Saturday, February 11, 2012

Genes Have Play, Stop and Pause Buttons

You probably remember from biology class that genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. What you may not have learned is the elaborate regulatory processes that occurs before, during and after this sequence of transcription, editing and translation. Genetic regulation is fascinating and you can read more here, here, here, here, here, here, here, here, here, here, here, here, here, here, here and here.

Background: Post translation regulation

Regulatory processes are constantly at work in the cell, practically at all levels. Consider the enzymes in the glycolysis pathway which metabolize food intake. There are about a dozen such enzymes and they team up to break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. So like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP, spent ATP, or the intermediate products.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Background: Pre translation regulation

The regulation of protein enzymes discussed above is the last in a sequence of processes that regulate genes and their products. Just before this there are processes that regulate the very production of proteins.

For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed. And microRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo.

And MicroRNAs, like instructions of use, can come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production.

And while microRNAs regulate the production of proteins from the RNA transcripts, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off —is incredibly naïve.”

Background: Pre transcription regulation

The next step upstream is the regulation of the transcription process, which copies the DNA gene into an RNA transcript. This is done with the help of transcription factors—proteins that bind to DNA and influence which genes are expressed (transcribed). These transcription factors bind to special, short, sequences of DNA that are before or after the gene they regulate. In so doing the transcription factors influence the huge molecular machine known as RNA polymerase which opens the DNA double helix and makes the RNA transcript copy of the gene.

Exactly how the transcription factors influence the RNA polymerase machine is a complicated topic. Equally complicated is the question of how the transcription factors know when and where to bind to the DNA. One way is with the help of DNA methylation in which a small molecule (a methyl group) is added to the DNA macromolecule at particular locations. Like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on. This DNA methylation is accomplished via the action of a protein machine that adds the methyl group at precisely the right location in the DNA strand.

The methylation occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by protein machines as they move along the DNA. The protein machine binds to the DNA, twists the helix so the DNA base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the DNA base.

In bacterial studies it has been found that the short donor molecule does more, however, than just supply a methyl group. It also helps to control the protein. First, the short donor molecule binds to the pocket of the protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed.

Furthermore, the methyl group marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information. For instance, the methyl group can be hydroxylated. And of course a different molecular machine is required for that task, and the information of when and where to go to work is needed.

All of this makes for a complex DNA methylation pattern which is superimposed on the DNA macromolecule. In addition to the DNA macromolecule, methyl groups are also used to tag the histone proteins about which the DNA is wrapped. The histones have a hub, around which the DNA wraps, and a tail that sticks out on which chemical markers are attached. As with DNA methylation, these histone markers are signals for the protein machinery. And like DNA, these tags are removed as well. Such modifications and removal of these chemical tags means that these codes are dynamic, and there are protein inspectors that double-check these complex encodings.

In addition to methylation, histones can also vary by tiny differences in their amino acid sequence. This histone sequence variation serves as yet another type of tag used for gene regulation.

Furthermore, histone variants are not merely static sign posts that influence gene expression. These variants are moved, by other proteins, between different locations in the genome, resulting in migration patterns that occur in the embryonic development phases. DNA methylation can also be transmitted across generations.

And finally this transcription factor binding and methylation patterns are heavily context dependent. In spite of expectations to the contrary, the transcription factor binding sites are not well conserved across different species. In fact, divergence between transcription factor binding sites even shows up in very similar species, such as different species of yeast.

Furthermore the methylation patterns vary substantially across different regions of the DNA and between the two alleles of a given gene and this allele-specific methylation can be tissue-specific. In one type of cell a histone modification may turn off a gene whereas in another type of cell the same histone modification may turn on the gene. As one writer put it, the regulatory architecture has been rewired on a substantial scale. Another explained, these findings “hint at an unimagined complexity of the genome.”

New finding: A pause button

Regulation of genes and their products is complex and occurs at all levels. At the level of transcription where the DNA gene is copied, genes can be turned off and on. It is as though they have a start and stop button. But new research now shows they also have a pause button. That is, transcription factors can not only start and stop the RNA polymerase copy machine, they can also pause the machine after it has begun. And other transcription factors turn off the pause, so the transcription process may continue. This pausing function, which may allow for a more rapid response when needs arise, seems to be a general feature of transcription.

With each new research study we learn more about evolution’s capabilities. There is, of course, no question that evolution created all of these regulatory processes and mechanisms because evolution is well known to be a fact. What is not known is the extent of evolution’s capabilities. No one would have thought evolution could have produced such elaborate designs. But as science advances so too does our knowledge of this incredible process.

160 comments:

  1. Cornelius Hunter

    With each new research study we learn more about evolution’s capabilities. There is, of course, no question that evolution created all of these regulatory processes and mechanisms because evolution is well known to be a fact. What is not known is the extent of evolution’s capabilities. No one would have thought evolution could have produced such elaborate designs. But as science advances so too does our knowledge of this incredible process.


    Congratulations Cornelius! After a long streak of posting nothing but anti-science caca you finally produced an honest, truthful entry!

    Of course we both know it was completely accidental on your part, but it is a refreshing change from your normal vapid propaganda.

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    1. Thorton
      it seems you are not very brite. When you don't see Cornelius is being sarcastic.

      Delete
    2. cita

      Thorton
      it seems you are not very brite. When you don't see Cornelius is being sarcastic.


      Then you must be even less 'brite' (sic). You missed me being sarcastic in response to CH's failed attempt at sarcasm. You must be especially dense to miss my third sentence where I specifically pointed this out. Uncommonly dense in fact. :)

      Delete
  2. Hilarious last paragraph! Two wicked 'put downs' by any standards in two days. Yesterday, W J Murray starred on UD.

    ReplyDelete
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    1. Paul

      Hilarious last paragraph! Two wicked 'put downs' by any standards in two days. Yesterday, W J Murray starred on UD.


      Yeah, it's just hilarious! You IDiot clowns have no positive evidence for your claims, have no testable hypotheses, make no predictions, do no research, produce no results. But you're happy because you can do blustering empty 'put downs'.

      I suppose when you're as hopelessly inept as you IDiots any small "victory" is a cause to cheer.

      Delete
  3. OT: Dr. Hunter, though not directly related to transcription, you may find the following interesting to the overall information flow in the cell;

    Quantum physicist explains $100K offer for proof scaled-up quantum computing is impossible - February 2012
    Excerpt: It’s all a matter of decoherence he says, where the quantum parts of the computer must of necessity interact with those that are not.
    http://www.physorg.com/news/2012-02-quantum-physicist-100k-proof-scaled-up.html

    I guess part of the reason for the skepticism against 'scaled-up quantum computing' is because, despite huge investment, so far man's attempt at quantum computation is very modest,,,

    NIST Scientists Use Microwaves to Quantum-Entangle Two Ions for the First Time - August 2011
    Excerpt: We’re still many years away from the first functioning quantum computer the size of a building, much less the first one the size of a desktop computer or a smartphone,
    http://www.popsci.com/science/article/2011-08/nist-scientists-use-microwaves-entangle-two-ions-first-time

    Quantum Computing Promises New Insights, Not Just Supermachines - December - 2011
    Excerpt: Unfortunately, while small quantum computations have already been demonstrated in the lab, they typically fall apart after only a few dozen operations. That’s why one of the most-celebrated quantum computations to date has been to factor 15 into 3 times 5 — with high statistical confidence! The problem is decoherence: basically, stray interactions that intrude prematurely on the computer’s fragile quantum state, “collapsing” it like a soufflé. In theory, it ought to be possible to reduce decoherence to a level where error-correction techniques could render its remaining effects insignificant. But experimentalists seem nowhere near that critical level yet.
    http://www.nytimes.com/2011/12/06/science/scott-aaronson-quantum-computing-promises-new-insights.html?pagewanted=all

    Perhaps these researchers, if they are looking for actual proof that 'scaled up quantum computing' can actually be done, should look to DNA, where 'scaled up quantum computing', on a massive scale, is happening right before our eyes!

    Quantum Information/Entanglement In DNA & Protein Folding - short video
    http://www.metacafe.com/watch/5936605/

    Quantum Computing in DNA – Stuart Hameroff
    Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist).
    Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement.
    http://www.quantumconsciousness.org/views/QuantumComputingInDNA.html

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    1. Biophotons - The Light In Our Cells - Marco Bischof - March 2005
      Excerpt page 2: The Coherence of Biophotons: ,,, Biophotons consist of light with a high degree of order, in other words, biological laser light. Such light is very quiet and shows an extremely stable intensity, without the fluctuations normally observed in light. Because of their stable field strength, its waves can superimpose, and by virtue of this, interference effects become possible that do not occur in ordinary light. Because of the high degree of order, the biological laser light is able to generate and keep order and to transmit information in the organism.
      http://www.international-light-association.eu/PDF/Biophotons.pdf

      The Real Bioinformatics Revolution - Proteins and Nucleic Acids 'Singing' to One Another?
      Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see' and ‘hear' each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1 000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions. ,,, The same results were obtained when regulatory DNA sequences were analysed.
      http://www.i-sis.org.uk/TheRealBioinformaticsRevolution.php

      Also of related note:

      Quote from following video: 'I was in a body and the only way that I can describe it was a body of energy, or of light. And this body had a form. It had a head. It had arms and it had legs. And it was like it was made out of light. And 'it' was everything that was me. All of my memories, my consciousness, everything.' - Vicky Noratuk

      Coast to Coast - Vicki's Near Death Experience (Blind From Birth) part 1 of 3
      http://www.youtube.com/watch?v=e65KhcCS5-Y

      "Miracles do not happen in contradiction to nature, but only in contradiction to that which is known to us of nature."
      St. Augustine

      Verse and Music:

      Luke 23:43
      Jesus answered him, "I tell you the truth, today you will be with me in paradise."

      FFH - One of These Days
      http://www.youtube.com/watch?v=CHdSgQVIb5c

      Delete
    2. Amazing how unintelligent, nay, unintelligible, randomalution makes monkeys of the very brightest software designers, isn't it? Back to the lab Messrs Magoo.

      Delete
  4. SWEET! This is an awesome blog entry. It seems that the more we learn about the cell and DNA, the greater appearance it gives of being an extremely complicated mechanism and having been designed for a purpose.

    ReplyDelete
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    1. W. Butler

      SWEET! This is an awesome blog entry. It seems that the more we learn about the cell and DNA, the greater APPEARANCE it gives of being an extremely complicated mechanism and having been designed for a purpose.


      I highlighted the key word for you.

      The real issues are

      1) We know that naturally occurring evolutionary processes can produce extremely complicated mechanisms.

      2) We have zero evidence that any such observed mechanisms were produced or manufactured by any guiding intelligence, let alone for any asserted "purpose".

      Personal incredulity will never be a basis for scientific understanding.

      Delete
    2. Thorton,

      There really is no point arguing about it. If you want to insist that such a complex system can come about from random processes all you have to do is demonstrate an organism in the lab that initially does not have the DNA system evolving a system like this using random, naturalistic processes that would have existed on the early earth.

      If you know of someone who has done this, feel free to point me in their direction and I'll be happy to read up on their research and concede your point.

      Delete
    3. Don't be nasty! Don't laugh, but here's what his nibs had to say, above:

      "You IDiot clowns have no positive evidence for your claims, have no testable hypotheses, make no predictions, do no research, produce no results."

      Did you notice that 'silence came the stern reply' to your invitation?

      Delete
    4. Do you realise if even less complex things took it upon themselves to assemble themselves, our car-repair bills would be so much cheaper. Heck, buying the car would be.

      I worked for a while on the assembly-line at Ford's truck plant at Langley, Berks, and we even had to get permission to go for a pee. If only someone had thought of asking the parts to assemble themselves, during our absence... What a cruel irony that it was Nature calling! Mother Nature, no less.

      Delete
    5. Patience Paul, so you really think that some sort of scary challenge?

