Genetics Intelligent Design

Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form

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Jonathan Wells Jonathan Wells, the author of The Myth of Junk DNA, offers some thoughts on the limitations of what DNA does. Read this before you pay attention to any more DNA fundamentalism:

We have rigorous experimental evidence that DNA does not even code completely for proteins; in most cases the final forms of proteins are not fully specified by DNA sequences.

After transcription, most multi-exon eukaryotic genes undergo alternative splicing, which changes the sequence. [1] We know of one DNA sequence (a “gene” in now-obsolete parlance) in Drosophila from which over 18,000 different proteins are derived, mostly through alternative splicing. [2]

After alternative splicing, some mRNAs undergo editing, in which various subunits are modified or removed and new subunits are added. [3] Because of alternative splicing and RNA editing, the sequences of most mRNAs are different from the original DNA sequence. Instead, their final forms are specified by processes mediated by huge epigenetic complexes (spliceosomes and editosomes) that respond to extracellular cues and operate differently in different developmental stages.

Even after RNAs are translated into proteins, the latter change in ways that cannot be traced back to DNA sequences. First, proteins with the same amino acid sequences can adopt different three-dimensional folding patterns; these are called “metamorphic proteins.” [4] Second, most proteins are glycosylated: That is, complex carbohydrates are chemically bonded to them to generate enormous diversity in protein functions. [5] Since carbohydrate molecules are branched, they carry many more orders of magnitude of information than linear molecules such as DNA and RNA. This has been called the “sugar code,” and although it is highly specified it is largely
independent of DNA sequence information. [6]

So DNA does not completely specify proteins; but even if it did, it would not specify their spatial locations in the cell or embryo. After a protein is transcribed in the nucleus, it must be transported to the proper location in the cell with the help of cytoskeletal arrays and membrane-bound targets that are not themselves specified solely by DNA sequences. The pattern of spatial information in the membrane — called the “membranome” — is known not to be specified by DNA [7] Since spatial localization is essential for proteins to function properly, this adds yet another layer of complexity to the specification of form and function. [8]

Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.

[1] Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, et al. (2013) Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153-165. doi:10.1038/nrm3525

[2] Sun W, You X, Gogol-Döring A, He H, Kise Y, et al. (2013) Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing. EMBO J Jun 21, 2013. doi:10.1038/emboj.2013.144

[3] Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253-260. doi:10.1038/nbt.2122

[4] Bryan PN, Orban J (2010) Proteins that switch folds. Curr Opin Struct Biol 20:482-488. doi:10.1016/j.sbi.2010.06.002

[5] Furukawa K, Ohkawa Y, Yamauchi Y, Hamamura K, Ohmi Y, et al. (2012) Fine tuning of cell signals by glycosylation. J Biochem 151:573-578. doi:10.1093/jb/mvs043

[6] Gabius H-J (2000) Biological information transfer beyond the genetic code: The sugar code. Naturwissenschaften 87:108-121. doi:10.1007/s001140050687

[7] Cavalier-Smith T (2004) The membranome and membrane heredity in development and evolution. In: Hirt RP, Horner DS, eds. Organelles, Genomes and Eukaryote Phylogeny. CRC Press (Boca Raton, FL) pp 335-351.

[8] Wells J (2013) The membrane code: A carrier of essential biological information that is not specified by DNA and is inherited apart from it. In: Marks RJ II, Behe MJ, Dembski WA, Gordon BL, Sanford JC, eds. Biological Information: New Perspectives. World Scientific (Singapore) pp 474-488.

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212 Replies to “Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form

  1. 1
    Dionisio says:

    spliceosomes and editosomes

    Basically a bunch of different kinds of ‘whateversomes’ – mind-boggling!
    Specially to think all that came up by accident…

  2. 2
    AVS says:

    Wow, what BS this is. Are these directly quoted from him? I guess I’m really not surprised. He knows his audience well; scientifically illiterate and completely lacking any knowledge in the field of biology.

  3. 3
    Upright BiPed says:

    Perhaps its time for a content-free attack.

  4. 4
    Joe says:

    And another devastating “refutation” by AVS. How can ID withstand such from an anonymous ass?

  5. 5
    CentralScrutinizer says:

    C’mon, AVS is a 14 year old. He still has water behind his ears. Don’t be too hard on him.

  6. 6
    AVS says:

    Every single one of his points is an equivocation, twisted to suit the point he is trying to make.
    “After transcription, most multi-exon eukaryotic genes undergo alternative splicing, which changes the sequence.”
    Yes they undergo alternative splicing, but the actual exons that become the protein coding mRNA retain completely retain their sequence. The introns are spliced out, which is his “change in sequence,” but the actual sequences of the protein coding region never changes. And the exons are never, to my knowledge, switched in order. Some genetic information is left out, some is included. The sequence that actually codes for the eventual protein never changes. This is exactly how Dscam alternative splicing works, there is just a large number of different possible exons.
    “After alternative splicing, some mRNAs undergo editing, in which various subunits are modified or removed and new subunits are added.”
    He completely overstates the findings in this paper. The study he sites found that over 90% of the RNA editing was a single nucleotide being switched from A to G. While this is a change in the actualy sequence, only a fraction of these changes will result in a change in the amino acid sequence of the protein and only a fraction of those residue changes will have an effect on the actual function of the protein.
    “Even after RNAs are translated into proteins, the latter change in ways that cannot be traced back to DNA sequences. First, proteins with the same amino acid sequences can adopt different three-dimensional folding patterns; these are called metamorphic proteins.”
    The paper he cites specifically demonstrates “that an amino acid sequence has more information content than previously thought.” And what controls amino acid sequence? Yup, you guessed it, nucleotide sequence.
    “Second, most proteins are glycosylated: That is, complex carbohydrates are chemically bonded to them to generate enormous diversity in protein functions.”
    Again, he blows the results of a study way out of proportion. Not only are significant sugar modification-induced changes in protein functionality rare, but in terms of the most common N-linked oligosaccharides, the initial addition of sugar residues is driven by the target Asparagine-X-Serine sequence. This is another sequence that is coded by…wait for it….DNA! The additional modifications of these sugar moieties is regulated by transport through the ER, Golgi, and other secretory organelles, which is largely driven by……yup…. signal sequences coded for by DNA and recognized in the amino acid sequence.
    “Since carbohydrate molecules are branched, they carry many more orders of magnitude of information than linear molecules such as DNA and RNA. This has been called the “sugar code,” and although it is highly specified it is largely independent of DNA sequence information.”
    He forgets to mention that the “many more orders of magnitude of information” is completely theoretical, as per the original paper: “As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers.” While I am not denying the fact that there is a sugar code, I am stating that Johnny here has blown its significance a bit out of proportion.
    “So DNA does not completely specify proteins; but even if it did, it would not specify their spatial locations in the cell or embryo. After a protein is transcribed in the nucleus, it must be transported to the proper location in the cell with the help of cytoskeletal arrays and membrane-bound targets that are not themselves specified solely by DNA sequences.”
    Yes, and this transport is driven largely by protein-protein or the protein-sugar interactions we just talked about, which can all be traced back to the amino acid sequence and therefore the DNA sequence.
    The eighth citation is straight out of the “discovery institute”…need I say more?
    “Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.”
    I’m not even sure what his point is here. Other than trying to be dogmatic in his claims that we’ve mutated every single nucleotide of these organism’s genome (which we haven’t even come close to) and have only learned that these three outcomes are possible…yeah.. we haven’t learned anything else from the study of these model organisms. I mean, what other outcome would you expect anyway? An alien fruit fly? His ability to gloss over the fact that huge, and I mean HUGE, amounts of information can be gained from studying “defective” and dead fruit flies at the molecular, cellular, tissue, and organismal level is astounding.
    Like I said, complete BS. This guy really knows how to blow it out his rear end.

