly, while clearly showing the limits of natural selection, these constraints on adaptation, in addition to the nested hierarchy and the specific predictions that have arisen from hypotheses about the hierarchy, are strong evidence that big-picture evolution has occurred.

    ReplyDelete
  19. I understand that Dawkins was very happy when Junk DNA was discovered because it meant that there was something that "God did it" doesn't explain well.

    ReplyDelete
  20. Could it be that the inferior laryngial nerve's path is the consequence of fetal development, and not a remnant of evolution? Just a thought.

    ReplyDelete
  21. natschuster: I understand that Dawkins was very happy when Junk DNA was discovered because it meant that there was something that "God did it" doesn't explain well.

    Dawkins writes for nonscientists, and is a vocal proponent of atheism, which is not a scientific topic. There are a few in the scientific community that think it unfortunate that the most prominent evolution writer is also one of the familiar exponents of atheism.

    ReplyDelete
  22. natschuster: Could it be that the inferior laryngial (sic) nerve's path is the consequence of fetal development, and not a remnant of evolution? Just a thought.

    The bizarre path of the recurrent (inferior) laryngeal nerve is indeed, in a proximal sense, a consequence of fetal development. The aorta migrates away from the pharyngeal region (where it first arises with a topology more like what we see in fishes) and toward the chest, the nerve goes with it. But this clumsiness is unnecessary. The superior laryngeal nerve services the same organ and does not suffer this strange and unnecessary entanglement. Even if you want to view this as "just a developmental issue" it speaks to a lack of oversight.

    Although this reaches its most ridiculous extreme in the giraffe, we see this same entanglement in all mammals, including humans. If all mammal species have separate origins, why would they all develop in this same, specific clumsy arrangement? Again, common descent of mammals from a fish ancestry provides a very good answer to this and other questions.

    ReplyDelete
  23. John said:

    "Dawkins writes for nonscientists, and is a vocal proponent of atheism, which is not a scientific topic. There are a few in the scientific community that think it unfortunate that the most prominent evolution writer is also one of the familiar exponents of atheism."
    =====================

    Spot on observation John. I agree.

    ReplyDelete

  24. Dawkins writes for nonscientists, and is a vocal proponent of atheism, which is not a scientific topic. There are a few in the scientific community that think it unfortunate that the most prominent evolution writer is also one of the familiar exponents of atheism.


    Doubtless true, but that doesn't mean he is wrong, does it?

    It may be unfortunate because it could well serve to enforce stupid people's association of the theory of evolution with atheism. The theory of evolution is not 'an atheistic theory' (whatever that might mean). Dawkins just happens to be both a leading expert on evolutionary biology and an atheist.

    And it doesn't mean there is a place for God in any kind of scientific field. There is no place for God in science. Unless you're a Creationist or ID advocate, in which case anything which can be spun or misrepresented to appear to support the existence of one is hailed as 'science' no matter how losely connected it is to the actual scientific method.

    ReplyDelete
  25. Espagnat

    did you read On Physics and Phylosophy ?

    ReplyDelete
  26. John

    While we are waiting on my buddy espagnat let me tell you that I think often about RNA world when I eat my minestrone soup. I do wonder how many spontaneous transcriptions are happening there. BTW I have good recipe for minestrone soup if somebody is interested.

    ReplyDelete
  27. Ritchie said,
    "I wonder if you are so ready to 'keep an open mind' to magic or fairies or invisible pixies as explanations for observed phenomena. You know what they say about having a mind so open your brain falls out."

    Rithchie, do you understand Quantum Mechanics well enough?
    If you do, then understand this, most quantum physicists are keeping an open mind because it's simply the smarter choice.
    Let me give you an intro to Quantum Mechanics.

    Quantum mechanics is astoundly successful and accurate as it plays an important role in the development of some of today's most amazing and important technologies, including lasers, transistors, microscopes, semiconductors, and computer chips.

