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  1. #1
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    Epigenetics and the problem of origins

    Every cell in your body contains the same DNA. So how does one cell know that it should be a muscle cell, and another cell know that it should be an eye cell and so on. In other words, how do the cells know which part of the body that they should make???

    Epigenetics is a branch of genetics that argues that signals from the environment of a cell tell the cell what kind of cells to make. Signals arrive at the membrane, and are relayed to the nucleus of the cell by a neat system of communication. The signals switch on or off various segments of the DNA.

    This makes perfect sense. However it still leaves us with a paradox - the origin of a system of signals in the membrane and the origin of appropriate responses from the DNA to those signals.

    To put this in perspective, realise that whilst DNA contains about 3 billion letters, the number of cells in your body numbers about 100,000 billion, and each of these cells must know it's proper place. So the signal response system must be able to sense the position and function of each cell and relay this to the nucleus, then activate just the right bits of the DNA in order to reproduce just the right kind of cell.

    It is hard to see how this could have evolved at all. Richards previous responses suggest that improbability is not an issue, however I beg to differ. We are not just faced with the improbability of the creation of the DNA code itself, we also have the vastly greater improbability of the creation of a signal response system capable of mapping the position and function of every cell in your body to on/off switches that activate or deactivate specific segments of DNA.

    Taking epigenetics into account, the complexity of life just increased by a factor of about 100,000 billion times.

    Faced with this paradox, some scientists have suggested the existence of a top-down process, whereby the position and function of individual cells is determined by a field. This field contains a kind of 3 dimensional template of what the organism should grow into, and cells read this field and relay the signals to the DNA. However, the DNA would still need to be preprogrammed with the specific appropriate responses to each signal - thats more than 100,000 billion different specific responses !!!

    And the existence of such a field is yet to be demonstrated - and as I just mentioned, it still leaves the extreme improbability unanswered.

    If anything, epigenetics raises an unforeseen problem - viz - how can a code containing 3 billion letters, also contain 100,000 billion different instructions. That would mean that each letter would have to code for 30,000 instructions ?

    Does the information required to create our bodies exceed the capacity of DNA? And if so, where else could the information reside?
    Last edited by Craig.Paardekooper; 05-27-2013 at 06:14 AM.

  2. #2
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    Quote Originally Posted by Craig.Paardekooper View Post

    Faced with this paradox, some scientists have suggested the existence of a top-down process, whereby the position and function of individual cells is determined by a field. This field contains a kind of 3 dimensional template of what the organism should grow into, and cells read this field and relay the signals to the DNA. However, the DNA would still need to be preprogrammed with the specific appropriate responses to each signal - thats more than 100,000 billion different specific responses !!!

    And the existence of such a field is yet to be demonstrated - and as I just mentioned, it still leaves the extreme improbability unanswered.

    If anything, epigenetics raises an unforeseen problem - viz - how can a code containing 3 billion letters, also contain 100,000 billion different instructions. That would mean that each letter would have to code for 30,000 instructions ?

    Does the information required to create our bodies exceed the capacity of DNA? And if so, where else could the information reside?
    Hello Craig

    every time facts like this are brought to my attention the verse from Psalm 139 comes to mind; (v14) I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well.
    When this was penned, the human writer could not have understood the complexity that has now been discovered. When you say; "Taking epigenetics into account, the complexity of life just increased by a factor of about 100,000 billion times.", the expression "fearfully and wonderfully made" cannot be bettered. We do not have the words to express greater wonder and increased complexity. All we might say is; "fearfully and wonderfully made" times a factor of a googol or in terms of "100,000 billion times" to shorten that to the mathematical number 1014 times.

    "Mind boggling" is also an expression that comes to my mind and the fact is also that the world's population is presently numbered at 6 billion and that excludes all the people that has ever lived and yet God knows from all those who are his and those who are sleeping in Christ have the spirits retained by God. Can the mind of man ever comprehend what God can do? Simple acceptance and faith in God and the admission of the Psalmist is all we can have.

    You have just made the understanding of the simplest cell 10? harder to explain.

    All the best

    David

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    A Pixel Analogy

    A computer generated picture is made of pixels - with each pixel having a specific colour in a specific position.