    Take note, BA, this is how comments are supposed to be done.

  7. 7
    Moose Dr says:

    I am a bit confused by Dr. Wells’ discussion that DNA does not contain the assembly instruction of life. It is clear that there must be a whole lot more than “protein coding” genes and even “RNA coding genes”. Beyond the genes, there must be assembly instructions. However, that “junk DNA” that Dr. Wells is so famous for debunking seems the most logical place to put the necessary assembly instructions. Does Dr. Wells not believe that “junk DNA” isn’t where this code, or much of it, is hidden?

  8. 8
    AVS says:

    Obviously, mooseknuckle, this guy has been talking in circles so much that he doesn’t know which end is up anymore.

  9. 9
    cantor says:

    Wow, what BS this is.

    Could you be just a tad more specific?

  10. 10
    AVS says:

    See above, Cant. Is that specific enough for you? Enough content for you upright?

  11. 11
    Dionisio says:

    Guys, y’all seem so much ahead on the cutting edge of scientific knowledge.
    Can someone please point to sources that provide a serious, accurate, reasonable, logical, understandable, detailed, complete, unambiguous, absolute, coherent, consistent, objective description of ALL the processes that take place during embryonic development?
    Please, also point to sources that provide a serious, accurate, reasonable logical, understandable, detailed, complete, unambiguous, absolute, coherent, consistent, objective description of how we got ALL that to begin with.
    Please, make sure the referred sources cover all current and future related discoveries.
    Thank you in advance.

  12. 12
    Dionisio says:

    Ok, let’s make it easier: just concentrate on the first week of development. That’s all for now.
    Now looking forward with great anticipation to your reply.

  13. 13
    AVS says:

    The fact that you are seriously asking that question, dionisio, tells me everything I need to know about your knowledge in the field of biology and science as a whole.

  14. 14
    Dionisio says:

    Guys, y’all seem so much ahead on the cutting edge of scientific knowledge.
    Can someone please point to sources that provide a serious, accurate, reasonable, logical, understandable, detailed, complete, unambiguous, absolute, coherent, consistent, objective description of ALL the processes that take place during the first week of embryonic development?
    Please, also point to sources that provide a serious, accurate, reasonable logical, understandable, detailed, complete, unambiguous, absolute, coherent, consistent, objective description of how we got ALL that to begin with.
    Please, make sure the referred sources cover all current and future related discoveries.
    Thank you in advance.

  15. 15
    Joe says:

    AVS- Alternative gene splicing requires knowledge- what to edit out and what to splice back together. Just how does blind watchmaker evolution explain that?

  16. 16
    Dionisio says:

    Dear AVS
    I’m not a biologist at all. Not even close. I’m an ignorant in the field. Middle school kids know more biology than I do.
    I have a degree in electrical engineering from a university in Eastern Europe.
    I have spent many years working on software development. Most of that time working on engineering apps. Lots of math, specially 3D geometry.
    A few years ago I quit my job (6-digit income) so I could study this fascinating field of biology. This should tell you I’m not joking. I’m craving for information. And I noticed most folks in this and other discussion forums can teach me a few things. Maybe that includes you too?
    Bottom line, I’m learning quite a bit from this experience.
    Did I make myself clear this time?
    Have a good day buddy.
    BTW, sometimes I write at different hours, because I commute between UTC+1 and UTC-5 😉

  17. 17
    Joe says:

    Which came first the genes that needed splicing or the complex protein machinery required to do the splicing?

    I can see it now, the early ribosomes started complaining:

    Hey you guys are sending me a lot of nonsensical crap, could you hire an editor already!?

  18. 18
    AVS says:

    Well, Joe, I can tell you right now that this conversation is going to require more knowledge in biology than you have and will probably devolve into an argument about what information is, but I’ll play along for now.
    Alternative splicing can be regulated by the use of different upstream promoters, the use of different transcription complexes composed of different proteins, the binding of different protein factors to the RNA chain, the binding of various alternative splicing factor proteins, the list goes on. These proteins are all subject to the typical mechanisms of evolution. Slight modifications can change binding specificity and affinity, and protein functionality can subsequently be altered.

  19. 19
  20. 20
    AVS says:

    You’re quite the character Joe.
    But anyways I can picture a scenario where genes do not need to be spliced, but a relatively simple protein evolves that is capable of modifying RNA at low levels, producing a new protein with a slightly different function that may benefit an organism. You’re problem is that you think these huge complex protein complexes we see in eukaryotes today had to all come about at once. No one is claiming this happened.

  21. 21
    Dionisio says:

    Dear all, (originally wrote this to AVS)
    I’m not a biologist at all. Not even close. I’m an ignorant in the field. Middle school kids know more biology than I do.
    I have a degree in electrical engineering from a university in Eastern Europe.
    I have spent many years working on software development. Most of that time working on engineering apps. Lots of math, specially 3D geometry.
    A few years ago I quit my job (6-digit annual income in US$), despite my wife’s and friends’ opposition, so I could study this fascinating field of biology. This should tell you I’m not joking. I’m craving for information. And I noticed most folks in this and other discussion forums can teach me a few things. Maybe that includes you too?
    Bottom line, I’m learning quite a bit from this experience.
    Did I make myself clear this time?
    Have a good day buddies.
    BTW, sometimes I write at different hours, because I commute between UTC+1 and UTC-5 😉
    P.S. I’m a very slow thinker. For example, it takes me a while just to figure out the missing number for the verification equation required for posting comments on this blog.

  22. 22
    Joe says:

    AVS:

    Alternative splicing can be regulated by the use of different upstream promoters, the use of different transcription complexes composed of different proteins, the binding of different protein factors to the RNA chain, the binding of various alternative splicing factor proteins, the list goes on.

    So you are saying that it just does it, no knowledge required to regulate it. No internal programming to run it.

    Is that science? How does blind watchmaker evolution explain it?

    These proteins are all subject to the typical mechanisms of evolution.

    And how was it determined that all those mechanisms are blind watchmaker mechanisms?

    Slight modifications can change binding specificity and affinity, and protein functionality can subsequently be altered.

    Still looking for a reference on how blind watchmaker evolution created alternative gene splicing. Knowing how something works doesn’t mean bwe didit.

    Try again

  23. 23
    AVS says:

    That’s a lovely story dionisio, I’m sure someone with half a brain would come to same decision as you and quit your “6-figure” job to come study biology. You commute across 6 time zones? Wow, that sounds completely not-made-up. Come back to planet earth, Dionisio

  24. 24
    Joe says:

    You are quite the joke AVS:

    But anyways I can picture a scenario where genes do not need to be spliced, but a relatively simple protein evolves that is capable of modifying RNA at low levels, producing a new protein with a slightly different function that may benefit an organism.

    LoL! Evolutionary “science” at its finest.

    You’re problem is that you think these huge complex protein complexes we see in eukaryotes today had to all come about at once.

    Your problem is that you don’t know jack, let alone what I think.

    No one is claiming this happened.

    Neither am I. Now tell us how bwe did it. How can we test the claim that happenstance mutations can do all of that?

  25. 25
    Dionisio says:

    AVS @ 20

    You’re problem is that…

    English is not my first language. Actually, it was the fourth language I learned. But I think the above highlighted expression -extracted from your comment- is grammatically incorrect. Isn’t it?