      Delete
    6. That would suck asking permission to pee. What did you do exactly? I've had Fords that appeared to have no intelligent design or assembly

      Delete
    7. wgbutler

      Thorton,

      There really is no point arguing about it. If you want to insist that such a complex system can come about from random processes all you have to do is demonstrate an organism in the lab that initially does not have the DNA system evolving a system like this using random, naturalistic processes that would have existed on the early earth.


      Er...no, I don't. To get to my tentative conclusion all science has to do is find evidence that the observed processes can create new features, which it has, then demonstrate evidence that such processes were working in the past, which it has.

      If you want to overturn science's conclusions all you need to do is provide an alternate detailed mechanism that explains the empirical data in a better more consilient manner.

      Pending that, you can get your Intelligent Designer to create another entire universe including a whole planet's worth of life forms from scratch in the lab. When do you think the demonstration will be ready?

      Delete
    8. Paul

      Do you realise if even less complex things took it upon themselves to assemble themselves, our car-repair bills would be so much cheaper. Heck, buying the car would be.


      LOL! Cars don't assemble themselves so that means ToE is disproven.

      Another candidate for "Fundies Say The Darndest Things" that's just about as stupid as everything else you post at Uncommonly Dense.

      I bet you UD IDiots must be so proud of Barry "the ass" Arrington after he went nuts and silently banned virtually every pro-science poster in the last two days. Especially when the gutless wonder issued call-outs and insults to them after they had been banned and couldn't reply. That really took a brassy set.

      Do you really wonder why you UD IDiots are the laughingstock of the whole scientific community?

      Delete

    9. I bet you UD IDiots must be so proud of Barry "the ass" Arrington after he went nuts and silently banned virtually every pro-science poster in the last two days. Especially when the gutless wonder issued call-outs and insults to them after they had been banned and couldn't reply. That really took a brassy set.



      Thorton,

      Do you really think that by acting obnoxious and hurling insults at people that you are ever going to persuade anyone to come over to your way of thinking?

      And exactly what is your way of thinking anyway? You profess to be an agnostic. An agnostic is a person who is open to the possibility of God existing. Every post you make absolutely reeks with hostility against any kind of evidence of a Designer and implies that you believe that our existence is one based upon random causation which ultimately has no meaning. That tells me that you are an atheist, NOT an agnostic.

      If you are an agnostic, explain to me why you are an agnostic instead of an atheist.

      Delete
    10. wgbutler777

      Do you really think that by acting obnoxious and hurling insults at people that you are ever going to persuade anyone to come over to your way of thinking?


      wgbutler777, do you really think that by having inappropriate physical relations with your pet chicken that you are ever going to get anyone to convert to your religion?

      See, I can ask stupid loaded questions too.

      Every post you make absolutely reeks with hostility against any kind of evidence of a Designer

      LOL! Of course they don't. They only reek with hostility against those who lie and misrepresent scientific evidence to push their IDC religious beliefs. I'll go to battle to defend your right to worship as you want, but I already told you I can't stand liars.

      If you are an agnostic, explain to me why you are an agnostic instead of an atheist.

      I've already answered that for you several times too. I see no evidence to believe in any of the thousands of different Gods that people have described over the centuries. Why do you think that if ask the same question enough times you'll get a different answer?

      Delete
    11. wgbutler -

      An agnostic is a person who is open to the possibility of God existing. Every post you make absolutely reeks with hostility against any kind of evidence of a Designer and implies that you believe that our existence is one based upon random causation which ultimately has no meaning. That tells me that you are an atheist, NOT an agnostic.

      You must think I'm picking on you. I apologise if that's how it comes across. But I did just want to clear up the definition of an atheist:

      1) Atheists are open to the possibility of God existing.
      2) An atheist is not, by definition, hostile to any form of evidence, even that of God (should any exist).
      3) An atheist does not believe existence ultimately has no meaning.

      There is only one thing that defines an atheist, and that is a LACK of belief in a God or gods. That is all. My opinion of God is like my opinion of fairies, or unicorns, or ghosts: if anyone came up with evidence for them existing I would be very interested. I cannot prove that any of them DEFINITELY don't exist, and I would never state such as a fact. It might even be nice to imagine these beings do possibly exist. But honestly I just don't believe it.

      Misconceptions of atheists as strident militarists with absolute faith in there being no God, or as stubborn fools desperately shutting their eyes and ears to all the evidence for God, or as desperately sad moral nihilists who see to point, value or meaning in life, are just ridiculous caricatures drawn up by religious folk to hide the fact that we are simply asking for solid evidence for God and reserving belief until such evidence can be presented - and that this is a perfectly reasonable thing to do.

      Delete
    12. btw, by contrast, an agnostic is a person who believes that the truth claims about God (and, possibly, other supernatural beings) are inherently UNKNOWABLE. It is the position that human reasoning is simply too limited to provide reasonable grounds for belief in God, and that therefore any opinion on his existence is equally (in)valid.

      It is a position one can hold AS WELL AS BEING a theist or an atheist.

      It is not merely a middle-ground of open-minded scepticism between the "faith-positions of theism and atheism" (since atheism is, of course, no such thing), though it does very often get portrayed that way.

      Delete
    13. Ritchie:

      I looked it up and found both of these definitions from Merriam Webster.com


      Definition of ATHEIST
      : one who believes that there is no deity


      Definition of agnostic:


      1
      : a person who holds the view that any ultimate reality (as God) is unknown and probably unknowable; broadly : one who is not committed to believing in either the existence or the nonexistence of God or a god


      I have yet to read anything from Thorton that implies that he is not committed to believing in the nonexistence of God.

      Delete
    14. Ritchie,

      y opinion of God is like my opinion of fairies, or unicorns, or ghosts: if anyone came up with evidence for them existing I would be very interested. I cannot prove that any of them DEFINITELY don't exist, and I would never state such as a fact. It might even be nice to imagine these beings do possibly exist. But honestly I just don't believe it.


      Regarding these other points, thank you for summarizing your position.

      I guess I am also an "atheist", so to speak, regarding the fairy tales of unicorns, fairies, ghosts, eternally existing universes, infinite multiverses that pop into existence uncaused out of nothing, primitive life forms that self-assemble out of non living components and then mutate into human beings, legendary Jesus myths, etc.

      I'm open to any and/or all of these possibilities. Indeed some of these possibilities are intriguing to me. I just don't see any evidence, sorry.

      Delete
    15. wg -

      I looked it up and found both of these definitions from Merriam Webster.com

      And look at all the comments underneath correcting it.

      From dictionary.com:

      a person who does not believe in God or gods

      I have yet to read anything from Thorton that implies that he is not committed to believing in the nonexistence of God.

      Then let's ask Thorton if he is committed to a belief in no God/gods, and to elaborate on his 'agnostic' position.

      Thorton?

      I guess I am also an "atheist", so to speak, regarding the fairy tales of...

      In a sense. The term specifically applies to a lack of belief in God/gods, but yes that's the general idea.

      I'm open to any and/or all of these possibilities. Indeed some of these possibilities are intriguing to me. I just don't see any evidence, sorry.

      That is why we study evidence. We go where the evidence leads us.

      Additionally, just while I have you, I wanted to ask your opinion on this:

      http://www.youtube.com/watch?v=kZY2eeozdo8

      This is a video from a man explaining his deconversion. It is one of an entire series, all well worth a watch. But this is the one I particularly wanted to hear your thoughts on.

      Check out his description for his sources.

      Delete
    16. Ritchie,

      Thanks for the link. In case anyone wants to know, it's a video arguing that the early Jewish religion was really a polytheistic religion rather than a monotheistic religion.

      I guess I'd put this video in the pile with all the other conspiracy stories that skeptics constantly come up with to discredit the Bible (Jesus didn't really exist, Jesus had a relationship with Mary Magdalene, Jesus was a homosexual, the Israelites were just a small, undistinguished tribe amongst the Canaanites, etc).

      It's heavy on conspiracy and speculation but extremely light on evidence. It's the archeological version of the "just so" story.

      In order to believe this narrative you have to buy in to the story that the monotheists were a cunningly resourceful group of masterminds who were plotting all along to overthrow the polytheists and have their favorite god become the predominate god of Judaism, taking advantage of every crisis and opportunity, rewriting entire books of the Bible and history, and mercilessly rooting out the other Jewish polytheistic sects.

      I guess if you are committed to materialism and absolutely want to think the Bible is false, and you have an imagination capable of thinking that a secret, mystical sect of 1st century Jews completely fabricated an imaginary Christ figure to deceive the world, this is par for the course.

      Meanwhile, real science continues to be done.

      Delete
    17. wg -

      I'm a little surprised you take this to be a just-so conspiracy theory. This is not a fanciful fringe belief, but one held by many Biblical scholars, including religious ones, such as Karen Armstrong.

      From the wikipage:

      http://en.wikipedia.org/wiki/History_of_ancient_Israel_and_Judah#Iron_Age_I

      Current models among scholars see the emergence of Israelite monotheism as a gradual process which began with the normal beliefs and practices of the ancient world.[76]

      The religion of the Israelites of Iron Age I, like many Ancient Near Eastern religions, was based on the cult of the ancestors and the worship of family gods (the "gods of the fathers").[77] The major deities were not numerous – El, Asherah, and Yahweh, with Baal as a fourth god in the early period.[78] By the early monarchy El and Yahweh had become unified and Asherah did not continue as a separate state cult,[78] although she continued to be popular at a community level until Persian times.[79]


      Even on the face of it, it is not a fanciful idea. The claim is merely that despite what the Bible claims, the ancient Israelite religion was NOT different at all from the religion of its neighbours.

      In order to believe this narrative you have to buy in to the story that the monotheists were a cunningly resourceful group of masterminds who were plotting all along to overthrow the polytheists...

      What!?!? No you don't. Who said anything at all about a great, cunningly masterminded conspiracy? That is utter nonsense. What a total strawman. Where on Earth did you get that from? The claim is merely that, just like their neighbours, the ancient Isrealites too were polytheistic, and following the destruction of Jerusalem by the Babylonians, became monotheistic - perhaps rationalising the destruction of their great holy city as divine judgement for worshipping other gods. Why is this such an outlandish claim? I think the only reason you find it so is because it contradicts your religious biases.

      Even many Biblical passages make considerably more sense when considered in this light.

      Exodus 12:12: And against all the gods of Egypt I will execute judgment.

      Exodus 15:11: Who is like unto thee, O LORD, among the gods?

      Exodus 20:3, 5: Thou shalt have no other gods before me. ... Thou shalt not bow down thyself to them, nor serve them.

      Numbers 33:4: Upon their gods also theLORD executed judgments.

      Joshua 24:2: They served other gods.

      1 Chronicles 16:25: The Lord ... is to be feared above all gods.

      Psalm 82:1: God standeth in the congregation of the mighty, he judgeth among the gods.

      What sense are we to make of these passages (and many, many more) under monotheism?

      Delete
    18. wg (cont)

      I guess if you are committed to materialism...

      ...which no evidence contradicts...

      ...and absolutely want to think the Bible is false...

      ...as can be demonstrated. It isn't even internally consistent...

      ...and you have an imagination capable of thinking that a secret, mystical sect of 1st century Jews completely fabricated an imaginary Christ figure...

      ...again with insisting I am pedalling conspiracy theories. There were many Mystery cults in the ancient world. That is a historical fact. Why then should the idea of Christianity having its roots as a Jewish Mystery cult be so outlandish?

      ...to deceive the world...

      Utterly untrue. I never said anything like that. I believe religious faith generally is sincere. It's just that that does not make it factually accurate.

      Meanwhile, real science continues to be done.

      Odd that you throw this out in defence of the Bible. What exactly is this bearing out? The claim is not that the Bible is utter fiction through and through. We already know that many people and places it talks of were indeed historical. The claim is that it is myth; legend; an attempt to explain the real world in terms of the supernatural.