    If we think of a cell as a pixel, then the human body is a picture made of 100,000 billion pixels, each pixel specified for it's colour and location.

    A billion bytes = 1 Gigabyte, so the information required to make a human body = 100,000 billion bytes = 100,000 Gigabytes.

    What puzzles me though, is that the DNA only contains 3 Gigabytes of storage = 3 billion letters (same as most laptop hardrives)



    The difference is a factor of 33 k or 33,000. So each letter in the DNA would need to be read in 33,000 different ways.



    Hypothetically,this might be possible if the signals from the cells environment don't just activate DNA instructions, but also determine the content of the instructions. ie the signals themselves form a second tier of data determining how each letter in the DNA is read. Then if there were 33,000 different signals from then membrane - when combined with each letter of the DNA, that would make 100,000 billion different combinations

    External signal x DNA letter = 30,000 permutations x 3 billion permutation = 100,000 billion possible instructions.


    Going back to the pixel analogy - this analogy only required two pieces of information for each pixel - it's location and it's colour. Cells are more complicated than pixels, so would require more information. So 100,000 billion is an under estimate.


    What we do know is that DNA without an environmental signalling system would never produce eukaryotes (multi cellular organisms) - because there would be no cell differentiation.
    Last edited by Craig.Paardekooper; 06-02-2013 at 09:26 AM.

  4. #4
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    Quote Originally Posted by Craig.Paardekooper View Post
    A computer generated picture is made of pixels - with each pixel having a specific colour in a specific position.

    If we think of a cell as a pixel, then the human body is a picture made of 100,000 billion pixels, each pixel specified for it's colour and location.

    A billion bytes = 1 Gigabyte, so the information required to make a human body = 100,000 billion bytes = 100,000 Gigabytes.

    What puzzles me though, is that the DNA only contains 3 Gigabytes of storage = 3 billion letters (same as most laptop hardrives)
    I think the answer is quite simple. The DNA is analogous to a computer program. A very short program can generate infinite complexity. For example, just a few lines of code can generate a Mandelbrot fractal:

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    Segmented organisms are a good biological example. They do not need a new block of DNA for each segment. They just need a small amount of information that says "scale and repeat." I think this is why many of the earliest organisms were segmented. It is very easy to simply repeat the same pattern over and over. Evolution is the most natural thing you could imagine. And when you understand it, it is obviously inevitable.

    Click image for larger version. 

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  5. #5
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    Segmented organisms are a good biological example. They do not need a new block of DNA for each segment. They just need a small amount of information that says "scale and repeat." I think this is why many of the earliest organisms were segmented. It is very easy to simply repeat the same pattern over and over. Evolution is the most natural thing you could imagine. And when you understand it, it is obviously inevitable.
    Hi Richard,

    I agree that it would make sense that repeated biological structures are coded for by repeated DNA sequences. However, I can cannot see how fractals can produce cell differentiation, since fractal is just another word for repetition.

    Cell differentiation means different cells in very specific places carrying out specific functions.

    How would fractals know to produce an ear in one place, and an eye in the other? Do you have any insight on this? - And I only want 2 eyes and two ears please - not an entire body made of eyes and ears of different sizes.
    Last edited by Craig.Paardekooper; 06-02-2013 at 11:00 AM.

  6. #6
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    Quote Originally Posted by Craig.Paardekooper View Post
    Hi Richard,

    I agree that it would make sense that repeated biological structures are coded for by repeated DNA sequences. However, I can cannot see how fractals can produce cell differentiation, since fractal is just another word for repetition.

    Cell differentiation means different cells in very specific places carrying out specific functions.

    How would fractals know to produce an ear in one place, and an eye in the other? Do you have any insight on this? - And I only want 2 eyes and two ears please - not an entire body made of eyes and ears of different sizes.
    Hey there Craig,

    I used fractals only as an example of how a small amount of code could produce complexity. It was not meant as a direct analogy to specific biological features.

    And to be clear, the "repeated biological structures" are NOT "coded for by repeated DNA sequences." It's just the opposite. Rather than repeating big chunks of DNA, all you need to do is have amount of code that says "repeat and scale using that one block of DNA."