  26. 26
    AVS says:

    My point was that alternative splicing is regulated largely by proteins, which are subject to the typical mechanisms of evolution. If you are truly asking for a play-by-play of how these systems evolved, then you are just as out of touch with reality as Dionisio.

  27. 27
    Joe says:

    Splicing and editing require knowledge. Proof-reading and error correction also require knowledge. Transcription and translation- yup more knowledge required.

    All AVS can say is it all “just happens” given the right chemicals in the right sequences.

  28. 28
    bornagain77 says:

    The problem that AVS failed to address, and tried to obfuscate the severity of, is that Body Plans ARE NOT reducible to the linear sequences of information on DNA. That is one of the major failures of the modern synthesis. Dr. Nelson addressed this very point just the other day in his debate that he had on Saturday with a Darwinist:

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    http://www.evolutionnews.org/2.....45581.html

    Dr. Meyer also addressed the fact that Body plans are not reducible to DNA sequences in his book ‘Darwin’s Doubt’

    Darwin’s Doubt (Part 8) by Paul Giem – developmental gene regulatory networks and epigenetic information – video
    http://www.youtube.com/watch?v.....38;index=8

    Darwin’s Doubt narrated by Dr. Paul Giem – The Origin of Body Plans – video
    http://www.youtube.com/watch?l.....page#t=290

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    Dr. Meyer also addressed this insurmountable ‘body plan’ problem for Darwinists here:

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Dr. Stephen Meyer comments at the end of the preceding video,,,
    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
    Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Dr. Nobel weighs in here

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    http://www.metacafe.com/w/10395212

    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.
    Professor Denis Noble is President of the International Union of Physiological Sciences.

    Dr. Shapiro weighs in here:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf
    Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

  29. 29
    Jul3s says:

    Fascinating. So AVS can make rebuttals that actually respond to the post he is replying to. Except, said posts are never about topics which are crucial to any particular worldview.

    Another interesting pattern is when responses amount to: “you are not smart/well educated enough to understand evolution” followed by a description of the biological feature mentioned previously without any actual answer to the question.

    The best part of all is the statement: “I can picture a scenario where . . . “

  30. 30
    bornagain77 says:

    Dr. Koonin weighs in here:

    These findings are a direct contradiction of the modern synthesis (central dogma) of neo-Darwinism,,
    Does the central dogma still stand? – Koonin EV. – 23 August 2012
    Excerpt: Thus, there is non-negligible flow of information from proteins to the genome in modern cells, in a direct violation of the Central Dogma of molecular biology. The prion-mediated heredity that violates the Central Dogma appears to be a specific, most radical manifestation of the widespread assimilation of protein (epigenetic) variation into genetic variation. The epigenetic variation precedes and facilitates genetic adaptation through a general ‘look-ahead effect’ of phenotypic mutations.,,,
    Conclusions:
    http://www.ncbi.nlm.nih.gov/pm.....MC3472225/

    Moreover, as if all that was not bad enough, even protein structure, something you would think would be amendable to Darwinian processes, is now known to only be ‘tenuously’ connected to the sequences in DNA:

    The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy
    http://darwins-god.blogspot.co.....rt-ii.html

    Thus, all in all, Darwinian explanations are almost completely useless as to explaining body plan formation.

    Supplemental note so as to make clear just how grossly inadequate is Darwinian explanatory power for Body Plan formation::

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

  31. 31
    Upright BiPed says:

    Good grief

    Enough content for you upright?

    You means where Wells said “After transcription, most multi-exon eukaryotic genes undergo alternative splicing, which changes the sequence and you jumped in his shit and said “Yes they undergo alternative splicing … Some genetic information is left out, some is included … This is exactly how Dscam alternative splicing works, there is just a large number of different possible exons.”

    I’m left wondering if including some information and leaving other information out changes the final sequence. THAT could not possible be what he meant, could it – exact what he said? Did he say that the sequence within the exons change? No he didn’t. That was all you.

    Nothing embarrasses an petulant ideologue.

    Enjoy yourself.

  32. 32
    AVS says:

    Thank you Dionisio, I am hereby appointing you as my editor in chief. Stick to attacking how I write things and not what I actually wrote though please, I don’t want you embarrassing yourself.

  33. 33
    AVS says:

    Upright, I thought you were smarter than that. Cmon. Johnny’s argument is that the DNA sequence that codes for protein is altered, it is not. The protein coding sequence remains the same, while non-coding regions are spliced out. He is trying to convince readers that the protein’s amino acid sequence is frequently altered from what the genome sequence is. This is a huge overstatement.

  34. 34
    AVS says:

    Another problem with his sentence is that he leaves it at “sequence.” Which sequence? The RNA or the amino acid? The majority of what he writes is written so ambiguously it makes it easy to argue from his standpoint. He, and you and your friends on here, can argue exactly what he meant however you see fit.

  35. 35
    Joe says:

    If exons are left out that alters the amino acid sequence.

  36. 36
    AVS says:

    Body plans? Body plans BA? Nowhere in the post or my comments is body plan mentioned.
    Oh, are you confusing this post with the more recent post about this crackpot? Yeah, you are huh. In your zeal to copy and paste your typical BS, you got completely confused as to what was going on. Did you forget to take your meds today BA?

  37. 37
    Dionisio says:

    AVS @ 23
    I spend a few months in Europe and a few months in the Eastern US every year. Have close relatives in both places. Perhaps the term ‘commute’ was an exaggeration, because I do the traveling only once a year.
    Anyway, you don’t have to believe my story, which is completely irrelevant.
    There’s a most relevant story we have to believe in order to be reconciled with our Maker. But that’s up to you.

  38. 38
    Jul3s says:

    Some exons are sometimes left out. This is always the very last exon if I recall correctly.

  39. 39
    AVS says:

    And it produces a different protein, Joe. I’m not sure what your point was. Try to make a point when you post and not just make single ambiguous statements that demonstrate your insecurities in talking about biology in such detail.

  40. 40
    AVS says:

    I’m pretty sure you are recalling incorrectly, Jules. Cmon guys, I need more than vague assertions that have no basis in reality.

  41. 41
    Jul3s says:

    Really, you have never even heard of mutually exclusive exons?

  42. 42
    bornagain77 says:

    Of related note to ‘top down’ body plan formation:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    An Electric Face: A Rendering Worth a Thousand Falsifications – September 2011 – video and article
    Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”
    https://www.youtube.com/watch?v=0VULjzX__OM
    http://darwins-god.blogspot.co.....usand.html

  43. 43
    AVS says:

    That would be when one exon is used and not another? Yeah, that has nothing to do with “the very last exon.” Unless you suspect I am a mind reader and can understand what you even mean by that.

  44. 44
    AVS says:

    BA! Did you not read my comment to you? We’re not even talking about body plans. You’re on the wrong post, my friend. You should try reading and thinking before you post, I know, there’s a first for everything right?

  45. 45
    Dionisio says:

    AVS @ 32

    Thank you Dionisio, I am hereby appointing you as my editor in chief. Stick to attacking how I write things and not what I actually wrote though please, I don’t want you embarrassing yourself.

    You have not answered my questions @ 14.
    Give up? “Don’t know” would count as an acceptable answer. However, you probable know the answer, but just forgot to reply. Right?
    Or maybe got too busy answering other comments?
    Remember. In my case, I really want to know the information I’m asking for. I’m trying to develop educational software using computer games technology, but lack the science part of the picture. I know many folks here, including you, can give me a hand with this. So please, let’s get serious and focus in on the right stuff. Can we stop all the childish arguments and decently exchange information? Thank you.