      It's as though you think validating the Bible's mundane claims therefore indirectly validates the Bible's extraordinary claims. But it does not, any more than the existence of London and King's Cross station validates the story of Harry Potter.

      Delete
    19. Ritchie,

      Thanks for your latest reply. I think your posts should be required reading for anyone thinking about giving up on theism and becoming an atheist. You really do a great job of highlighting what one has to believe in order to be an atheist.

      You seem willing to believe virtually anything about the scriptures other than what they say. You have a keen ability to read secret messages, meaning, and conspiracies into the scriptures that have somehow eluded the best scholars in the world who have learned all the ancient languages and devoted their lives to the study of scripture. And to think that a random internet atheist would be the one to finally discover the secret meanings and get to the truth after all these centuries!

      Regarding this latest conspiracy theory, you have me at a loss for words. I never thought you could outdo your "Jesus was an imaginary person" hypothesis, but you've managed to do it. Color me impressed.

      Delete
    20. wg -

      This is not a conspiracy theory. This is not a fringe belief. It is a very well-backed opinion of Biblical historians and scholars. The only people who do NOT widely accept it are the religious community who are committed to their tenets.

      Because when evidence clashes with dogma, we all know which the religious side with.

      Nor do I do not claim to be coming up with anything original here. I am just relaying the work of others. For someone who put such faith in the opinion of experts when it came to the historicity of Jesus, you seem pretty damn quick to withdraw it whenever they say something you DON'T like.

      Please stop portraying me as a conspiracy theorist spouting lunatic ideas that I have invented myself. I realise it may soothe your conscience to invent excuses to shoot the messenger and completely ignore out of hand whatever I say just because you don't like it, but it is neither accurate nor fair. I am providing sources for my claims, so you have no excuse for not examining the evidence yourself. Is it laziness, or fear of discovering something you don't want to find?

      You really do a great job of highlighting what one has to believe in order to be an atheist.

      One does not have to believe anything to be an atheist. That's kinda the point.

      You seem willing to believe virtually anything about the scriptures other than what they say.

      Virtually any alternative hypothesis is MORE PLAUSIBLE than the idea that the Bible's claims are true. I could sit and make up a hundred naturalistic explanations for any Biblical story you could mention, and the Bible would always be LESS LIKELY to be true than any one of them.

      Delete
    21. Ritchie,

      My previous post was a little too snarky. I apologize for that.


      Virtually any alternative hypothesis is MORE PLAUSIBLE than the idea that the Bible's claims are true. I could sit and make up a hundred naturalistic explanations for any Biblical story you could mention, and the Bible would always be LESS LIKELY to be true than any one of them.


      This is why its probably a waste of time to discuss any of this stuff with you. Your mind is made up and you will latch on to anything and everything that discredits the Bible and points to atheism.

      Regarding your latest theory, it seems patently ridiculous to me because the entire old testament is replete with admonishments against polytheism and establishes that there is only one God who created the heavens and the earth.

      And yes many of the early Israelites were polytheistic, AGAINST the tenets of Judaism which is why they were constantly being punished! The entire message of the old testament speaks against polytheism and holds it up as a road to folly and yet you manage to find a way to believe that ancient Judaism was a polytheistic religion. It boggles the imagination.

      For a more scholarly response to some of the arguments in your video, I direct you to this and this.

      Delete
    22. wg

      My previous post was a little too snarky. I apologize for that.

      No worries. I can feel my patience fray on here sometimes too.

      This is why its probably a waste of time to discuss any of this stuff with you. Your mind is made up and you will latch on to anything and everything that discredits the Bible and points to atheism.

      Ahh, the supreme confidence of the theist. That everyone who disagrees with them is doing it out of a stubborn refusal to think as they do.

      I am not the one being stubborn in the face of evidence here.

      Regarding your latest theory, it seems patently ridiculous to me because the entire old testament is replete with admonishments against polytheism and establishes that there is only one God who created the heavens and the earth.

      Indeed. But so what? This is only a problem if you assume, as you seem to, that the Bible is the inerrant word of God in the first place.

      Do you adhere to the traditional belief that the first five books of the Old Testament were written by Moses, or even any single source? Because if you do, I have bad news: this is most definitely a fringe belief in academic circles:

      "Today, the majority of scholars agree that the Torah does not have a single author, and that its composition took place over centuries."

      http://en.wikipedia.org/wiki/Torah#Composition

      It is pretty well established that the Torah is a collection of books spanning many years subject to revision, rewrites and editing. The Torah, and by extension the Old Testament, are products of human societies. A jump from polytheism (even a monolaturalist one) to monotheism would require extensive editing of holy books - and that is exactly what we can in fact see in the Bible's pages.

      Here is a reasonable programme on the subject:

      http://www.youtube.com/watch?v=VtEsQT5M2IQ

      It is a little verbose, and as the title suggests it does take a rather feminist slant. Nevertheless, it does illustrate some of the evidence that shows the early Israelites were polytheists.

      The entire message of the old testament speaks against polytheism and holds it up as a road to folly and yet you manage to find a way to believe that ancient Judaism was a polytheistic religion. It boggles the imagination.

      I'm not saying Judaism was ALWAYS polytheistic. I'm saying it used to be and BECAME monotheistic. If that were the case, then of course we would find many admonitions of polytheism in the Bible. Please at least try to follow my argument. Your objection amounts to little more than 'It's true because it says it's true'.

      As to your links, Dr Richard Hess admits many scholars believe in Judaism's ploytheistic roots. It is no mere fringe belief. And he seems to avoid this problem by claiming 'some' were polytheistic, while others were not. As for the second, it seems to centre around how unlikely he (she?) considers editing and revising of the Torah to be, and yet that is exactly what most scholars agree happened.

      Delete
    23. WG: The entire message of the old testament speaks against polytheism and holds it up as a road to folly and yet you manage to find a way to believe that ancient Judaism was a polytheistic religion.

      Apparently, you've never read The Evolution of God, by Robert Wright. He presents a strong argument that monotheism was sanitized from the Bible by monotheists. And, it would appear that this process is continuing today.

      For example, from the King James Version….

      Joshua 10:12 Then spake Joshua to the LORD in the day when the LORD delivered up the Amorites before the children of Israel, and he said in the sight of Israel, Sun, stand thou still upon Gibeon; and thou, Moon, in the valley of Ajalon.

      But why would Joshua, supposedly with Yahweh's help, command other gods to stand still? Specifically, both the sun and moon were thought to be gods at this time.

      If you're a monotheist, this doesn't make sense. So, we get new translations such as this from the New International Version….

      On the day the LORD gave the Amorites over to Israel, Joshua said to the LORD in the presence of Israel: "O sun, stand still over Gibeon, O moon, over the Valley of Aijalon."

      Delete
  5. BA ,
    Miracles do not happen in contradiction with nature,but only in contradiction to that which is known to us of nature.... St Augustine

    Funny , that sounds like even St Augustine thinks Dr Hunter's belief that life is too complicated to have happened by " nature" is a weak argument. I never thought I would write this but thanks for the link BA

    This research in the post,it was conducted by scientists using naturalism ,correct? When is naturalism permitted in the scientific world? Is your belief that micro naturalism is permitted ,but macro naturalism is not? To paraphrase Smith" There and then here preferably -- whenever both those might be"

    ReplyDelete
    Replies
    1. On the contrary. You have completely misunderstood Augstine's point. He meant that we think of them as miracles in defiance of nature, only because our knowledge of nature is so exiguous.

      Don't mind my asking, but is English your first language?

      Delete
    2. Ouch! So, something is considered a miracle because man's knowledge of nature has exiguososity ? So the muy grande our knowledge, the less miracles are miraculous . They are explained by natural causes. Ch says life is too miraculous to be formed by nature. St Augustine ( correctly spelled) says not so fast miho. Am I still confused? Help please!

      Delete
    3. It couldn't be simpler or more straight-forward, Vel. Creation and its very sustenance could scarcely be more miraculous, could it.

      When Christ 'rebuked the wind and the waves' - love that passage (Alright. That's enough!) - he was using what our media people today call, 'visual aids' (and, as primarily in this case, 'auditory aids'.

      Christ could have caused his miracles with a mere act of the will, as he did when he cast all his captors to the ground in the garden of Gethsemane, but he understood our need for, well... 'visual aids'.

      I've been patient, too, but still no response from you to the challenge to replicate in a laboratory your phantasmagorical conjectures concerning evolution... Or was it 'natural selection..?'

      The failure to understand that Grace builds upon nature, was one of the greatest failings of Karl Marx, when he tried to 'gut' Christianity of the divine; but that's tangential.

      I was handling some thin, curled pipes which had something to do with the air-brakes I think. But I can't remember what added-value I contributed to their existence.

      "So the muy grande our knowledge, the less miracles are miraculous . They are explained by natural causes."

      You've learnt nothing from quantum physics, have you, Vel? I'm sorry to see that, because, you see, it's kind of magic, you know?

      Delete
    4. "LOL! Cars don't assemble themselves so that means ToE is disproven.

      Another candidate for "Fundies Say The Darndest Things" that's just about as stupid as everything else you post at Uncommonly Dense.

      I bet you UD IDiots must be so proud of Barry "the ass" Arrington after he went nuts and silently banned virtually every pro-science poster in the last two days. Especially when the gutless wonder issued call-outs and insults to them after they had been banned and couldn't reply. That really took a brassy set.

      Do you really wonder why you UD IDiots are the laughingstock of the whole scientific community?"

      Tee hee! Love it Thorton. More! More! Emotional, nay hysterical diarrhoea of the first water. That irascible Olive Hardy tone is a knock-out. No contest! You win, hands down..

      Can we make Thor our mascot on here?

      Delete
    5. Thor, the first rule of all p*ss-taking is to remain light-hearted.

      Invective is a whole nother discipline, for which, I suspect you have congenitally scant aptitude. I mean, of course, literary invective. Not just bawling jejune insults.

      Christ was, understandably enough a master at it, but so, on a still deeply impressive level, was Hunter Thompson.

      How about this, for example:

      'Richard Nixon has never been one of my favorite people anyway. For years I've regarded his existence as a monument to all the rancid genes and broken chromosomes that corrupt the possibilities of the American Dream; he was a foul caricature of himself, a man with no soul, no inner convictions, with the integrity of a hyena and the style of a poison toad. The Nixon I remembered was absolutely humorless; I couldn't imagine him laughing at anything except maybe a paraplegic who wanted to vote Democratic but couldn't quite reach the lever on the voting machine. '

      Thompson later came to realise that Republican presidents could get a whole lot worse.

      and this:

      'The TV business is uglier than most things. It is normally perceived as some kind of cruel and shallow money trench through the heart of the journalism industry, a long plastic hallway where thieves and pimps run free and good men die like dogs, for no good reason. There's also a negative side.'

      The last sentence didn't appear in its original publication.

      Delete
  6. Thorton

    "...I bet you UD IDiots must be so proud of Barry "the " Arrington after he went nuts and silently banned virtually every pro-science poster in..."

    How do you play a soccer game if you eliminate the opposing team?

    In the light of latest chistka on UD , Cornelius deserves even more respect for allowing ID challengers to freely comment.

    ReplyDelete
  7. Eugen

    Thorton

    "...I bet you UD IDiots must be so proud of Barry "the " Arrington after he went nuts and silently banned virtually every pro-science poster in..."

    How do you play a soccer game if you eliminate the opposing team?


    Exactly. The UD management isn't interested in honest scientific discussion, only making sure their anti-science garbage is the only side heard. That's certainly their right, but it's amazingly hypocritical for them to then bitch about how everyone else is censoring/expelling them for their views.

    In the light of latest chistka on UD , Cornelius deserves even more respect for allowing ID challengers to freely comment.

    Indeed. I've commended him many times for at least having the decency to do that. I personally think he does it to assuage his guilty conscience for taking the DI's money and doing their propaganda dirty work. Deep down I believe he knows how wrong it is, but he needs the cash.