    Yet it reveals a truly weird world of micro entities: entities that can be at two places at once, that can "travel" from here to the anywhere in an instant without traversing the space in between, that behave differently when observe.

    The interpretation of this weirdness will differ depending on the theoretical physicist you ask.
    In one, the world is not real until people look at it. In another, signals travel backwards in time to connect every particle in the universe.
    There's also one where multiple universes are created every moment.
    All interpretation have their skeptics because they cannot be proven.

    Bernard D'Espagnat, Professor Emeritus of Theoretical Physics at the University of Paris-Sudwho, suggests something different.
    For him, quantum physics shows us that reality is ultimately "veiled" from us. The equations and predictions of the science, super-accurate though they are, offer us only a glimpse behind that veil. Moreover, that hidden reality is, in some sense, divine. Along with some philosophers, he has called it "Being". For more details, refer to the link below.


    http://news.bbc.co.uk/2/hi/uk_news/magazine/7955846.stm

    ReplyDelete
  28. Thank you Espagnat. I was hoping a little you would be Bernard but I know he would not be on this forum.
    I wish some people would read little more about quantum physics and cosmology. It would help them understand how wierd is this stuff we are made of.

    ReplyDelete
  29. Espagnat -


    Rithchie, do you understand Quantum Mechanics well enough?


    There is, I believe, a rather famous quote that runs something along the lines of, "If you think you understand quantum mechanics, you don't understand quantum mechanics." The upshot, basically, being that quantum mechanics is fantastically complicated, counter-intuitive, and for the most part, unexplained.

    I feel I do have an appreciation that the world of quantum mechanics is phenominally bizarre and intricate - without, I confess, actually knowing too much about it in depth. Basically, it is a puzzle. What I reject is that this is therefore evidence for a divine being.

    The fallacy you are committing is of the God of the Gaps reasoning - that is, to come across a mystery, to account for it with a total guess, and then to claim the mystry is evidence for your guess because 'no-one has come up with a better explanation'. In fact, the only truly honest thing to do would be to conclude that it is a mystery and try to solve it, not claim it as evidence for a favourite guess.


    For him, quantum physics shows us that reality is ultimately "veiled" from us. The equations and predictions of the science, super-accurate though they are, offer us only a glimpse behind that veil. Moreover, that hidden reality is, in some sense, divine.


    See, here is where I think the bone of contention lies. Saying reality is 'veiled' from us, implies the existence of someone doing the veiling. Why not just say 'We don't understand this yet?'

    And the assertion that 'that hidden reality is, in some sense, divine', seems utterly unsupported, totally speculatory, and frankly logically irrational.

    ReplyDelete
  30. Ritchie, this is not a God of the Gaps argument and it's not based on total guess. The thrust of d’Espagnat’s work on experimental tests of Bell’s theorem. The theorem states that either quantum mechanics is a complete description of the world or that if there is some reality beneath quantum mechanics, it must be nonlocal – that is, things can influence one another instantaneously regardless of how much space stretches between them, violating Einstein’s insistence that nothing can travel faster than the speed of light. For more details refer to the link below.

    You stated that this is logically irrational, most quantum physicist agree with you on this but they also find other interpretation are just as logically irrational. Which is why, most of them are be humble in the face of these mysteries.



    http://blogs.discovermagazine.com/80beats/2009/03/16/quantum-physicist-wins-14m-templeton-prize-for-writing-on-veiled-reality/

    ReplyDelete
  31. Espagnat -

    You are leaping to far too many conclusions here. I think a little wishful thinking is colouring your interpretation of Espagnat's conclusions.

    D'Espagnat's argument is that quantum mechanics cannot describe the world as it really is - it can merely make predictions for the outcomes of our observations. If we want to believe, as Einstein did, that there is a reality independent of our observations, then this reality can either be knowable, unknowable or veiled. D'Espagnat subscribes to the third view. Through science, he says, we can glimpse some basic structures of the reality beneath the veil, but much of it remains an infinite, eternal mystery.