  46. 46
    bornagain77 says:

    AVS, seeing as how disrespectful you are to people who disagree with you, I’m getting to the point of not really caring to read what you have to say, save for to get the overall gist to refute,,, but anyways this video in the OP must have slipped your notice,,

    Body Plans Are Not Mapped-Out by the DNA Jonathan Wells – video
    http://www.youtube.com/watch?v=meR8Hk5q_EM

  47. 47
    Moose Dr says:

    Dionisio, I too develop computer software. ‘Kinda gave up my 6 figure job too, but to raise the kids, not to study biology. That said, I do find the study of biology to be fascinating.

    Sometime AVS actually spits out something that causes me to believe that he knows something about biology. But his communication skills, and his ability to have a respectful conversation make dialog with him useless.

    This whole evolutionary theory thing causes my software developer sense to cringe. I recognise DNA as, well, source code. There seems to be a central processor in there which tracks through the DNA, finds a start codon, reads triplets, and assembles protein. That all makes sense.

    I also recognize proteins as, well, parts. They are intricate like the parts of any machine. Like the parts of a machine, some are not all that intricate, not all that precise. Like other machine parts, incredible precision, incredible material properties, etc. are all critical.

    As such, a gene appears to be most like the instructions sent to a cnc mill. Change the code, get a very different part.

    The idea that one gene, one piece of source code, could render 18,000 different parts is rather incredible to consider. The closest analogy I have found in my source code is the universal search or universal sort functions which take a comparator function as a parameter. Because there can be many comparator functions, the one universal sort function can sort differently in different contexts.

    Where evolution looks whacked in the head is when we look at making software one change at a time. Each change must work at least as well as the pre-changed version. If I were coding a cnc machine, I can’t fathom making individual changes in one part, and having the machine work at least as well as its well tuned predecessor.

    But then the theory gets really weird. The theory says that random bunches of text periodically gets a start codon at its start by accident. The cnc machine is then run with the resulting code until a stop codon is encountered (about 100 steps down the road.) The resultant part just happens to be a part that makes the machine better. These orphan genes are not painfully rare. They make up as much as 10% of genes in some organism. Yes, 10% of the genes in organism A will be unique to that organism over another species in the same genus. Yup, this just happens. Nope. No, this kind of data is an absolute Darwin killer.

    Dionisio, if you are who you describe yourself to be then this post makes a lot of sense to you.

  48. 48
    AVS says:

    After reading the nonsense you quoted from him, no, I did not bother to see what he says in some youtube video and I don’t plan to. The complete lack of academic integrity he demonstrates in the misleading and ambiguous text was enough to make me sick. I rebutted everything he claimed in the text and since not a single person has refuted anything I have said. Joe has tried, I’ll give him that. A+ for effort Joe.

  49. 49
    AVS says:

    Dionisio and mooseknuckle, I get where you guys are coming from, but your IT background puts you at an extreme disadvantage. We are talking about the living world here in biology, while at the surface it may seem similar to the computer world, there are a vast amount of differences. The best way I can sum it up is the fact that biology is concerned with living things, to which there is no real comparison in the non-living world.

  50. 50
    AVS says:

    Dionisio, on the off chance that you are being sincere in your request I will explain:
    Asking for a complete description of all the process that occur in the first week of development and how they evolved is absolutely absurd. Not only do we not know exactly how a lot of these things work, but what we do know would fill stacks and stacks of books. In fact they do. That’s part of what the problem is with teaching you guys about evolution; we don’t know a lot about how things are happening in cells currently, this makes putting together a picture of the evolution of these biological systems extremely difficult. Anyway here are some terms you can look up to get you on your path to knowledge:
    transcription factors, cell determination, cell differentiation, fate maps, ectoderm, endoderm, and mesoderm, gastrulation, mitosis, hox genes, and morphogens
    Wiki is a good resource, goodluck

  51. 51
    bornagain77 says:

    something for you computer programmers to enjoy

    Animusic’s “Pipe Dream” Made Real – video
    http://makezine.com/2012/02/20.....made-real/

    The extremely sophisticated hardware and software systems that enable life simply cannot be built by any trial and error system. In particular – it is very clear that software can never be developed one binary bit at a time. Apart from a fully functional pre-existing hardware/software system, a single bit has absolutely no meaning. I feel that if we are to preserve our scientific integrity, we must acknowledge that we have a major explanatory problem, and we need to go back to the drawing board in terms of understanding the origin of biological information.
    John Sanford – Inventor of the ‘Gene-Gun’
    http://www.uncommondescent.com.....integrity/

  52. 52
    AVS says:

    Yes, BA, let’s just continue the cycle of misunderstanding.

  53. 53
    AVS says:

    What happened? Nobody wants to play ball when actual science is brought to the table? Why am I not surprised?

  54. 54
    Dionisio says:

    Dear Moose Dr,

    Yes, your post does make a lot of sense to me. Thank you!
    I commend you for considering the time with your children more valuable than your professional career.

    In my case my children were grown up and independent when I decided to change career so drastically. Initially my wife was not excited by my decision, but eventually she understood that “money can’t buy me love” and stood by me 🙂

    I have given many personal details about myself here in this blog, so that AVS and others could understand my craving for information. I don’t want to engage in silly discussions that lead nowhere. I want specific information, so I can learn more.
    You and I seem to have a similar IT background, which allows us to understand each other better. Also the computer software development background seems to be an advantage when it comes to looking at complex systems.
    But sometimes I’ve gotten the impression that biologists don’t think the same way, hence it’s difficult to communicate with them.
    Sometimes I think they should make information theory, set theory and math logics required subjects in all undergraduate majors.
    When I asked a similar question (as posted @ 14) to a biology doctor a few years ago, he asked me if I was interested in philosophy? Only after I told him I wanted purely scientific answers, where “don’t know” was an acceptable option, he invited me to visit his institute and introduced me to his research colleagues. We had a very productive meeting where I learned much from them.
    We had lunch together at a restaurant near their university. At one point the professor noticed I wasn’t eating much, so he asked me if I didn’t like the meal, to what I responded that I wasn’t eating because I was listening to his interesting descriptions of the research work they do in their labs, and got so absorbed by his talk, that completely forgot about the food. He laughed out loud. He said it was the first time a non-biologist sat with him for so long, paid so much attention to his talk, and asked so many questions as I did.
    My budget is limited, hence I’m taking different approaches to gather information. Online searching is one of them. This forum is another approach.
    Again, I appreciate the time you took to write to me. If you can see my email address, feel free to write, so we can exchange more info outside this public venue. If you don’t see it, I will write it.

  55. 55
    Dionisio says:

    Dear Moose Dr,

    Yes, your post does make a lot of sense to me. Thank you!
    I commend you for considering the time with your children more valuable than your professional career.