    ReplyDelete
  8. Actually there is a very good reason for Barry's actions, actions that are perhaps lost on people who cannot ground morality in the first place. Here is a clue as to what started the heads rolling:

    Taylor Swift - Mean
    http://www.youtube.com/watch?v=jYa1eI1hpDE
    http://www.youtube.com/watch?v=jYa1eI1hpDE

    ReplyDelete
    Replies
    1. Hey Phil Cunningham (ba77), why are you so crazy and dishonest?

      Delete
  9. bornagain77

    Actually there is a very good reason for Barry's actions


    Like what Batspit? Give us Barry Arrington's "good reason" for banning at least eight pro-science posters in the last two days, including those like Dr. Elizabeth Liddle who's never done anything but engage in the most kind, polite manner.

    Give us Barry Arrington's "good reason" for cowardly deleting the accounts of at least five of those posters with no warning, no message, just them discovering they could no longer log on.

    Give us Barry Arrington's "good reason" for banning Dr.REC, then publishing Dr.REC's real name and contact info that Dr.REC had never made public in an attempt to "out" him as an ID critic. This was after UD had previously banned others merely for posting GEM of TKI's name that *IS* publicly available on the web page GEM always pimps.

    Give us Barry Arrington's "good reason" for starting a call-out thread against Eigenstate, another poster who has been nothing but civil, deleting Eigenstate's answers, then lying and claiming Eigenstate ran away without answering.

    The simple fact is that Arrington is a spineless jackass and bully who only knows how to win by abusing his moderator powers. The really sad thing the number of UD IDiots supposedly interested in "honest" discussion who cheered him on during the backstabbing.

    Go ahead Batspit, try to defend his absolutely craven and disgusting behavior.

    ReplyDelete
    Replies
    1. This was after UD had previously banned others merely for posting GEM of TKI's name that *IS* publicly available on the web page GEM always pimps.

      That "kairosfcous" guy is quite a character. I haven't yet had the stomach to read one of those dense and pompous (and apparently repetitive) treatises, but I did enjoy his robo-swan. END.

      Delete
    2. Well Thorton, Does it even strike you as odd, in the least, that I point out being mean was a primary cause that 'started' the heads rolling, and that you, in response, would start off your post by calling me the derogatory name 'batspit', or is the irony of what you have just done completely lost on you? Just what in blue blazes makes you think that I would want to stick around and tolerate such treatment from you? I certainly would not tolerate it in person from you to any overbearing degree save in good natured fun, and on the internet I certainly tolerate it even less since I can just go somewhere else where the company is much more respectful.,,, Dr. Hunter has the patience of Job in tolerating such treatment from you, but perhaps Dr. Hunter realizes that having you constantly belittling people here actually exposes just how dogmatic some neo-Darwinists can be in their views and he realizes that you prove his overriding point, of evolution being a religion, much more effectively that he ever could on his own.

      Delete
    3. Yes. The fact that Thorton is disrespectful is proof that other, completely independent people deserved what they got.

      Delete
    4. I just found the apparent source of what has to be the world's most scrolled-over prose, boreagain77's daily random copy-and-paste jobs. A single webpage with close to a 100,000 words or 250 A4 pages.

      The sheer derangedness of it all is awesome.

      Delete
    5. bornagain77

      Well Thorton, Does it even strike you as odd, in the least, that I point out being mean was a primary cause that 'started' the heads rolling


      LOL! So all those poster that pompous ass Arrington banned (the count is up to 11 now I believe) deserved it because they were mean??

      Please provide examples of all 11 being mean. You can start with Dr. Liddle.

      Just what in blue blazes makes you think that I would want to stick around and tolerate such treatment from you?

      Batspit, I think it's safe to say no one would lose one wink of sleep if you took your 10,000 word rambling posts full of inane blithering and Christian music videos and went elsewhere. Anywhere.

      BTW, is it OK if I call you Philip Cunningham? After all, if Arrington is "fair and respectful" in posting Dr.REC's name, shouldn't I be equally fair and respectful and use yours?

      Delete
    6. Venture Free

      Yes. The fact that Thorton is disrespectful is proof that other, completely independent people deserved what they got.


      It's that Biblical 'original sin' thing.

      Since GOD can murder thousands of innocent children and babies because of something their great-great-great-great-grandfathers did, what's Arrington's little temper tantrum by comparison?

      Delete
    7. I see that Phil Cunningham (ba77) says that being mean is what got 20+ people banned from UD. Hey Phil, what about joe's meanness, or the meanness of gordon mullings, o'leary, stephenb, uptightbiped, you, and all the other IDiots? After all, you all constantly attack, insult, ridicule, and falsely accuse anyone who doesn't worship you and your imaginary god.

      Of course you self-righteous, pontificating, sanctimonious god-wannabes don't see that as being mean, do you? You believe that you're authorized by your imaginary god to be as malicious and vicious as you want to be, right?

      You no doubt believe that you're a special agent for your imaginary god and that you're doing that imaginary god's will, no matter how despicable and two-faced your behavior is.

      You IDiots actually are like your imaginary god, as he is depicted in the bible; monstrous, contradictory, jealous, petty, insane, two-faced, dishonest, selfish, vile, arrogant, shallow, cowardly failures.

      Oh, and I'm not being mean. My imaginary god, Fifi the pink unicorn, authorized me to speak to you in this way. I am one of her special agents.

      Delete
  10. In spite of expectations to the contrary, the transcription factor binding sites are not well conserved across different species. In fact, divergence between transcription factor binding sites even shows up in very similar species, such as different species of yeast.

    That last bit of info comes from a paper (Borneman et al. 2007) that begins with:

    Differences in related individuals are generally attributed to changes in gene composition and/or alterations in their regulation.

    Way to downplay the expectations contradicted by the data of their own shiny paper!

    But moreover, Cornelius, some estimates of human intra-specific variation in binding regions are rather high: 25% and 7.5% for the case of RNA PolII and NFκB, respectively (compare to the 0.025 of variation among coding sequences, according to the same paper, Kasowski et al. 2010). How can be such great variation in the tight molecular machinery of individuals of the same species? More evidence of exquisite fine-tuning within our species? That must be it! What an obsessive chap this designer is!

    ReplyDelete
  11. Geoxus:

    But moreover, Cornelius, some estimates of human intra-specific variation in binding regions are rather high: 25% and 7.5% for the case of RNA PolII and NFκB, respectively (compare to the 0.025 of variation among coding sequences, according to the same paper, Kasowski et al. 2010). How can be such great variation in the tight molecular machinery of individuals of the same species? More evidence of exquisite fine-tuning within our species? That must be it! What an obsessive chap this designer is!

    So the paper shows that intra specific variation in binding regions >> intra specific variation in coding regions. Under creation or design, this would imply not fine-tuning at the global / universal level (e.g., the electron charge to mass ratio across the entire universe), but rather at the local level repeated billions of times (i.e., specific nucleotides for every person on the planet). That kind of fine-tuning is more like evidence against design (because it really amounts to manual tinkering on a massive scale) than for design. Is that your point?

    If so, could it not also be an issue for evolution? IOW, not only does evolution create all of these incredible regulatory mechanisms and machinery in the first place, but it also creates mechanisms that induce just right levels and types of SNPs, at just the right places (i.e., at the binding regions), to bring about the right levels of binding variations for intra specific phenotypic variation between individuals. Do you think that is reasonable under evolutionary theory?

    ReplyDelete
    Replies
    1. I wrote:

      [...] some estimates of human intra-specific variation in binding regions are rather high: 25% and 7.5% for the case of RNA PolII and NFκB, respectively (compare to the 0.025 of variation among coding sequences, according to the same paper, Kasowski et al. 2010).

      Sorry, those figures I provided can be misleading. You were talking about variation in binding sites, but those figures included other sources of variation in binding. The corrected figures (only binding variations associated to sequence differences) are 6.5% and 2.63%, respectively (still two orders of magnitude greater than 0.025).

      Cornelius wrote:

      That kind of fine-tuning is more like evidence against design (because it really amounts to manual tinkering on a massive scale) than for design. Is that your point?

      Of course not, Cornelius. You know me better. Nothing could possibly be evidence against design, such is the beauty of the design hypothesis. This can easily be explained by millions of tiny miracles, which in turn could be explained by a control freak designer or an army of designers (or something in between).

      it also creates mechanisms that induce just right levels and types of SNPs, at just the right places (i.e., at the binding regions), to bring about the right levels of binding variations for intra specific phenotypic variation between individuals

      Not "just the right levels and types at just the right places". I recall there's a little thing called natural selection, and that binding sites are quite short in sequence and often degenerate at certain positions.

      I don't know what the "right" levels of intra-specific phenotypic variations are.

      Delete
    2. Geoxus:

      I recall there's a little thing called natural selection, and that binding sites are quite short in sequence and often degenerate at certain positions.

      I thought the binding region variations called for locally elevated mutation rates because the variation was so high. No?

      Delete
    3. Got me there, Conrelius! That does look like something interesting. I do confess I'm not well-read on human genetic variation, and, sadly, I can't easily find a meaningfully comparable figure for "normal" non-coding sequence variation (I also skimmed through Venter's 2007 paper, the reference for the 0.025 figure, but failed to find its calculation... I trusted Kasowski et al. on that).

      Delete
  12. Neo-Darwinism is to biology what stone knives and bear skins are to the publishing industry.

    It's time to move on.

    ReplyDelete
  13. Tedford the idiot

    Neo-Darwinism is to biology what stone knives and bear skins are to the publishing industry.

    It's time to move on.


    Considering that the alternative you're offering is like being unarmed and buck naked, I think we'll keep what we've got.

    ReplyDelete
  14. Thorton

    You insulted bornagain 77 immediately.
    Generally, insults to others reveal character of insulter more than the insulted .

    ReplyDelete
  15. Eugen

    You insulted bornagain 77 immediately.
    Generally, insults to others reveal character of insulter more than the insulted


    The way I see it Batspit and the rest of the IDiots at UD have been doing a lot worse insulting of myself and my fellow science professional for years. It's hard to find a post by them that doesn't insinuate we're hopelessly incompetent, willful frauds, moochers off the public dole, etc.

    The tone of my responses are based solely on how I am addressed to begin with. What goes around comes around as the saying goes.

    ReplyDelete
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    1. My karma ran over their dogma. :)

      Delete
    2. He is the Ethan Edwards to their Chief Scar

      Delete
    3. A two dimensional mouse-like creature to a green, two dimensional elephant... to a slightly smaller elephant, but still green and two dimensional.

      Delete
    4. Yes. Apparently, but - no, don't laugh - that was by his own side!!!!

      Can you imagine Planck, Bohr, Einstein, Godel or any of the greats, the ID, theistic scientists, encouraging a nursery of screaming Kevins like that, in the first place?! Water finds its own level.

      Delete
    5. This comment has been removed by the author.

      Delete
    6. He is the Macaulay Culkin to their Joe Pesci and Daniel Stern.

      Delete
  16. Didn't Dawkins shut down his blog due to foul and abusive language?

    ReplyDelete
  17. natschuster

    Didn't Dawkins shut down his blog due to foul and abusive language?


    No.

    ReplyDelete
    Replies
    1. Do you mean he didn't shut down blog, or didn't shut it down because of language?

      Delete
  18. As one writer put it, the regulatory architecture has been rewired on a substantial scale. Another explained, these findings “hint at an unimagined complexity of the genome.”

    But ID has been asserting this kind of hidden complexity for decades now. It's only the Darwinists who have trouble "imagining" how complex the genome is.

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    Replies
    1. But ID has been asserting this kind of hidden complexity for decades now.

      No, it hasn't.

      Delete
    2. Hawks:

      What do you base your assertion on?

      Delete
    3. Some negatives just can't be shown. You made an assertion. Back it up.

      Delete
    4. Actually, let me say something different. ID has not been making that assertion for the simple reason that ID can't make that assertion. What ID does assert is that we should not expect such complexity without intelligence. What ID does NOT assert is what we should expect given intelligence.