    For one thing, there is no indication that spirituality is a viable means to access this 'veiled reality'. There is nothing here to support the veracity of prayer, evelations, visions, etc.

    Worse, there isn't anything to support the Judeo-Christian concept of God. D'Espagnat's 'veiled God' is partially – but still fundamentally – unknowable. And thus it cannot be superimposed over the personal God attested to in the Judeo-Christian religions, or associated with any specific commandments, creeds or ethics.

    In layman's terms, d'Espagnat's work seems to hint (and not terribly convincingly, frankly) at the existence of a mostly unknowable 'something' outside of time and space which underlies quantum mechanics. Nothing about it validates the blind assumption that this is God.

    Finally, just a word on the Templeton Foundation. I find it curious that there is foundation at all specifically set up to try to harmonise science and religion. Doesn't that, in itself, suggest that such a conclusion is not self evident?

    And though the Templeton Foundation does, naturally, tend to fund scientists who are religious, it has flatly tried to disassociate itself with the scientifically vaccuous ID: "We do not believe that the science underpinning the intelligent-design movement is sound, we do not support research or programs that deny large areas of well-documented scientific knowledge, and the foundation is a nonpolitical entity and does not engage in or support political movements," said Pamela Thompson, Templeton Foundation spokesperson, in her letter to the LA Times. "In the past we have given grants to scientists who have gone on to identify themselves as members of the intelligent-design community. We understand that this could be misconstrued by some to suggest that we implicitly support the movement, but this was not our intention at the time, nor is it today."

    If an organisation as clearly religiously motivated as the Templeton Foundation sees no scientific credibility in ID, what does that say about it?

    ReplyDelete
  32. Ooops, forget to post a link for that final quote. Here it is:

    http://articles.latimes.com/2007/feb/04/business/fi-letters4.2

    ReplyDelete
  33. Ritchie

    you are all over the place here especially with the Judeo –Christian god thing.. It's not about that. Why don’t you instead study delayed choice quantum eraser experiment a bit and think what it means.

    ReplyDelete
  34. Ritchie,
    There's no wishful thinking on my part. It's more like a misunderstanding on your part.

    Following is my understanding which you can also research it at the link below from New Scientist.

    So what is it, really, that is veiled? At times d'Espagnat calls it a Being or Independent Reality or even "a great, hypercosmic God".

    "Independent Reality plays, in a way, the role of God – or 'Substance' – of Spinoza," d'Espagnat writes. Einstein believed in Spinoza's God, which he equated with nature itself, but he always held this "God" to be entirely knowable. D'Espagnat's veiled God, on the other hand, is partially – but still fundamentally – unknowable.

    I have never said that this "veiled reality", is an absolute proof of God for any religion. I'm just saying to keep an open mind and be humble.

    Let me relate a true story to you so that you understand my point.
    There's this atheist quantum physicist,who confided in me that he used to make fun of religious people, calling them idiots. However, after being spooked by quantum weirdness on a daily basis, he's convinced that the smarter choice is to be humble. Although he's still an atheist, he has learned to respect other people's faith.

    I've never said that you should believe d'Espagnat just because he won the Templeton prize. Therefore, we should not include the late Sir John Templeton's legacy in this debate. True d'Espagnat gain publicity by winning it, but his work has always been a hot topic among those who delve into quantum physics.

    http://www.newscientist.com/article/dn16769-concept-of-hypercosmic-god-wins-templeton-prize.html

    ReplyDelete
  35. Espagnat -


    I have never said that this "veiled reality", is an absolute proof of God for any religion. I'm just saying to keep an open mind and be humble.


    And I am not saying that Espagnat's research fails to provide proof for 'God' - I am saying it fails to provide any support at all for one.