    In my case my children were grown up and independent when I decided to change career so drastically. Initially my wife was not excited by my decision, but eventually she understood that “money can’t buy me love” and stood by me 🙂

    I have given many personal details about myself here in this blog, so that AVS and others could understand my craving for information. I don’t want to engage in silly discussions that lead nowhere. I want specific information, so I can learn more.
    You and I seem to have a similar IT background, which allows us to understand each other better. Also the computer software development background seems to be an advantage when it comes to looking at complex systems.
    But sometimes I’ve gotten the impression that biologists don’t think the same way, hence it’s difficult to communicate with them.
    Sometimes I think they should make information theory, set theory and math logics required subjects in all undergraduate majors.
    When I asked a similar question (as posted @ 14) to a biology doctor a few years ago, he asked me if I was interested in philosophy? Only after I told him I wanted purely scientific answers, where “don’t know” was an acceptable option, he invited me to visit his institute and introduced me to his research colleagues. We had a very productive meeting where I learned much from them.
    We had lunch together at a restaurant near their university. At one point the professor noticed I wasn’t eating much, so he asked me if I didn’t like the meal, to what I responded that I wasn’t eating because I was listening to his interesting descriptions of the research work they do in their labs, and got so absorbed by his talk, that completely forgot about the food. He laughed out loud. He said it was the first time a non-biologist sat with him for so long, paid so much attention to his talk, and asked so many questions as I did.
    My budget is limited, hence I’m taking different approaches to gather information. Online searching is one of them. This forum is another approach.
    Again, I appreciate the time you took to write to me. If you can see my email address, feel free to write, so we can exchange more info outside this public venue. If you don’t see it, I will write it.

  56. 56
    AVS says:

    Dionisio, if you really want to learn about biology, take some classes at an accredited university. Definitely do not rely on UD as a source for information on how biology works. As you can see from this page alone it would seem none of the regulars here at UD have the slightest of knowledge as to molecular biology.

  57. 57
    Eric Anderson says:

    . . . your IT background puts you at an extreme disadvantage. We are talking about the living world here in biology, while at the surface it may seem similar to the computer world, there are a vast amount of differences. The best way I can sum it up is the fact that biology is concerned with living things, to which there is no real comparison in the non-living world.

    I love this refuge argument of the clueless. It essentially says, “You understand information systems and engineering and computation. I don’t understand them (evidently). Therefore, you are at a disadvantage. No, make that an extreme disadvantage.”

    This is the kind of backdoor argument put forth by someone who doesn’t understand that building an organism is, at the end of the day, an engineering problem.

    No. Instead of dealing with real issues, let’s stick to fanciful vague notions, completely void of detail and analysis, about how the Sun gives energy to the Earth, and so life is inevitable. That’s the ticket.

    It would be hard to even parody this stuff.

    You guys have a lot more patience than I could muster to deal with this level of nonsensical rhetorical bluster . . .

  58. 58
    AVS says:

    Yet another person who tells me I have no idea what I am talking about, and yet I am the only person to actually demonstrate any knowledge of biology in the 60 comments above this one. It’s quite comical.
    I’ll play along and agree that at the end of the day, building a cell is an “engineering problem,” but it is not a type of engineering any of you are familiar with. It would be classified as biological engineering, which I’m sure the computer engineers here would be just as familiar with as they are chemical engineering or civil engineering.

  59. 59
    jerry says:

    I haven’t read all the comments but what Wells is talking about here is covered in Meyer’s book. Somehow the body plans are in the cell walls and other places in the egg but not in the DNA. Meyers spends a couple chapters on this in his book and is one of the truly novel ideas of the book. Meyer provides lot of references from the published literature.

    Meyer, in his book credits Wells with this insight as Wells got his Ph. D. at Berkeley and studied developmental processes as part of getting his Ph. D. Meyers quotes Wells as saying that this is where Darwinian ideas will fall apart.

    I once saw a lecture about the development of the brain. There is about 100 billion brain cells and as they are formed each of these 100 billion cells know exactly where to go. Biologists have no idea what directs this process but whatever it is, it is very precise and does not appear to be in any part of the genome.

  60. 60
    AVS says:

    Jerry, you should try supplementing your information on biology with textbooks and journal articles. When you get your information from the type of people you have mentioned, you tend to gain a misunderstanding of actual biological events and functions.

  61. 61
    Dionisio says:

    AVS @ 49

    Dionisio and mooseknuckle, I get where you guys are coming from, but your IT background puts you at an extreme disadvantage. We are talking about the living world here in biology, while at the surface it may seem similar to the computer world, there are a vast amount of differences. The best way I can sum it up is the fact that biology is concerned with living things, to which there is no real comparison in the non-living world.

    This does not answer the second part of my questions posted on # 14.

  62. 62
    Dionisio says:

    AVS @ 50

    Dionisio, on the off chance that you are being sincere in your request I will explain:
    Asking for a complete description of all the process that occur in the first week of development and how they evolved is absolutely absurd. Not only do we not know exactly how a lot of these things work, but what we do know would fill stacks and stacks of books. In fact they do. That’s part of what the problem is with teaching you guys about evolution; we don’t know a lot about how things are happening in cells currently, this makes putting together a picture of the evolution of these biological systems extremely difficult. Anyway here are some terms you can look up to get you on your path to knowledge:
    transcription factors, cell determination, cell differentiation, fate maps, ectoderm, endoderm, and mesoderm, gastrulation, mitosis, hox genes, and morphogens
    Wiki is a good resource, good luck

    This does not answer the second part of my questions posted on # 14.

  63. 63
    Dionisio says:

    AVS @ 56

    Dionisio, if you really want to learn about biology, take some classes at an accredited university. Definitely do not rely on UD as a source for information on how biology works. As you can see from this page alone it would seem none of the regulars here at UD have the slightest of knowledge as to molecular biology.

    This doesn’t answer the second part of my questions posted on # 14.

  64. 64
    AVS says:

    See comments 50 and 56 Dionisio

  65. 65
    Dionisio says:

    AVS
    Please, answer the second part of my questions posted on # 14. Please, take a break on your discussions with other guys in this thread and give me a hand with the second part of my questions posted on # 14. Thank you.

  66. 66
    AVS says:

    Dionisio, please read comments 50 and 56. Thank you.

  67. 67
    Moose Dr says:

    Eric Anderson, “It essentially says, “You understand information systems and engineering and computation. I don’t understand them (evidently). Therefore, you are at a disadvantage. No, make that an extreme disadvantage.”

    Well said.

  68. 68
    Moose Dr says:

    BA77, love the “pipe dream” video.

    AVS, tell me honestly, is there any living organism that is less complex than the machine in BA77s video?

  69. 69
    AVS says:

    Moosey, if you and EA put my quote back in context, you’d realize I was saying that it puts you at a disadvantage in thinking about biology. Computer engineering lends itself better to a different way of thinking than biology does, just as math and chemistry lend themselves to different ways of thinking. And these guys have spent their lives in computer engineering.

  70. 70
    Dionisio says:

    AVS
    That’s fine. You’re not supposed to know the answers to my questions posted on # 14. Because actually no one knows them. The school biology textbooks contain false claims and half truths. That’s why you keep pointing to online sites I have seen for the last few years. Because there’s nothing else under the sun that could answer my questions.
    I have taken free online biology classes. Have read a number of peer-reviewed journals I’m subscribed to.
    In software development you can’t pretend knowing, can’t claim to know. They’ll fire you right away. You have to know exactly the ‘what’ and ‘how’ of everything you are dealing with.
    Anyway, thank you for your effort to help. I appreciate it.

  71. 71
    Moose Dr says:

    AVS, in response to your post #56, please ponder this link a bit: http://www.uncommondescent.com.....y-biology/

    AVS #50, “That’s part of what the problem is with teaching you guys about evolution; we don’t know a lot about how things are happening in cells currently…”

    So what you are saying is that y’all don’t have a clue how biology works* but you are certain that you know how it got there?

    *Oh I know, you know tons of stuff about how biology works, you just realise that for every ton you know, there’s another 10 tons that you don’t.

  72. 72
    AVS says:

    Dionisio, do everyone a favor and stick to computer engineering. You are absolutely clueless.