      Delete
    5. And actually, it doesn't follow that if something is designed it should be highly complex. Cdesign proponentists say that in the hope complexity becomes more and more difficult to explain for evolutionary biology, but what is the theoretical justification for that assertion from the design paradigm? Aren't boomerangs and hula-hoops designed?

      Delete
    6. An abstract Intelligent agent can choose to design things simply, poorly, etc., or even look *as if* it wasn't designed, on purpose. So, whether something is well designed isn't a good indication of design.

      However, what we're pointing out is that the "explanation" that the biosphere was designed by an intelligent agent, because it was very well designed, is in error.

      We do not universally observe very well designed things in the biosphere. Nor is it clear why human designs ought to be the criteria for concluding something is well designed.

      This doesn't "prove" that biosphere wasn't designed, but we shouldn't conclude this is the case due to this particular explanation, because it was found in error. As such we discard it.

      Now, someone might claim that the biosphere is designed because they present an explanation as to why human beings are a criteria for good design. And they might present an explanation as to why a designer would only design some things that meet this criteria, but not others, such as the designer had yet to create the knowledge of how to design things very well. However, neither of these has yet to occur to my knowledge. Nor do I expect the later to occur because this would exclude the ID proponent's favorite designer.

      Delete
    7. Hawks:

      Some negatives just can't be shown. You made an assertion. Back it up.

      I see. I must back up my assertion, but you don't hold yourself to that same standard. Is that it?

      As to what ID has asserted. If you read the literature, you will see that the notion of a "front-loaded" genome has been around since at least the middle 90's. "Front-loading" would view genes/proteins as basic building blocks, with the actual production of a life form coming about as a result of a genetic program built upon genetic networks present in the genome. This is simply the argument ID has had against Darwinian "junk-DNA" for ages now.

      Personally, I've been on the internet espousing these ideas for almost ten years. Once you step outside of the Darwinian mindset, then you very quickly assume that genetic networks, tantamount to routines and sub-routines in a computer program, are the only way significantly different phenotypes can emerge. It's a non "gene-centric" view. And it implies that "the regulatory architecture has [to be] rewired on a substantial scale."

      Delete
    8. Lino: As to what ID has asserted. If you read the literature, you will see that the notion of a "front-loaded" genome has been around since at least the middle 90's. "Front-loading" would view genes/proteins as basic building blocks, with the actual production of a life form coming about as a result of a genetic program built upon genetic networks present in the genome. This is simply the argument ID has had against Darwinian "junk-DNA" for ages now.

      Lino, perhaps you'll be the ID proponent that answers my question.

      How was the knowledge used to build the biosphere, which you claim was front-loaded into the genome, created?

      Saying a designer "just was", complete with the knowledge of how to build the biosphere, already present, serves no explanatory purpose. This is because one could more economically state that organisms "just appeared", complete with the knowledge of how to build themselves, already present.

      Delete
    9. Scott:

      Saying a designer "just was", complete with the knowledge of how to build the biosphere, already present, serves no explanatory purpose. This is because one could more economically state that organisms "just appeared", complete with the knowledge of how to build themselves, already present.

      I would disagree. In fact, I think you have it backwards. IOW, to state that organisms "just appeared" doesn't explain how they came to appear; hence, an absence of "explanatory purpose". If you are sympathetic to the idea of an infinite regress, I would only point out that if you posit an infinite regress, then, mathematically there is a zero chance that anything happened, since it would take an infinite amount of time to come out of the regress, and we know the universe to be finite, not infinite.

      Thus positing of an intelligent designer at least explains all the hallmarks of intelligence we find in the genome.

      Delete
    10. Lino: I would disagree. In fact, I think you have it backwards. IOW, to state that organisms "just appeared" doesn't explain how they came to appear; hence, an absence of "explanatory purpose".

      Except your not disagreeing with me.

      Again, saying a designer "just was", complete with the knowledge of how to build the biosphere, already present, serves no more explanatory purpose than saying, organisms "just appeared", complete with the knowledge of how to build themselves, already present.

      In other words, saying the knowledge was previously located here, then moved there, doesn't actually add to the explanation because it does not actually address the origin of the knowledge in question. All you've done is push the problem into some unexplainable mind in some unexplainable realm. It's as if you've pushed the food around on your plate, then claimed you've ate it. But it's still there staring you in the face.

      However, that organisms "just appeared", complete with the knowledge of how to build themselves, already present, isn't the underlying explanation behind evolutionary theory.

      Lino: If you are sympathetic to the idea of an infinite regress, I would only point out that if you posit an infinite regress, then, mathematically there is a zero chance that anything happened, since it would take an infinite amount of time to come out of the regress, and we know the universe to be finite, not infinite.

      I'm not sympathetic to an infinite regress.

      The underlying explanation behind evolutionary theory is that the knowledge of how to build the biosphere, as found in the genome, was created via a variation of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection.

      Lino: Thus positing of an intelligent designer at least explains all the hallmarks of intelligence we find in the genome.

      Does it? Why don't you start out by explaining how knowledge is created, then point out how evolutionary theory doesn't fit this explanation.

      Delete
    11. Scott:
      Except your not disagreeing with me.

      Again, saying a designer "just was", complete with the knowledge of how to build the biosphere, already present, serves no more explanatory purpose than saying, organisms "just appeared", complete with the knowledge of how to build themselves, already present.


      Except that you're missing the point that no one has ever seen some organism "just appear", complete with the knowledge of how to build themselves already present within. This is an Origin of Life question, one that Darwinism, because of its reliance on a kind of feedback mechanism, is hopeless to explain. OTOH, we are completely familiar with intelligent beings bringing about functional machines. So to say that biological life bears the hallmarks of being designed---something that Dawkins readily admits---is to say that a Designer had a hand in its production. Whereas, not having any possible way of explaining the OOL---even Darwin punted on this---nor how the biosphere came about, the explanatory power of RV + NS is very, very limited. Common sense tells us that invoking a Designer is more logical than invoking a poorly understood feedback mechanism that is so limited in its scope.

      S:The underlying explanation behind evolutionary theory is that the knowledge of how to build the biosphere, as found in the genome, was created via a variation of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection.

      I see. But this can explain nothing of OOL. Where did the genome come from? Please explain your answer.

      S:Does it? Why don't you start out by explaining how knowledge is created, then point out how evolutionary theory doesn't fit this explanation.

      How about I ask a question? Is it possible for knowledge to exist if no intelligent beings exist?

      A moment's reflection tells you that knowledge can only exist if intelligence exists. So, where did the intelligence come from? If you want to answer that intelligence arose from lifeless matter all by itself, then you're arguing that knowledge sprang up into being out of that which did not possess knowledge. Does this make sense?

      As to explaining how"knowledge is created", why don't you tell us exactly how Darwinism explains this? If I say an intelligent designer brought about knowledge of knowledge, at least that makes sense. How does Darwinism explain the "creation of knowledge". But, of course, since NS is tantamount to the Grim Reaper=Death, Darwinists posit that life comes through death. So nothing will surprise me. Although it will likely bore me.

      Delete
    12. I see. I must back up my assertion, but you don't hold yourself to that same standard. Is that it?

      No. You made an assertion and didn't back it up. In my second comment I explained why ID can't make these assertions. Did you read it?

      I'll say it to you again:

      ID has not been making that assertion for the simple reason that ID can't make that assertion. What ID does assert is that we should not expect such complexity without intelligence. What ID does NOT assert is what we should expect given intelligence.

      Some ID supporters might have been saying this for years. However, they don't base their assertions on ID. ID itself doesn't make the assertion more than it asserts the exact opposite and everything in between.

      Once you step outside of the Darwinian mindset, then you very quickly assume...

      YOU make that assumption. ID doesn't.

      Delete
    13. Lino: Except that you're missing the point that no one has ever seen some organism "just appear", complete with the knowledge of how to build themselves already present within.

      I never claimed we had. My point is, for the purpose of explaining the origin of the knowledge used to build the biosphere, they are equivalent.

      However, I would note that organisms contain the knowledge of how to build themselves, unlike cars, in which the knowledge of how to build them resides in us, books and the robots we build and program to construct them.

      Lino: This is an Origin of Life question, one that Darwinism, because of its reliance on a kind of feedback mechanism, is hopeless to explain.

      I'm not following you. It's unclear why the explanation for the knowledge of how to build the concrete adaptations we observe and the OOL would necessarily be exactly the same. Why would you expect this to be the case? You seem to be holding some presupposition that you have yet to disclose.

      Lino: So to say that biological life bears the hallmarks of being designed---something that Dawkins readily admits---is to say that a Designer had a hand in its production. Lino: Whereas, not having any possible way of explaining the OOL---even Darwin punted on this---nor how the biosphere came about, the explanatory power of RV + NS is very, very limited.

      You're objecting to the idea that we can explain why the biosphere appears *as if* it was designed.

      In doing so, you're essentially claiming the biosphere was created in a way that makes a theory of biological complexity impossible. However, this is like claiming that atoms were created in a way that makes atomic theory impossible. Why is this the case for the biosphere, but not atoms? A voice in a whirlwind told you so?

      Again, how do you explain how knowledge is created? I'm asking because both how we, as people, and how neo-darwinism creates information are variations of the same process: conjecture and refutation. This is the explanation for why it the biosphere appears *as if* it was deigned.

      Delete
    14. Lino: Common sense tells us that invoking a Designer is more logical than invoking a poorly understood feedback mechanism that is so limited in its scope.

      First, poorly understood? Speak for yourself. Apparently, you don't have an explanation as to how knowledge is created, but you know evolutionary process isn't an example of it?

      Second, It's precisely the limitations of evolutionary process that makes it the best explanation.

      One of the unique things about people is that we're universal explainers. That we we can create explanations and use them as a criteria for what possibilities we test.

      For example, it's unlikely that anyone has performed research to determine if eating a square meter of grass each day for a week would cure the common cold. Why is this? Is it because it's logically impossible? No. Is it because it's unfalsifiable? No, this would be trivial to test. Is it because it's a non-natural? No. Why then is it unlikely to be the subject of research? Because we lack an explanation as to how and why eating a square meter of grass each day for a week would cure the common cold. As such, we discard it, a priori, even before we bother to test it. And we do this for a near infinite number of mere possibilities every day, in every field of science.

      However, unlike people, natural process cannot create explanations. As such it cannot discard conjectured genetic variations due to the lack of a good explanation, a-priori, before being tested by natural selection.

      Regardless of these differences, both processes still fall under the same explanation of knowledge creation. Neither is "magic."

      Lino: I see. But this can explain nothing of OOL. Where did the genome come from? Please explain your answer.

      If the truth about the physical world doesn't consist of long chains of hard to vary explanations, then how do you explain our ability to make progress? Is that just what God must have wanted?

      Scott: Why don't you start out by explaining how knowledge is created, then point out how evolutionary theory doesn't fit this explanation.

      Lino: How about I ask a question? Is it possible for knowledge to exist if no intelligent beings exist?

      Wouldn't that depend on one's explanation as to how knowledge is created, or if one thinks it's even possible for knowledge to be created in the first place. Do you see why I keep asking you this question?

      Delete
    15. Lino: A moment's reflection tells you that knowledge can only exist if intelligence exists.

      It does? Let me guess, a moments reflection also tells us that God exists, has always existed, and has the knowledge of everything that could possibility be conceived? And we know this because the Bible has divinely revealed that we're without excuse?

      Lino: So, where did the intelligence come from? If you want to answer that intelligence arose from lifeless matter all by itself, then you're arguing that knowledge sprang up into being out of that which did not possess knowledge. Does this make sense?

      Does it make "make sense" that knowledge has always existed, rather than having been created? What empirical observations indicate that knowledge has always existed? Please be specific.

      Lino: As to explaining how"knowledge is created", why don't you tell us exactly how Darwinism explains this?