    As for your question concerning cell differentiation - that is a very complex topic that would require some serious knowledge of genetics and biology. But I'd be happy to explore it with you if you are so inclined (though I think there are more important points to address, such as the overwhelming body of evidence that contradicts the flood). In any case, I would start with your desire for bilateral symmetry (2 eyes, 2 ears, etc.). That is one of the earliest advances in mulitcellular evolution. It is governed by the Hox Genes. Are you familiar with them?

    From the wiki: Hox genes (from an abbreviation of homeobox) are a group of related genes that control the body plan of the embryo along the anterior-posterior (head-tail) axis. After the embryonic segments have formed, the Hox proteins determine the type of segment structures (e.g. legs, antennae, and wings in fruit flies or the different vertebrate ribs in humans) that will form on a given segment. Hox proteins thus confer segmental identity, but do not form the actual segments themselves.
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  7. #7
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    Hi Richard

    Cool, I must learn all about development and hox genes.

  8. #8
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    Quote Originally Posted by Craig.Paardekooper View Post
    Hi Richard

    Cool, I must learn all about development and hox genes.
    Absolutely!

    And while we are chatting - I am curious if you understand how "devolution" really works. You seem to think that devolving organisms would keep all their functions just in a "weaker and smaller" way. But that's obviously false because in some environments smaller is more fit. And more importantly, would we not expect a general loss of functionality like we see when fish live in dark caves? When natural selection is removed, random mutations quickly accumulate and the organ loses all functionality. Does this not PROVE that natural selection works to prevent devolution?
    • Skepticism is the antiseptic of the mind.
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  9. #9
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    Hi Richard,

    I found a video on Hox Genes, which shows that the body plan is programmed into DNA. The scientists studying flies found that a body part can be made to grow from a different part of the body when hox genes are suppressed. Very cool to know this.

    http://www.youtube.com/watch?v=pa9uPnIeVKU

    So DNA for a particular limb can be activated or deactivated. This means that one day they will be able to regrow limbs that were amputated, or organs that were damaged through accidents. Very exciting.

    I agree that mechanisms are at work to help protect us from the ravages of mutation - and one such mechanism is natural selection. My question would be - is natural selection a sufficient protection to prevent the accumulation of errors with each passing generation.

    And while we are chatting - I am curious if you understand how "devolution" really works. You seem to think that devolving organisms would keep all their functions just in a "weaker and smaller" way. But that's obviously false because in some environments smaller is more fit. And more importantly, would we not expect a general loss of functionality like we see when fish live in dark caves? When natural selection is removed, random mutations quickly accumulate and the organ loses all functionality. Does this not PROVE that natural selection works to prevent devolution?

    You seem to think that devolving organisms would keep all their functions just in a "weaker and smaller" way. But that's obviously false because in some environments smaller is more fit
    The only reason that size might be related to fitness, is that fit creatures would live longer, and so they would grow for longer, and hence reach bigger sizes. This is particularly so for reptiles that continue to grow through out their lifespans.

    I would say that devolving organisms loose their functions quicker - ie they die younger before reaching a large size.

    So even if size is not a cause of fitness, I would still argue that size is an effect of fitness. I would say that size is also an effect of the fitness of the environment for life. In a very supportive environment creatures might grow much bigger, ie in paradise conditions. Often, when I look at the fossils of bigger plants, bigger insects, bigger fish, bigger reptiles and bigger mammals I
    get the impression that the environment was so much more supportive then because it allowed life to floursh so much more.


    would we not expect a general loss of functionality like we see when fish live in dark caves?
    Devolution is the same as ageing, but on a species scale. There would be a maintenance of vital functions until near the end.

    I would say that random mutation operates in both light and dark, but natural selection removes harmful mutations in the light, but does not do so in the dark. So I agree that natural selection slows down the process of devolution.

    But the question still remains as to whether natural selection can HALT devolution or even REVERSE it. Such a question can only be answered by counting harmful mutation rates between each generation for a chosen species.

    And even if natural selection cannot halt devolution, then there is still hope that unnatural selection can (ie via Gene Therapy)
    Last edited by Craig.Paardekooper; 06-02-2013 at 03:40 PM.