  73. 73
    AVS says:

    What exactly does that link have to do with UDers and their understanding of molecular biology?
    Anyway, no I’m saying we have learned a lot about how the cell works and there is a lot still to learn. What we have learned about cells and organisms tells us that we seem to have evolved from a common ancestor and the theory of evolution is what explains this process of descent.
    Do you or anyone else have anything to refute my original rebuttal of Johnny Wells’ BS, or have you realized what a load of crap everything that comes out of his lot’s mouths are?

  74. 74
    Moose Dr says:

    Dionisio, I cannot see your e-mail, but would be interested in a one on one.

  75. 75
    TSErik says:

    It’s nice to see GoAVS! back, again, trolling the site. He comes here from Yahoo! Answers now and again, embarrasses himself by parroting stuff he doesn’t understand, then disappears before answering anything of merit.

    It’s funny, because in all my time in academia, and surfing the internet, the only time I’ve ever come across the assertion, “you don’t understand biology” or the many variations where you use the actual term, “biology”, has been when encountering kids, usually high school age, or people of very limited exposure or understanding of the subject in which they claim to be an expert.

    It’s the classic overcompensation dialogue.

    Jerry, you should try supplementing your information on biology…

    I am the only person to actually demonstrate any knowledge of biology… It’s quite comical. (ed. Classic deflection)

    if you really want to learn about biology…

    We are talking about the living world here in biology…

    I could keep going. Let’s examine other dialogue:

    My point was that alternative splicing is regulated largely by proteins

    And:

    Jerry, you should try supplementing your information on biology with textbooks and journal articles. When you get your information from the type of people you have mentioned, you tend to gain a misunderstanding of actual biological events and functions.

    Good advice you should take yourself. Where do you cite such sources here? Also, this is a deflection and logical fallacy. Consider the source does not an argument make.

    This is a common equvocation tactic GoAVS! uses when he realizes he’s been caught spouting stuff in which he is quite ignorant.

    Further arguments from GoAVS! is ad hominem with vulgar insults, (EG: Mooseknuckle)and stamping of feet shouting, “You just don’t get it!” That way he can sit behind his copypasta, poorly understood and parroted tripe and maintain the delusion of superiority.

    AVS is just a poor pseud-intellectual who probably never made it past community college, if that. He ventured to message boards like “Yahoo! Answers” berating people, inflating his fragile ego in an attempt to give validation that he “is one of the smart kids” and “above the rest”.

    He found hardcore atheist forums, reddit, TSZ, and the like, where he felt automatically “part of the cool kids” group. He takes in the information there, even copying stuff here then posting it there and taking the responses, and parrots it back over here. It’s all a way to validate his dirt-low self-esteem and need to feel superior.

    We see this in the inability to argue effectively, or produce unique thought with regards to scientific data or analysis, the language of overcompensation, and deflection when asked on specifics of his stated arguments.

  76. 76
    AVS says:

    Oh don’t worry Erik, everything I say comes straight from my own head. I am well versed in “biology,” which apparently I shouldn’t call by name because it makes me seem unintelligent when I refer to a field of science by its name…? I don’t really follow your thinking on that one, but Ok.

    Once again I find it very interesting that when I step in to the world of UD, I apparently am a highschooler with limited exposure to biology. In fact, I take great solace in this because it reminds me that you and your buddies on here wouldn’t recognize biology if it slapped you across the face.

  77. 77
    AVS says:

    In all seriousness, Erik, if you can’t read my commments, yes you have to ignore the inner asshole in me, but if you can’t read my comments and realize that at the very least I know what I am talking about than you are in the same boat as the rest of your buddies here.

  78. 78
    Moose Dr says:

    AVS, “What we have learned about cells and organisms tells us that we seem to have evolved from a common ancestor…”

    I have analyzed the science behind the common ancestor theory. I agree that the case for common ancestry is rather strong, at least when it is summarized. I understand that there are disease producing individual point mutations that are shared between chimps and humans. Certainly the easiest explanation for this fact is that chimps and humans descended from a common ancestor.

    This is the kind of data that convinces me. This is the kind of evidence that makes sense.

    I am sooo not buying the theory that random mutational events (like duplication, inversions, horizontal gene transfer) accounts for the genetic data I see. I personally believe that you have bought the baby and the bathwater. You recognize the case for common ancestry, and you presume that the other huey that your teachers present are as well established.

    Now please understand, I am convinced that gene frequency is influenced by natural selection as well as by random drift. I am convinced that some genetic alleles are produced by random mutations. I am convinced that the disease producing mutations that I discussed earlier were the product of random chance.

    However, as I mentioned earlier, the ubiquitous phenomenon of orphan genes, especially de novo genes, seems to be painfully in disagreement with your theory. Other similar pieces of data seem to painfully disagree with your theory.

    Calling names, and schpittin’ with folk will not convince me of anything. You’ve got to put rich nuggets of evidence on the table if you are going to be heard.

  79. 79
    TSErik says:

    I am well versed in “biology,” which apparently I shouldn’t call by name because it makes me seem unintelligent when I refer to a field of science by its name…? I don’t really follow your thinking on that one, but Ok.

    I explained above my reasoning of overcompensation above. Surely you have a modicum of reading comprehension and analytical abilities to figure it out. I believe in you.

    Once again I find it very interesting that when I step in to the world of UD, I apparently am a highschooler with limited exposure to biology.

    I vote for community college drop-out. I simply said your behavior and the way you argue is reminiscent of high school students.

    it reminds me that you and your buddies on here wouldn’t recognize biology if it slapped you across the face.

    Fantastic. I’ll alert my bio-med sci. program then.

  80. 80
    AVS says:

    First off, I don’t think that is how the “baby and the bathwater” saying works.
    Anyway, I completely agree, the few basic mutations you mention are definitely not the whole story. It is much more complex than that. As your friends love to point out here, a lot of non-coding regions are extremely important and it is also important to note that the orphan or “de novo” genes you speak of are not necessarily being created out of “nothing.” I commented on a post about this a long time ago actually and I think some people thought that new genes were just popping into existence. As you have demonstrated, the devil is in the details and i think the strength of the argument for evolution is in the huge amount of details that have been collected in every field of biology that have all become a part of the theory as a whole. What people don’t understand is that evolution started off as a single idea and eventually grew to become what it is today because of the huge support it has gotten from every field of biology. I’m not an evolutionary biologist, but I do understand enough of it to know that it makes sense and puts biology in perspective. It is the link between all fields in biology.
    Sorry for using the phrase “biology” so many times Erik, I must be a kindergartener now by your scale.

  81. 81
    AVS says:

    You should let them know Erik, that way they’re not surprised when you drop out of the program.

  82. 82
    Dionisio says:

    Moose Dr

    I’m out of here, but first let me share these proverbs:

    Proverbs 12:15

    The way of a fool is right in his own eyes, but a wise man listens to advice.

    Proverbs 13:20

    Whoever walks with the wise becomes wise, but the companion of fools will suffer harm.

    Proverbs 14:7

    Leave the presence of a fool, for there you do not meet words of knowledge.

    Proverbs 15:2

    The tongue of the wise commends knowledge, but the mouths of fools pour out folly.

    Proverbs 15:14

    The heart of him who has understanding seeks knowledge, but the mouths of fools feed on folly.

    Proverbs 16:22

    Good sense is a fountain of life to him who has it, but the instruction of fools is folly.

    Proverbs 17:10

    A rebuke goes deeper into a man of understanding than a hundred blows into a fool.

    Proverbs 18:2

    A fool takes no pleasure in understanding, but only in expressing his opinion.

    Proverbs 20:3

    It is an honor for a man to keep aloof from strife, but every fool will be quarreling.