      Why didn't the first appearance of advanced multi-celled life appear along side the least complex single celled organisms? If the designer already had the knowledge of how to build each species, there would be no need to create them in the order of least complex to most complex. In fact, the designer could have created the entire biosphere, or the entire universe, last Thursday, complete with the appearance of age, implanted memories, etc. How do you explain this observation?

      Evolutionary theory explains this in that the knowledge of how to build complex multi-celled organisms had yet to be created by evolutionary processes. It's impossible to build something unless you have the knowlege of *how* to build it.

      Why is there so much time between the simplest single celled organisms and the most complex? Again, if the designer already had the knowledge of how to build each specs, they could have been created concurrently, within the same month, year, etc., rather than over billions of years appart. How do you explain this observation?

      Evolutionary theory explains this in that, unlike people, evolutionary processes cannot create explanations. As such, they were unable to discard genetic variations, a priori. Testing each and every variation takes time.

      Why have over 98% of all species that have ever existed gone extinct? How do you explain this?

      Evolution explains it in that, again, evolutionary process cannot discard genetic variations a priori. Nor does it exhibit foreknowledge or "planning".

      How was the knowledge of how to build each species, as found in the genome, created?

      Evolution explains this in that evolutionary processes are a form of knowledge creation similar to the scientific method. Genetic variation creates "theories" of how to build an organism. These "theories" are tested by by natural selection and those with errors are "discarded"

      I could go on, but I think you get my point.

      Lino: If I say an intelligent designer brought about knowledge of knowledge, at least that makes sense.

      It does? If the designer used knowledge to bring about knowledge, then what is the origin of the knowledge the designer used?

      Despite being an intelligent agent that exhibits intent, magicians cannot perform a magic trick without the knowledge of how that trick is performed. If they did, it would no longer be a magic trick, but actually magic. The knowledge of how to "build" the rabbit being pulled out of the magician's hat would have been spontaneously generated, as the magician lacks the knowledge of how to instantaneously create entire rabbits where none existed before.

      So, a "magic man did it" makes sense?

      Or are you suggesting the designer "just was" complete which the knowledge of how to build the biosphere, already present?

      However, as I've already pointed out, this doesn't serve any explanatory purpose, as one could just as simply state organisms, just appeared, complete with the knowledge of how to build themselves already present.

      Delete
    16. Hawks:
      ID has not been making that assertion for the simple reason that ID can't make that assertion. What ID does assert is that we should not expect such complexity without intelligence. What ID does NOT assert is what we should expect given intelligence.

      So now you make another assertion. And you tell us just exactly what ID can do, and not do. You must be an expert.

      ID "asserts" that only intelligence can produce specified complexity. Hence, the genome is the product of an intelligent being.

      Do you agree with this much?

      If so, then, the genome, being the product of an intelligent being---which ID asserts---should show the hallmarks of intelligent design, one of which is the avoidance of huge amounts of wasteful excess. Further, since genes produce proteins in a machine-like way, they can be viewed as basic building blocks of complexity. Intelligent design takes those basic building blocks and "fashions" them into a purposeful whole.

      And, again, this kind of thinking has been around ID since the 90's.


      Some ID supporters might have been saying this for years. However, they don't base their assertions on ID. ID itself doesn't make the assertion more than it asserts the exact opposite and everything in between.

      You seem to want to quibble about a word, rather than to deal with facts. I don't.

      Delete
    17. Scott:

      You've responded in three separate posts. My reaction to all three is to say that your thinking on all of this appears to be muddled. And I don't think you're open-minded enough for the muddle to be corrected.

      So, let me just point out what I mean by being muddled:

      Evolution explains this in that evolutionary processes are a form of knowledge creation similar to the scientific method. Genetic variation creates "theories" of how to build an organism. These "theories" are tested by by natural selection and those with errors are "discarded"


      This creation process you're touting can only be of value if replication is possible. And replication is only possible if life comes into existence. But life cannot come into existence unless the right creation theory is stumbled upon. But the right creation theory can only be stumbled upon if something knows how to create itself.

      You have no way of accounting for how this process begins.

      I'll leave you to muddle through this.

      Delete
    18. ID "asserts" that only intelligence can produce specified complexity. Hence, the genome is the product of an intelligent being.

      Do you agree with this much?


      This much, ID asserts.

      If so, then, the genome, being the product of an intelligent being---which ID asserts---should show the hallmarks of intelligent design, one of which is the avoidance of huge amounts of wasteful excess.

      No, this does not follow. The "hallmark of design" you're talking about is simply the existence of specified complexity and ID is trying (and failing, btw) to find ways to detect it. ID gives you no clue what-so-ever what intelligence should do. Intelligence could design specified complexity - or not. It could design without waste - or not. Even Dembski realised this back in 2001 when he wrote(http://www.arn.org/docs/dembski/wd_isidtestable.htm):

      But what about the predictive power of intelligent design? To require prediction fundamentally misconstrues design. ...Yes, intelligent design concedes predictability.

      How about that?

      You seem to want to quibble about a word, rather than to deal with facts. I don't.

      Wrong. I am dealing with the fact that ID can't do predictions. Dembski agrees. Unfortunately, lots of ID supporters totally fail to grasp this very simple point.

      Delete
    19. Lino: You've responded in three separate posts. My reaction to all three is to say that your thinking on all of this appears to be muddled.

      Is that so? Then you should have no problem pointing out exactly where my comments were "muddled", right?

      Lino: And I don't think you're open-minded enough for the muddle to be corrected.

      That's quite a jump there. You've gone from the vague claim of "muddled" to closed-minded and in need of correction. So, before you get ahead of yourself, let's address where my arguments were muddled, shall we?

      Lino: So, let me just point out what I mean by being muddled:

      Scott: Evolution explains this in that evolutionary processes are a form of knowledge creation similar to the scientific method. Genetic variation creates "theories" of how to build an organism. These "theories" are tested by by natural selection and those with errors are "discarded"

      Lino: This creation process you're touting can only be of value if replication is possible. And replication is only possible if life comes into existence. But life cannot come into existence unless the right creation theory is stumbled upon. But the right creation theory can only be stumbled upon if something knows how to create itself.

      Lino,

      There's a reason why I keep asking you to explain how knowledge is created. The remainder of my comments elaborate on why this question is relevant, along with responding to what appears to be your attempt to avoid it.

      So, again, why don't you start out by explaining how knowledge *is* created, then point out how evolutionary theory doesn't fit this explanation?

      Could it be that you're close-minded in presupposing that knowledge has always existed, but don't want to disclose it because you do not want to expose it to criticism?

      Delete
    20. To address your comment...

      Lino: This creation process you're touting can only be of value if replication is possible. And replication is only possible if life comes into existence. But life cannot come into existence unless the right creation theory is stumbled upon. But the right creation theory can only be stumbled upon if something knows how to create itself.

      That's like arguing we can understand nothing about how umbrellas work unless we have an exhaustive understanding of meteorology. It's a fallacious, disingenuous argument. Not to mention that we've made significant progress in explaining the OOL, which is also a variation of conjecture and refutation, but with different mechanisms.

      Again, why don't you start out by expelling how we create knowledge? Specifically, how do you explain our relatively recent, rapid increases in the creation of knowledge?

      For example, "An abstract designer did it", is a bad explanation, in that it's similar to the Greek myth of the seasons: they are both shallow and easily varied, the cast of characters are only connected to seasons though the myth itself, and the roles they play could be varied without significantly reducing it's ability to explain seasons, or the biosphere, respectively.

      This is in contrast to our current explanation of the seasons, which represents a long chain of hard to vary explanations across multiple fields. The earths rotation is titled in respect to it's orbit around the sun. A spinning sphere retains it's tilt. Surfaces titled away from radiant heat are headed less. The origin of star light (nuclear fusion), etc. If we break any part of this chain, there is no easy way to vary this explanation without significantly impacting it's ability to explain the seasons. There is no where go.

      In other words, our explanation for the seasons is good not only because it's falsifiable, but because it's hard to vary.

      Why would the explanation for biosphere be any different? Could it be that you think a voice in a whirlwind told you this was the case?

      So, how could we make progress if shallow, easily varied (bad) explanations are true? Is that just what God must have wanted?

      Delete
    21. Hawks:

      ID gives you no clue what-so-ever what intelligence should do. Intelligence could design specified complexity - or not.

      This is what I wrote:

      If so, then, the genome, being the product of an intelligent being---which ID asserts---should show the hallmarks of intelligent design, one of which is the avoidance of huge amounts of wasteful excess.

      You're twisting the argument. Intelligence tells us what intelligence does and does not do. IOW, is it intelligent to write a computer program with a whole bunch of useless code? How do you answer? (But, of course, you'll run away from the question ---in one way or another).

      You quote Dembski as saying:

      But what about the predictive power of intelligent design? To require prediction fundamentally misconstrues design. ...Yes, intelligent design concedes predictability.



      And in the very next sentence from the arn page you're quoting, Dembski said:

      But this represents no concession to Darwinism, for which the minimal predictive power that it has can readily be assimilated to a design-theoretic framework.

      How about that?


      Did I say anything about ID predicting "junk-DNA"? I said it would assert that "junk-DNA" would turn out to have function. Why? Because that's who intelligent being's design.

      And Dembski also said:

      To be sure, designers, like natural laws, can behave predictably (designers often institute policies that end up being rigidly obeyed).

      How about that?

      (And, of course, this is part of the ellipsis in your above quote of Dembski. Isn't that called "quote-mining"?)

      And the genome, per Bill Gates, is a computer program beyond anything human intelligence could design. So we're dealing with a supreme intellect at work.

      These are common sense arguments. To be a Darwinist, you have to leave common sense behind. Darwin tells us that varieties are incipient species, not the end of the line for what species can do and still survive. Does this jive with your everyday experience? Not mine.

      Delete
    22. Scott: Why don't you start out by explaining how knowledge is created, then point out how evolutionary theory doesn't fit this explanation. I

      Lino: I'll leave you to muddle through this.

      Poor Lino. Apparently, my question is too muddled for you. So, you've run off after failing to even acknowledge the questions I asked you. At all. Period.

      Or are you afraid to disclose your position as it would open it to criticism it cannot withstand?

      Delete
    23. You're twisting the argument. Intelligence tells us what intelligence does and does not do. IOW, is it intelligent to write a computer program with a whole bunch of useless code? How do you answer? (But, of course, you'll run away from the question ---in one way or another).

      No, and that was the point of the Dembski quote. Even Dembski agrees that ID doesn't predict what intelligence would do. ID says that given something that is specified and complex (SC), we can conclude that it was intelligently designed. What ID does not say is that given something intelligent, we can expect something SC - for the simple reason that intelligence can easily design things that are neither complex nor specified. It's really simple...

      And in the very next sentence from the arn page you're quoting, Dembski said:

      But this represents no concession to Darwinism, for which the minimal predictive power that it has can readily be assimilated to a design-theoretic framework.

      How about that?


      What about it? It tells you nothing about what ID expects.


      Did I say anything about ID predicting "junk-DNA"? I said it would assert that "junk-DNA" would turn out to have function. Why? Because that's who intelligent being's design.

      No, ID doesn't tell you to expect that. ID tells you that given something SC, intelligence designed it. It does not say that given intelligence, we expect SC. Simple....

      And Dembski also said:

      To be sure, designers, like natural laws, can behave predictably (designers often institute policies that end up being rigidly obeyed).

      How about that?

      (And, of course, this is part of the ellipsis in your above quote of Dembski. Isn't that called "quote-mining"?)


      No, it's not quote-mining. It's you failing to understand a very simple concept. What Dembski is saying is that given some sort of specific intelligence, we can make predictions. ID, however, does NOT make any assumptions what-so-ever about the designer. ID, therefore, does not make predictions. Simple...

      And the genome, per Bill Gates, is a computer program beyond anything human intelligence could design. So we're dealing with a supreme intellect at work.

      Well, you've got to love "argument from Bill Gates".

      These are common sense arguments.