  10. #10
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    Quote Originally Posted by Craig.Paardekooper View Post
    Hi Richard,

    I found a video on Hox Genes, which shows that the body plan is programmed into DNA. The scientists studying flies found that a body part can be made to grow from a different part of the body when hox genes are suppressed. Very cool to know this.

    http://www.youtube.com/watch?v=pa9uPnIeVKU

    So DNA for a particular limb can be activated or deactivated. This means that one day they will be able to regrow limbs that were amputated, or organs that were damaged through accidents. Very exciting.
    Hey there Craig,

    Thanks for the link. It was great. I'm constantly amazed at the amount of free information available. I could easily spend all my time studying everything.

    The potential of genetic manipulation is both exciting and scary. If we ever gain full control I have no doubt that folks will want to transform themselves into anything that can be imagined. Just look at what folks are willing to do with painful surgery! Imagine if they could do it genetically? Like the guy who wanted to look like a cat:

    Click image for larger version. 

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    Quote Originally Posted by Craig.Paardekooper View Post
    I agree that mechanisms are at work to help protect us from the ravages of mutation - and one such mechanism is natural selection. My question would be - is natural selection a sufficient protection to prevent the accumulation of errors with each passing generation.
    Is it not obvious that natural selection is sufficient? It takes somewhere between 10-100 thousand years for cavefish to lose their eyesight. The only difference between them and the surface fish is natural selection.

    Quote Originally Posted by Craig.Paardekooper View Post
    The only reason that size might be related to fitness, is that fit creatures would live longer, and so they would grow for longer, and hence reach bigger sizes. This is particularly so for reptiles that continue to grow through out their lifespans.
    There is a correlation between size, metabolism, and longevity. You can read one study here. But there are other factors as you well know. For example, insects and plants are much bigger in the tropics. Environmental factors play an important role.

    Quote Originally Posted by Craig.Paardekooper View Post
    I would say that devolving organisms loose their functions quicker - ie they die younger before reaching a large size.
    But is there any science backing you up?

    Quote Originally Posted by Craig.Paardekooper View Post
    So even if size is not a cause of fitness, I would still argue that size is an effect of fitness. I would say that size is also an effect of the fitness of the environment for life. In a very supportive environment creatures might grow much bigger, ie in paradise conditions. Often, when I look at the fossils of bigger plants, bigger insects, bigger fish, bigger reptiles and bigger mammals I
    get the impression that the environment was so much more supportive then because it allowed life to floursh so much more.
    Again, I think it's just because it was more tropical.

    Quote Originally Posted by Craig.Paardekooper View Post
    Devolution is the same as ageing, but on a species scale. There would be a maintenance of vital functions until near the end.
    I could see similarities perhaps between aging and devolution. But there is no evidence for this actually happening as far as I know. The biggest problem with your thesis is that the smaller animals are not descendants of the larger ones that went extinct. E.g. smaller modern elephants are not the descendants of the mammoths. Horses are not descended from the giant horse but rather from much smaller horses that evolved into bigger modern horses. Etc.

    The most difficult thing about your theory is that it directly contradicts the entire body of evolutionary science. How could you have any confidence that it is correct?

    Quote Originally Posted by Craig.Paardekooper View Post
    I would say that random mutation operates in both light and dark, but natural selection removes harmful mutations in the light, but does not do so in the dark. So I agree that natural selection slows down the process of devolution.
    Again, you seem to have a false understanding of "harmful and beneficial" mutations. Did you watch that video that explained how evolution is a random exploration of genetic phase space? It explains why evolution is as certain as the second law of thermodynamics.

    The strangest thing in all this is that I don't get the impression that you actually have any real understanding of the science you are seeking to overthrow. How is your project any different than a school kid thinking to overthrow relativistic cosmology?

    Quote Originally Posted by Craig.Paardekooper View Post
    But the question still remains as to whether natural selection can HALT devolution or even REVERSE it. Such a question can only be answered by counting harmful mutation rates between each generation for a chosen species.
    You assumption that "devolution is a fact" is very problematic. You seem to have latched onto it merely because it coheres with what you want to believe. But if it were true it would mean that tens of thousands of working biologists have missed something that you have found. Doesn't that seem a little unlikely?

    Great chatting!

    Richard

    PS: It would be great if you could answer my previous post where I went point by point. Especially the many proofs that the flood could never have happened. If you don't deal with those issues how could you hope to right a book that anyone would take seriously?
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