    Your advice that I keep an open mind implies that you think I have closed my mind off to the possibility of there being a God. Let me assure you I have not. I deem it perfectly possible that a God exists. However there is a practically infinite number of things which might possibly exist. So how do we identify the ones which really do exist from the ones which don't? The logical answer, surely, is evidence (which is not the same as proof). The more evidence there is of something the more likely it is to really exist.

    Faith is a belief in something despite a lack of evidence for its existence.

    Now, I am an atheist because I do not believe in things for which there is no (or extremely scant, circumstancial, anecdotal, or otherwise just plain bad) evidence. And 'God' is extremely poor on the evidence front. And d'Espagnat's research does not help here - it does not provide anything in the way of supportive evidence.

    I really do try to keep a humble, open mind. Present evidence for practically any hypothesis and I will eagerly listen. But without evidence there is no compelling reason to think something is true.

    ReplyDelete
  36. you said:

    Faith is a belief in something despite a lack of evidence for its existence.

    You have strong faith in materialism even there is no evidence that materialism explains quantum non local effects.
    What materialistic explanation are you waiting for regarding quantum non local effects?Flying spaghetti monster?

    This illogical guy is so irritating. I'm going out for beer!

    ReplyDelete
  37. Ritchie,
    Picture this, quantum physicist have to consider the possibility that a cat could be made to be both dead and alive at the same time. Based on d'Espagnat research, this is determined by an unknown reality which is beyond the reach of empirical science.

    D'Espagnat also says that human intuitions in art, music and spirituality can bring us closer to this ultimate reality, but it is so mysterious we cannot know or even imagine it.

    "I believe we ultimately come from a superior entity to which awe and respect is due and which we shouldn't try to approach by trying to conceptualize too much," he said. "It's more a question of feeling."

    Although they cannot be tested, the intuitions people have when they are moved by great art or by spiritual beliefs help them grasp a bit more of ultimate reality, d'Espagnat said.

    I guess this is not the hard evidence which you are seeking but I have never said that there was absolute proof. Currently, there's no absolute proof for any interpretation of quantum physics. If you believe in d'Espagnat's veiled reality, you might also keep an open mind about his assertion on the importance of human intuitions in art, music and spirituality.

    http://www.reuters.com/article/idUSTRE52F2GC20090316

    ReplyDelete
  38. Eugen -


    You have strong faith in materialism even there is no evidence that materialism explains quantum non local effects.


    Unless we assume materialism then we would never get out of bed in the morning. Why assume our legs will work lie they did yesterday? Why assume you need to eat? Why assume we are not living inside the Matrix? Some thnigs you just have to take as red in order to get through the day.

    That does not justify making up whatever nonsense you like and claiming is as equally reasonable.


    What materialistic explanation are you waiting for regarding quantum non local effects?Flying spaghetti monster?


    I don't know. It is a mystery. That's that a mystery means. But what I am NOT going to do is make up some fanciful explanation (such as a flying spaghetti monster, or... say... God) and then insist that the mystery proves me guess correct under the logic of 'what else could it be? It's a mystery, so OBVIOUSLY the explanation is [insert nonsense here]).


    This illogical guy is so irritating. I'm going out for beer!


    You need more than that, my friend!

    ReplyDelete
  39. Espagnat -


    Picture this, quantum physicist have to consider the possibility that a cat could be made to be both dead and alive at the same time. Based on d'Espagnat research, this is determined by an unknown reality which is beyond the reach of empirical science.


    Okay. So...?


    D'Espagnat also says that human intuitions in art, music and spirituality can bring us closer to this ultimate reality, but it is so mysterious we cannot know or even imagine it.


    This is an assertion. Not evidence. How does he KNOW human intuitions in art, music and spirituality bring us closer to this ultimate reality? How could anyone know such a thing? How could we measure how close we are to an unknown 'reality', whatever that means?


    I believe we ultimately come from a superior entity...


    Notice his first two words - 'I believe...'. He is expressing his faith. This is not a conclusion of his research.