      It might be common sense to confuse the arguments "A given B" with "B given A". Common sense would then be wrong.

      Delete
    24. Hawks: Well, you've got to love "argument from Bill Gates".

      Agreed. After all...

      "The Internet? We are not interested in it" - Bill Gates, 1993

      "I see little commercial potential for the Internet for at least 10 years" - Bill Gates, 1994

      "Anybody who thinks a little 9,000-line program that's distributed free and can be cloned by anyone (Java) is going to affect anything we do at Microsoft has his head screwed on wrong." - Bill Gates

      However, Microsoft's C# was highly influenced by Java.

      Delete
  19. Thorton:

    1) We know that naturally occurring evolutionary processes can produce extremely complicated mechanisms.

    Can you please tell us how you "know" this? Evolution via Darwinian mechanisms is the issue; not the answer.

    ReplyDelete
    Replies
    1. Hi PaV! Finally over that embarrassing thrashing you took at the hands of a real population geneticist? I bet you couldn't sit properly for weeks after that caning.

      PaV Lino

      Thorton:

      1) We know that naturally occurring evolutionary processes can produce extremely complicated mechanisms.

      Can you please tell us how you "know" this? Evolution via Darwinian mechanisms is the issue; not the answer.


      Because it's been demonstrated with the use of evolutionary algorithms.

      Go ahead PaV, say something really stupid like "that doesn't count because you used intelligence to program the computer!" You know you want to.

      Delete
    2. He is the hammer to Pav's nail.

      Delete
    3. He is the hammer to Pav's nail.

      A pot to his kettle.

      You're so full of yourselves over here. It's called, "compensation".

      Delete
  20. Cornelius, is there a way to turn off full text justification for comments?

    This is terribly unintelligent graphic design.

    ReplyDelete
    Replies
    1. Geoxus:

      Cornelius, is there a way to turn off full text justification for comments?

      This is terribly unintelligent graphic design.


      I completely agree. I don't know why they did that, and unfortunately I don't think there is a way to turn it off.

      Delete
    2. This is proof that Google IS evil.

      Delete
  21. Thorton:

    It seems to me that the computer generated evolutionary algorithms are different than what happens in organisms. In evolutionary algorithms each iteration produces a result which is an improvement. They are programmed to pick the best result or each iteration. In organisms, however, even beneficial mutations that can give a protein a new ability can cause he protein to loose stability. The residues that need to line up the right way become misaligned. You have a floppy protein floating around the cell. So you need other mutations to compensate. So you don't get the benefit until a number of mutations have occurred. And it might be even more complicated than that. You also have to change the control genes and other control things like microRNA to make sure that the new protein is produced at the right time and in the right amounts.

    ReplyDelete
    Replies
    1. natschuster

      It seems to me that the computer generated evolutionary algorithms are different than what happens in organisms.


      What your ignorance makes it seem like to you doesn't really concern science. If you want to demonstrate that EAs can't produce complex mechanisms, be my guest.

      Delete
    2. Has it been demonstrated that they can build complex mechanism when several "mutations" are required before there is any benefit? If not, then we can't say that the same process can create complxity in organisms.

      Delete
    3. natschuster

      Has it been demonstrated that they can build complex mechanism when several "mutations" are required before there is any benefit?


      Yes. Just as in real life, neutral mutations can get carried along at no evolutionary cost until either 1) an environmental change makes them beneficial, or 2) they combine with a second, later mutation and the combination is beneficial.

      Really nat, with all the info readily accessible online there's no reason for you to remain this ignorant. Unless you're happy being ignorant

      Delete
  22. Listen, evamolutionsists. Don't you think that, in summary, Cornelius has presented your case most eloquently?

    "With each new research study we learn more about evolution’s capabilities. There is, of course, no question that evolution created all of these regulatory processes and mechanisms because evolution is well known to be a fact. What is not known is the extent of evolution’s capabilities. No one would have thought evolution could have produced such elaborate designs. But as science advances so too does our knowledge of this incredible process."

    If not, what criticism of it would you raise?

    ReplyDelete
  23. Still none of you able to take up wqbutler777's challenge?

    "There really is no point arguing about it. If you want to insist that such a complex system can come about from random processes all you have to do is demonstrate an organism in the lab that initially does not have the DNA system evolving a system like this using random, naturalistic processes that would have existed on the early earth.

    If you know of someone who has done this, feel free to point me in their direction and I'll be happy to read up on their research and concede your point."

    I could see it would all end in tears before bed-time.

    ReplyDelete
    Replies
    1. Paul

      Still none of you able to take up wqbutler777's challenge?


      LOL! Why would anyone try to take up such a ridiculous straw man "challenge'?

      Tell you what Paul. I'll do it, as soon as you demonstrate your Intelligent Designer creating another entire universe including a whole planet's worth of life forms from scratch in the lab.

      When do you think your lab demonstration will be ready? You're not going to run from the challenge, are you?

      Delete
    2. Paul,

      It's absolutely astonishing, isn't it, that they have the gall to act superior and call us stupid for not believing their fantastic claims, and then get all offended when we ask for proof.

      Centuries from now people will be absolutely amazed that anyone could ever have been dense enough to believe any of this stuff.

      Delete
  24. Thorton:

    Because it's been demonstrated with the use of evolutionary algorithms.

    And, then:

    Go ahead PaV, say something really stupid like "that doesn't count because you used intelligence to program the computer!" You know you want to.

    How could I say anything more stupid than your response. You're telling us that we "know" Darwinian mechanisms work because of computer programs.

    BTW, Thorton, bumblebees aren't supposed to be able to fly.

    As to my discussion with a "real" population geneticist, besides being an amicable discussion, and somewhat informative, we ended up agreeing to disagree. But, of course, if it isn't on Wikipedia, then you can't figure it out; and as to our discussion, I'm sure most of it went over your head.

    So, now, bottom line: Thorton, you have no basis for asserting that we "know" evolutionary mechanisms can produce extremely complicated objects. Just as I thought.

    ReplyDelete
    Replies
    1. PaV Lino

      How could I say anything more stupid than your response.


      Yet you managed to somehow.

      You're telling us that we "know" Darwinian mechanisms work because of computer programs.

      Yes, that's what I'm telling you. Go argue with the hundreds of companies who successfully use EAs each day to produce complex new products if you think differently.

      BTW, Thorton, bumblebees aren't supposed to be able to fly.

      Figures an IDiot would fall for that old unban legend.

      Who says bumblebees can't fly?

      As to my discussion with a "real" population geneticist, besides being an amicable discussion, and somewhat informative, we ended up agreeing to disagree. But, of course, if it isn't on Wikipedia, then you can't figure it out; and as to our discussion, I'm sure most of it went over your head.

      LOL! You got your fanny kicked into next Tuesday. If was fun watching you eat a whole case of humble pie and slink off in disgrace. Especially when it turned out you didn't even understand the basic terminology.

      So, now, bottom line: Thorton, you have no basis for asserting that we "know" evolutionary mechanisms can produce extremely complicated objects. Just as I thought.

      Go tell that to NASA.

      NASA Evolvable Systems group

      You're every bit as ignorant yet every bit as arrogant as ever PaV. Some things never change.

      Delete
    2. Thorton:

      LOL! You got your fanny kicked into next Tuesday. If was fun watching you eat a whole case of humble pie and slink off in disgrace. Especially when it turned out you didn't even understand the basic terminology.

      You wouldn't know anything of what happened because you don't understand the concepts well enough. The terminology borders on being equivocal, and I wonder if it isn't by design in an effort to obfuscate what is otherwise a huge problem for neo-Darwinism.

      Be that as it may, our population geneticist believes in the neo-Darwinian orthodoxy; I don't; and I don't see how it is reasonable to do so. As it turned out, he was still left with the problem of the time of fixation, which he chooses not to see as a problem, assuming that neutral mutations will always be at the ready. This is where we disagree. I don't disagree because of any preconceived notions, but only because it doesn't make sense, and there's nothing to demonstrate that we see this happening in real populations.

      But population genetics is as good as dead anyway. It is hopeless to explain the diversity and complexity present in succeeding generations of organisms. Evo-devo is the "great white hope" these days. It, too, of course, doesn't have enough explanatory power to tell us how Hox genes came about in the first place, or where these regulatory mechanisms came about either.

      Figures an IDiot would fall for that old unban legend.

      Oh, but it was a legend---and, in fact, conventional wisdom---until it was shown to be otherwise. My point is that what we know about physics and what we know about biology are not commensurate, and evolutionary algorithms have precious little to do with biology.

      Go argue with the hundreds of companies who successfully use EAs each day to produce complex new products if you think differently.

      Well, you've stepped into it.

      Usually, an initial population of randomly generated candidate solutions comprise the first generation. The fitness function is applied to the candidate solutions and any subsequent offspring. Here


      The reason that genetic algorithms are not a lazy way of performing design work is precisely because of the effort involved in designing a workable fitness function. Even though it is no longer the human designer, but the computer, that comes up with the final design, it is the human designer who has to design the fitness function. If this is designed wrongly, the algorithm will either converge on an inappropriate solution, or will have difficulty converging at all.

      In the absence of a designer, nothing at all happens in these EAs. Wake up and smell the coffee.

      Delete
    3. Pav Lino

      T: "Go ahead PaV, say something really stupid like "that doesn't count because you used intelligence to program the computer!" You know you want to."

      In the absence of a designer, nothing at all happens in these EAs. Wake up and smell the coffee.


      BWAHAHAHA!!

      I knew the IDiot couldn't stop himself from saying it!

      Sometimes this script just writes itself.

      Delete
    4. Thorton:

      Aren't you the chum that complains so loudly about "quote mining"? So why do you only quote what I say at the end, while completely ignoring what is easily found on Wikipedia concerning EAs?

      You're intractable and incorrigible. You think smugness is the equivalent of correctness. I can't help you there, except to say: move beyond liberalism; you might like the truth.

      Delete
    5. PaV Lino

      Aren't you the chum that complains so loudly about "quote mining"? So why do you only quote what I say at the end, while completely ignoring what is easily found on Wikipedia concerning EAs?


      Because the Wiki article had nothing to do with my prediction, that you'd whine EA processes aren't evidence for evolution because human intelligence was involved. True to IDiot form, you did exactly as predicted.

      You're a mindless IDC dolt who can't reason for himself. You think regurgitating ID crap you've read but can't defend is the equivalent of knowledge. I can't help you there except to say - try reading some actual science journals instead of the Discovery Institute web page for your science understanding. You wouldn't look so ignorant and clueless if you did.

      Delete
    6. Thornfulness:

      Because the Wiki article had nothing to do with my prediction, that you'd whine EA processes aren't evidence for evolution because human intelligence was involved.

      Mendacious mental midget that you are, you've tried to change the subject because of what is found in the Wikipedia link. Not so fast, Thornfulness:

      From my link to Wikipedia on EAs:

      Implementation of biological processes:

      Usually, an initial population of randomly generated candidate solutions comprise the first generation. The
      fitness function is applied to the candidate solutions and any subsequent offspring.

      Then we click on "fitness function" and go to the Wikipedia page that tells us:

      The reason that genetic algorithms are not a lazy way of performing design work is precisely because of the effort involved in designing a workable fitness function. Even though it is no longer the human designer, but the computer, that comes up with the final design, it is the human designer who has to design the fitness function. If this is designed wrongly, the algorithm will either converge on an inappropriate solution, or will have difficulty converging at all.

      Is this too difficult for you to understand and grasp? Or didn't you even bother to read it?

      One of the things that has become increasingly clear to me as I've grown older is just how much liberals end up describing themselves when they attempt to characterize their opponents. And, so, we simply have to read the above quote to find out who you are.

      Isn't it you who regurgitates Darwinian [nonsense]?

      Aren't you the one who can't effectively defend it?

      Do you actually read science journals, or do you read Talk.Origins instead and wikipedia instead?
      (You're the Wikipedia master here; and the first thing you suggest to Eugen is......Talk.Origins. com).