    Proverbs 23:9

    Do not speak in the hearing of a fool, for he will despise the good sense of your words.

    Proverbs 26:4

    Answer not a fool according to his folly, lest you be like him yourself.

    Proverbs 26:5

    Answer a fool according to his folly, lest he be wise in his own eyes.

    Taken together these verses illustrate the point that no proverb is intended to cover every possible situation. The apparent contradiction in the two proverbs indicates that proverbs must be appropriately applied. One situation demands that we avoid playing the fool’s game by giving an answer, while another demands that we expose the folly so that the fool is not considered wise.

    Proverbs 26:11

    Like a dog that returns to his vomit is a fool who repeats his folly.

    Proverbs 29:9

    If a wise man has an argument with a fool, the fool only rages and laughs, and there is no quiet.

    Proverbs 29:11

    A fool gives full vent to his spirit, but a wise man quietly holds it back.

  83. 83
    TSErik says:

    First off, I don’t think that is how the “baby and the bathwater” saying works.

    Being pedantic is another tool of the pseudo-intellectual.

    Sorry for using the phrase “biology” so many times Erik, I must be a kindergartener now by your scale.

    Quite a fatuous remark that shows you may not understand my reasoning, which would denote a lacking analytical mind. Or (more likely) I struck a nerve and in a desperate move to save face, you are attempting to ridicule away the point’s validity. Which, funny enough, is another signature of overcompensation.

    With each post you simply make the case for me.

  84. 84
    TSErik says:

    You should let them know Erik, that way they’re not surprised when you drop out of the program.

    Ouch. You wound me so.

  85. 85
    Dionisio says:

    Moose Dr @ 74

    Dionisio, I cannot see your e-mail, but would be interested in a one on one.

    dshared@ymail.com

  86. 86
    AVS says:

    Do I really need to explain your own reasoning for you?
    You claimed that people who often used the word “biology” were overcompensating for their lack of knowledge in the field. You often found they were highschoolers. I was merely continuing your train of thought and saying that the more I used the word, the less mature you thought I was.
    And I was only letting the guy know that he wasn’t using the saying right, I wouldn’t want him to sound like an idiot in person would I?
    Don’t worry, you haven’t bothered me in the slightest. The fact that you claim to have a background in biology, oh woops said it again, and yet you don’t bother to refute anything I have said speaks volumes.

  87. 87
    AVS says:

    Well have a nice day guys, it’s been fun. Don’t forget to ask the customers if they want paper or plastic tomorrow.

  88. 88
    TSErik says:

    Do I really need to explain your own reasoning for you?
    You claimed that people who often used the word “biology” were overcompensating for their lack of knowledge in the field. You often found they were highschoolers.

    Wait…seriously? No.

    This is seriously the extent of your analysis of my comments? I was being facetious when I said you didn’t get it, but if this is it, well, you really don’t get it.

    I was merely continuing your train of thought and saying that the more I used the word, the less mature you thought I was.

    This has nothing to do with my comments. I said that you displayed behavior of overcompensation, illustrated by your argument patterns.

    What you exhibit is textbook overcompensation. How can such an erudite person not be familiar with this? Should I give you some of your own advice and suggest you open a book?

  89. 89
    TSErik says:

    I was merely continuing your train of thought and saying that the more I used the word, the less mature you thought I was.

    Seriously!? You can’t really think THIS was the point of my comments.

    I feel bad now.

  90. 90
    AVS says:

    You are a class A troll Erik. I can’t believe I let the conversation go for this long. Oh well, enjoy whatever it is you call a life, bye now.

  91. 91
    TSErik says:

    You are a class A troll Erik. I can’t believe I let the conversation go for this long. Oh well, enjoy whatever it is you call a life, bye now.

    Hah! Ok, smart guy. Come back soon.

  92. 92
    The Karaite Heretic says:

    OK, this was a very constructive session…

  93. 93
    Querius says:

    TSErik and Dionisio,

    Frankly, it’s becoming blatantly obvious that you’re having to endure vacuous insults and puffery from people who have little else to offer than cutting and pasting from who knows where.

    And to think that I used to also believe the 19th century fantasy that they’re defending with such vehemence and unquestioning faith.

    I personally went through several stages of scepticism before completely losing my faith in Darwin’s plagiarized theory:

    1. Geological dating being dependent on dating the fossils and vice versa.

    2. The struggle between the supporters of spontaneous generation and biogenesis…and that OOL is simply looking for another recipe for Von Helmont’s experiment.

    3. Learning some of the amazing array of interrelated and complex chemical cycles essential for cellular metabolism. (later biology)

    4. Learning the incredibly destructive effects of ionizing radiation in a nuclear safety class.

    5. Finding out that a lot of the Darwinist “truths” were only half truths or outright frauds when I delved into the details. There are so many of these! For example, how can the chimpanzee genome be 98-99% the same as the human genome when the chimpanzee genome is 6-10% larger (by weight) than the human genome? “We don’t count those.” LOL

    6. The overuse of the word “musta” when speculating about improbable or fanciful explanations for Darwinian evolution. For example, fossils that are virtually identical with contemporary species are arbitrarily assigned a to different species or even genus purely on the reasoning that they “musta” been different genetically.

    The whole sorry mess is so contrived and lame. And then you get attacked by the rabid, abusive supporters…

    -Q

  94. 94
    wallstreeter43 says:

    Stephen Meyer was the main reason I left evolution after being a believer for 41 years. People like AVS who feel the need to insult an ridicule others confirm my suspicions that when you feel the need to insult others that you are really insecure about your own views.

    It’s is the typical tactic is the atheist/materialist/Darwinist

    How would you like it AVS if I said that if we debates and discussed the shroud of turin that I would make you look like an amateur nimrod idiot that would have to abandon science , logic and reason to stick to your belief taint the shroud is a forgery and a fraud.

    I would be able to that easily but is it how someone who is confident in what he believes in acts? Definitely not

    For you to claim that wells and meyer don’t know squat about biology or evolution is ridiculous.

    I am getting an image in my mind and this is the only way I picture you by yoir personality and actions on this blog. This image fits you best

    http://mlkshk.com/p/CEK

  95. 95
    wallstreeter43 says:

    Querius, don’t feel bad man, I was brainwashed for 41 years.
    I was a theistic evolutionist who actually debated young earth creationists until I actually started to take a long, hard and quiet look at some of the claims of Evolutionists and my faith in evolution started to crumble.

    Some of evolution is actually good science but much of it is more philosophy then anything else. It’s actually an ambolucetas of a tale, opps , I meant a whale of a tale 😉

  96. 96
    Dr JDD says:

    I find it a shame when we feel the need to throw around insults. Sorry, this is only my second post and I’m not sure of what value I can add but I feel a bit sad when things descend into insults (both sides) and it seems as though we forget the purpose of why we look into things, perhaps. There is also a danger with these discussions, that we are all so biased that we grasp onto any piece of information that supports (or we think supports) our views, and argue it until we are blue in the face. Secondly, we often as biased people will not accept anything the other side has to say.

    On that note, and please before you jump on me, remember I am a complete theist and one who rejects (macro) evolution (very much accept evolution on the “micro-scale” just not for arisal of new functional pathways and complex genes especially in a naturalistic setting) – I actually agree and see where AVS is coming from initially (I just wish his first post was a bit less patronising). In the context of the quotes, I think the argument Dr Wells makes here is somewhat weak. As AVS points out in his second post, the genetic information does in fact determine the final protein form by in large. Even things like carbohydrate modifications (not to mention palmitoylation, myristolation, prenylation, geranylgeranylation, ubiquitination, sumoylation, and all other manner of post-translational modifications of proteins) are in fact dictated by the amino acid motifs that allow these additions, which are in fact dictated by the DNA. Even the splicing is dictated by DNA code. So perhaps I would agree, the way this argument is portrayed does not make, in my scientific mind, the point that Dr Wells is trying to make.