    I guess this is not the hard evidence which you are seeking but I have never said that there was absolute proof.


    Oh come on, let's be honest here - this doesn't just fall short of being 'absolute proof', or even 'hard evidence'. This falls short of being evidence of any kind. This is not evidence at all. These are the whismical meditations and unverifiable assertions of a religious man. Nothing more.

    ReplyDelete
  40. Ritchie,
    Finding evidence of God is like finding evidence of how reality really works, which is the currently the domain of quantum physics.
    Theoretical physicists employ mathematical models and abstractions of physics to come up with theories and interpretations so that it can be further applied in research and experiments.

    d'Espagnat's interpretation points out that the secret of reality is beyond the reach of empirical science. What does this mean? A quantum physics researcher is suppose to evaluate all interpretations and proceed with the next step.
    However, in this case if one can't use empirical science, what is the choice? d'Espagnat is asking them to think out of the box, beyond empirical science. An atheist might think it is weird to use spirituality, but in quantum physics, it is normal to be weird.

    I think I have said enough, even if you don't believe me, it doesn't matter

    ReplyDelete
  41. Espagnat -


    Finding evidence of God is like finding evidence of how reality really works, which is the currently the domain of quantum physics.


    We don't have any evidence of God.


    d'Espagnat's interpretation points out that the secret of reality is beyond the reach of empirical science.


    ie, God is unproveable. Therefore we can never take His existence as a fact, since we will never have evidence for it. Therefore it is thoroughly unreasonable to believe in Him.


    An atheist might think it is weird to use spirituality, but in quantum physics, it is normal to be weird.


    My objection is not that it is 'weird', but that we have absolutely no reason to think spirituality is an accurate way of acquiring knowledge about the world. It's like saying 'If science cannot tell us about the cause of the Big Bang, let's turn to a Magic 8 ball for our answers'.


    I think I have said enough, even if you don't believe me, it doesn't matter


    As you wish.

    ReplyDelete
  42. Ritchie,
    I'm merely asking for an atheist to be open and humble about the possibility that God might exist.
    There are many mysteries science cannot explain especially in quantum physics. Prior to d'Espagnat's discovery, the scientific community has never been confronted with a scientific explanation that in order to solve these mysteries in quantum physics, we have to think out of the box, beyond empirical science.

    This is all I have to say.

    ReplyDelete
  43. Espagnat -


    I'm merely asking for an atheist to be open and humble about the possibility that God might exist.


    Believe me, I am open to that possibility. I am also open to the possibility that Zeus exists, or that Allah exists, or that Vishnu and the Hindu pantheon exists, or that unicorns exist...

    But I won't actively BELIEVE in any of them until there is reasonable evidence.


    There are many mysteries science cannot explain especially in quantum physics.


    This is no evidence at all. We have faced scientific mysteries before, and solved them. And the answers have always turned out to be NOT magic/miracles/the handiwork of God.


    Prior to d'Espagnat's discovery, the scientific community has never been confronted with a scientific explanation that in order to solve these mysteries in quantum physics, we have to think out of the box, beyond empirical science.


    You extrapolate too far. D'Espagnat has not discovered the existence of a deeper reality - he is hypothesising one. It may well turn out to not really exist. But in any case 'thinking outside the box' does not translate to 'automatically claim God did it'.

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

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

    ReplyDelete
  46. Ritchie said:
    But in any case 'thinking outside the box' does not translate to 'automatically claim God did it'.

    I've never said that 'thinking outside the box' translate to 'automatically claim God did it'.
    I said we should heed d'Espagnat's personal advice that the human intuitions in art, music and spirituality can bring us closer to this ultlimate reality. Many quantum physicists have the same opinion but they are afraid that voicing it out publicly will affect their career. Established physicists like Brian Josephson have a Nobel prize which gives him the confidence to publicly discuss his interests in the paranormal and scold the scientific community for its skepticism.

    ReplyDelete