      And, isn't it you who are the mindless Darwinian dolt who refuses to reason for himself?

      You haven't acquitted yourself well here. Your entire contribution to this board seems to be insulting people. Somehow you think that proves Darwinian theory.

      Intellectual thuggery is the refuge of scoundrels.

      Delete
  25. Its interesting how the article sited says that they need to run on supercomputers to get around the time constraints. Do organisms have supercomputers. And I didn't see anything about how a benefit that requires more than one mutation to be a benefit works. And aren't unstable proteins harmful, if for no other reason that they are a waste of resources? So meaybe you need several mutations before you get something that isn't negative. I'm just asking.

    ReplyDelete
    Replies
    1. Weather models also run on supercomputers. Does weather have a supercomputer?

      Delete
    2. I understood Thorton to be saying that evolutionary algorithms aren't just models of evolution, but actual evolution. Weather models are just that, models, not actual weather. Bit of a difference.

      Delete
    3. natschuster

      I understood Thorton to be saying that evolutionary algorithms aren't just models of evolution, but actual evolution. Weather models are just that, models, not actual weather. Bit of a difference.


      You're lying nat. Again.

      Do you think lying is going to help you get into heaven?

      Delete
    4. First, there is a difference between lying and being mistaken. Next, what exactly did you mean, then?

      Delete
  26. natschuster

    Its interesting how the article sited says that they need to run on supercomputers to get around the time constraints. Do organisms have supercomputers.


    Aah, couldn't help but revert back to your asinine trolling, could you?

    Why don't you argue "Boeing 777s fly using jet engines. Birds don't have jet engines, so therefore birds can't fly". That's just as stupid.

    Stay ignorant nat. It's what you do best.

    ReplyDelete
  27. I guess a little knowledge is a dangerous thing. I read the article you posted. It said that evolutionary algorithms need to run on supercomputers or else they run into time constraints and such. The numbers begin to work against you. That prompted me to ask whether there time constraints for evolution to happen among organisms. It seems that time constraints area a real factor in the real world. I would imagine that it takes longer for mutations, natural selection, reproduction, fixation, etc to take longer in the real world. But that's just me,

    ReplyDelete
    Replies
    1. Thorton is hiding the truth ,Nat . There are time constraints. Several thousands of millions of years. Most engineers are unwilling to wait for the algorithms to work out in real time.

      Delete
  28. natschuster

    I guess a little knowledge is a dangerous thing.


    How would you know? You've run from every bit of scientific knowledge presented to you.

    I read the article you posted. It said that evolutionary algorithms need to run on supercomputers or else they run into time constraints and such.

    "Birds don't have jet engines, so they can't fly!!"

    Stay ignorant nat. It's what you do best.

    ReplyDelete
    Replies
    1. Birds don't have jet engines, so they don't fly as fast or as high as jets. So too organisms don't have super computers, so they can't "evolve" as fast as genetic algorithms on a computer platform. Maybe they evolve so slowly that even geological time isn't enough. I'm just wondering.

      Delete
  29. natschuster

    Birds don't have jet engines, so they don't fly as fast or as high as jets. So too organisms don't have super computers, so they can't "evolve" as fast as genetic algorithms on a computer platform. Maybe they evolve so slowly that even geological time isn't enough. I'm just wondering.


    Maybe if you weren't so lazy and intellectually dishonest you'd research the topic instead of just trolling the board about it. I'm just wondering.

    Stay ignorant nat. It's what you do best.

    ReplyDelete
  30. I did read the article you posted. That's where learned that evolutionary algorithms run on supercomputers because of time constraints and such. Are you sure you want me to do more research?

    ReplyDelete
  31. natschuster

    I did read the article you posted. That's where learned that evolutionary algorithms run on supercomputers because of time constraints and such. Are you sure you want me to do more research?


    No nat. I want you to stay a dirt-ignorant trolling jerk who lies about being interested in scientific topics. Why change now?

    ReplyDelete
  32. natschuster

    First, there is a difference between lying and being mistaken.


    Yes, there is. You're lying.

    Sorry troll, you've been caught in this little "pretend you don't understand" game too many times. You even admitted it once before, remember? I do. Go lie to someone else, someone who isn't aware of your dishonesty.

    ReplyDelete
  33. I still don't understand what you meant if you didn't mean that evolutionary algorithms are not actual evolution.

    ReplyDelete
  34. natschuster

    I still don't understand what you meant if you didn't mean that evolutionary algorithms are not actual evolution.


    Too bad. Go lie to someone else, someone who isn't aware of your dishonesty.

    ReplyDelete
  35. Either it is real evolution or it isn't. When I said I thought you meant it was real evolution, you called me a liar. So I guess it means that you mean it isn't real evolution, just a model. But models are wrong a lot of the time. And anyone can program a model to give any sort of result. So if it isn't real evolution, just a model, then it is doubtful how reliable it is.

    Thorton:

    "Your still a lying little troll."

    There, I saved you the trouble.

    ReplyDelete
  36. natschuster

    "Your still a lying little troll."


    You are a lying little troll nat. You already admitted it. You also spelled "you're" wrong.

    Some teacher.

    ReplyDelete
  37. I do have a life outside of blogging. Sometimes I don't have time to edit out my typos. When I teach, I'm usually more careful. Any more nits you want to pick?

    ReplyDelete
    Replies
    1. natschuster

      I do have a life outside of blogging. Sometimes I don't have time to edit out my typos. When I teach, I'm usually more careful.


      Heh. You mean like the time you took it upon yourself to "edit" and removed material from the school board approved science curriculum because it didn't match your Creationist views. A despicable action that by all rights should have gotten you fired. Yeah, you're one heck of a teacher alright.

      Any more nits you want to pick?

      Go ahead and keep lying and trolling the board if that's how you get you jollies. Just don't expect any answers to your dishonesty from me.

      Delete
  38. Hmm, I wonder if IDiots are ever going to do their own science, instead of just trying to find things wrong with science that is done by real scientists?

    Oh wait, there isn't any science to be done when it comes to intelligent design creation, because it's all based on wacky, antiquated fairy tales.

    ReplyDelete
  39. Thorton:

    I only skipped the page that contained the faked drawings because I don't like to lie to children. I did mention that scientists say that since some embryos look alike at some point in their development, it is considered evidence for evolution. I also mentioned that they don't look alike at other points. The books left that part out. I gave the students all the facts and let them decide for themselves. So I didn't remove anything imformation. Just the opposite, I added information. And the school boards consist almost entirely of political appointee who know nothing about education or the subjects we teach, so I'm not impressed by anything the Board of Ed approves.

    You really have got to get a life. Yoru obsession with me is really unhealthy.

    ReplyDelete
  40. natschuster

    I only skipped the page that contained the faked drawings because I don't like to lie to children.


    Except there weren't any "fake" drawings. In your ignorance you removed part of the established lesson plan, something you had neither the training nor authority to do. You didn't add information, you added your own personal Creationist propaganda. You screwed those kids out of part of their science curriculum. You deserved to be fired.

    You also sure don't have any problems lying to anyone else, like you lied to people on this board when you pretended to be interested in learning. You already flat out admitted you were trolling. I remember it very well, and so do you. So don't act surprised when you get treated like a lying troll.

    You really have got to get a life. Yoru obsession with me is really unhealthy.

    Nobody is holding a gun to your head and forcing you to lie and troll the board. That's slime of your own choosing Bunky.

    ReplyDelete
  41. The real embryos don't look like the drawings.
    That much I know, so they are faked. They are not accurate. When the textbooks used photos instead of drawings, I didn't skip them.In each case, I did say that the scientists do say that since they kinda look alike, it is evidence for evolution. When I told them that they don't look alike at other points in their development I was adding information. Its simple arithmetic.

    I must confess I kinda enjoy baiting you. I know its immature. But its fun. And, Like I tell my students, "just ignore it, and he'll stop," you could ignore me.

    But now I'm getting concerned over your obsession. You really need to get a life.

    ReplyDelete
  42. natschuster

    I was adding information. Its simple arithmetic.


    Natschuster arithmetic:

    1. Screw his kids, unilaterally delete part of their approved science curriculum.
    2. Lie to them, put in your own dishonest Creationist spin.
    3. Go online and brag about it like it was something to be proud of.

    You should be legally barred from ever teaching children again. Misusing the trust of a teacher like that is truly despicable. You deserve to be fired.

    I must confess I kinda enjoy baiting you.

    I'm sure in your mind you're a master baiter. But reality seems to be you're just mad because no one will fall for your lying and trolling anymore.

    ReplyDelete
  43. How did I delete part of the apporved curriculum? I just didn't use the inaccurate drawings? How is including information that is not in the textbooks lying? How is giving them all the information lying? And, again, the curriculum is written by people who know nothing about anything. They are politicians.

    And you keep responding, so you obviously are falling for it.

    ReplyDelete
  44. natschuster

    How did I delete part of the apporved curriculum?


    You already admitted to skipping it. If you're going to keep lying you need a better memory.

    I just didn't use the inaccurate drawings? How is including information that is not in the textbooks lying? How is giving them all the information lying?

    When your added "information" is just Creationist BS, it's lying.

    And, again, the curriculum is written by people who know nothing about anything. They are politicians.

    LOL! I suppose you're a specialist in embryology? Enough so that you can unilaterally declare science textbook material to be fraudulent? You're a real hoot there master baiter.

    You deserve to be fired and legally restrained from ever teaching children again.

    And you keep responding, so you obviously are falling for it.

    Pointing out your continued dishonesty and trolling isn't the same as falling for it.

    ReplyDelete
  45. I think, since you are not an educator, you are missing the distinction between methodology and content. The content was the assertion that the embryos look alike. The methodology was the use of faked drawings. You don't have to be an embryologist to see that they don't look like photos. You just need eyes. I covered the content. I just didn't use faked drawings, a dishonest methodology. And the fact that the embryos don't look all that much alike, and go through different developemental pathways and such at other stages of development, e.g. blastula, gastrula, is biological fact. No spin, just fact.In fact mammal blastulas are so different they are called blastocists.

    Now, it occured to me that I am enabling very unhealthy behavior on your part. Your obsession with me is becoming pathological. If no one is fooled by me, then why do you keep responding? My baiting you into responding, is not only immature on my part, but encouraging pathological behavior on your part. So I'm thinking, for your sake, that I will no longer respond, when you get all ad hominum, insulting, etc. I'm concerned.

    ReplyDelete
  46. natschuster

    I think, since you are not an educator, you are missing the distinction between methodology and content.


    Since you have no formal scientific training in the subject you're not qualified to judge content. You're a Creationist who lied to and screwed his kids based solely on your religious beliefs. You deserve to be fired.

    BTW nat, you are the one who keeps knee-jerk responding. I only post to you when it's necessary to point out your lies and trolling, like now.

    You like to lie and troll the board for kicks. I like to point out your dishonest behavior. To each his own.

    ReplyDelete
  47. I just said I wasn't judging the content. I taught the content. I was rejecting the methodology because I have eyes. Adn I was under the impression that you start by responding to my posts on the topic, then I respond on topic, then you start with the name calling. That's when I start baiting you and you bring up things like my teaching. If you woudl limit your responses to the topic, y'know, prove me wrong, then I wouldn't feel the need to bait you. I know I said that I wouldn't respond, but i just can't help it.

    ReplyDelete
    Replies
    1. natschuster

      I just said I wasn't judging the content. I taught the content. I was rejecting the methodology because I have eyes.


      You're vastly unqualified to make that judgement either. You're a Creationist who lied to and screwed his kids based solely on your religious beliefs. You deserve to be fired.

      You keep lying and trolling the board for kicks. I'll keep pointing out your dishonest behavior. You and Tedford make perfect examples of the type of dishonest bullcrap science has to put up with from Creationists.

      Delete
  48. Sorry, laughing out loud was me. My daughter forgot to sign out.

    ReplyDelete