     

    Personally, what I think ID-ists should be focusing on with respect to the complex nature of this is there for the taking though. For example, think about all these different post-translational modifications, such as lipid anchoring modifications which are in some cases, absolutely necessary to anchor a protein in a membrane for a particular orientation and to “see” its substrate correctly, and be useful as a protein. How did this arise? If the protein’s function is dependent upon these modifications, the original machinery and genetic code had to be in place when this gene came into existence. For example, the enzymes needed to attach this modification to the specific amino acid motif present on the protein. It is a network that again, seems somewhat irreducible and therefore makes its gradual appearance by evolution much more difficult to believe/explain. It points more to design (in my opinion).

    Secondly, intron-exon existence in genes to me, does provide a difficult process to explain by natural selection alone. Even prokaryotes (archaea) possess introns despite for many years people assuming/thinking that this was one thing that separates eukaryotic cells from prokaryotic ones. Furthermore, how do introns arise? Surely an early assembly of a DNA-based code due to naturalistic evolution would simply have code with start and stop codons perhaps (another issue difficult to understand) but as soon as you introduce introns you have to have the machinery to deal with splicing those out from the RNA, and the machinery allowing the exons to be joined together.

    Then we have to take all of these other important aspects of gene regulation into account. Much of the “non-coding” DNA is necessary for proper gene control and many genes if over or under-expressed are detrimental to the organism. Even more than this it is often the relative gene expression to another gene (or sets of genes) that needs to be perfectly in balance by transcription factors and regulatory factors (not even getting into issues like DNA methylation, imprinting etc – all touted as evolutionary mechanisms yet can also point to complexity and intelligent design). Thus changing just one nucleotide may severely alter these processes, perhaps for the better but more likely for the worse. Furthermore, the recent description of the genetic “duon” that DNA codons have in fact more than just the role of defining an amino acid but also contribute to the gene regulation is also a paradigm for evolutionary changes. No longer are DNA mutations resulting in amino acid changes either detrimental or beneficial to a protein’s function ALONE, but also can have impact on the gene regulation given this duon effect. To me, that makes the probability of beneficial mutations even less likely to produce different functional proteins from one protein and give a favourable advantage.

     

    The argument would make more sense if Dr Wells focused on the incredible complexity of everything the DNA encodes for as screaming of design, rather than try (in my humble opinion) to make this assertion that it isn’t just the DNA. There are better and other arguments that can be made that allude to this point (e.g. protein orientation, organisation, cell circuitry etc). I feel this argument, or rather the evidence presented in quotes above can be easily picked apart like AVS is done. So I agree with him on those points (that even carbohydrate addition is down to the DNA as it is a specific sequence, etc.) but I interpret that as complexity of DNA outside the reach of a naturalistic evolution. It is not proof of either, it is merely adding complexity which makes one theory more difficult to rationalise and the other easier to believe (to my simple mind).

    Does agreeing with AVS on some points make me a non-IDer?! No, of course not, but if we wish to be true scientists I think we have to accept some arguments do us little favours by over-interpreting data. It would be nice if the evolutionists could do the same, but hey, some of us scientists have to take the moral high-ground!! 😉

     

    JD

  97. 97
    Dr JDD says:

    I find it a shame when we feel the need to throw around insults. Sorry, this is only my second post and I’m not sure of what value I can add but I feel a bit sad when things descend into insults (both sides) and it seems as though we forget the purpose of why we look into things, perhaps. There is also a danger with these discussions, that we are all so biased that we grasp onto any piece of information that supports (or we think supports) our views, and argue it until we are blue in the face. Secondly, we often as biased people will not accept anything the other side has to say.

    On that note, and please before you jump on me, remember I am a complete theist and one who rejects (macro) evolution (very much accept evolution on the “micro-scale” just not for arisal of new functional pathways and complex genes especially in a naturalistic setting) – I actually agree and see where AVS is coming from initially (I just wish his first post was a bit less patronising). In the context of the quotes, I think the argument Dr Wells makes here is somewhat weak. As AVS points out in his second post, the genetic information does in fact determine the final protein form by in large. Even things like carbohydrate modifications (not to mention palmitoylation, myristolation, prenylation, geranylgeranylation, ubiquitination, sumoylation, and all other manner of post-translational modifications of proteins) are in fact dictated by the amino acid motifs that allow these additions, which are in fact dictated by the DNA. Even the splicing is dictated by DNA code. So perhaps I would agree, the way this argument is portrayed does not make, in my scientific mind, the point that Dr Wells is trying to make.

     

    Personally, what I think ID-ists should be focusing on with respect to the complex nature of this is there for the taking though. For example, think about all these different post-translational modifications, such as lipid anchoring modifications which are in some cases, absolutely necessary to anchor a protein in a membrane for a particular orientation and to “see” its substrate correctly, and be useful as a protein. How did this arise? If the protein’s function is dependent upon these modifications, the original machinery and genetic code had to be in place when this gene came into existence. For example, the enzymes needed to attach this modification to the specific amino acid motif present on the protein. It is a network that again, seems somewhat irreducible and therefore makes its gradual appearance by evolution much more difficult to believe/explain. It points more to design (in my opinion).

    Secondly, intron-exon existence in genes to me, does provide a difficult process to explain by natural selection alone. Even prokaryotes (archaea) possess introns despite for many years people assuming/thinking that this was one thing that separates eukaryotic cells from prokaryotic ones. Furthermore, how do introns arise? Surely an early assembly of a DNA-based code due to naturalistic evolution would simply have code with start and stop codons perhaps (another issue difficult to understand) but as soon as you introduce introns you have to have the machinery to deal with splicing those out from the RNA, and the machinery allowing the exons to be joined together.

    Then we have to take all of these other important aspects of gene regulation into account. Much of the “non-coding” DNA is necessary for proper gene control and many genes if over or under-expressed are detrimental to the organism. Even more than this it is often the relative gene expression to another gene (or sets of genes) that needs to be perfectly in balance by transcription factors and regulatory factors (not even getting into issues like DNA methylation, imprinting etc – all touted as evolutionary mechanisms yet can also point to complexity and intelligent design). Thus changing just one nucleotide may severely alter these processes, perhaps for the better but more likely for the worse. Furthermore, the recent description of the genetic “duon” that DNA codons have in fact more than just the role of defining an amino acid but also contribute to the gene regulation is also a paradigm for evolutionary changes. No longer are DNA mutations resulting in amino acid changes either detrimental or beneficial to a protein’s function ALONE, but also can have impact on the gene regulation given this duon effect. To me, that makes the probability of beneficial mutations even less likely to produce different functional proteins from one protein and give a favourable advantage.

     

    The argument would make more sense if Dr Wells focused on the incredible complexity of everything the DNA encodes for as screaming of design, rather than try (in my humble opinion) to make this assertion that it isn’t just the DNA. There are better and other arguments that can be made that allude to this point (e.g. protein orientation, organisation, cell circuitry etc). I feel this argument, or rather the evidence presented in quotes above can be easily picked apart like AVS is done. So I agree with him on those points (that even carbohydrate addition is down to the DNA as it is a specific sequence, etc.) but I interpret that as complexity of DNA outside the reach of a naturalistic evolution. It is not proof of either, it is merely adding complexity which makes one theory more difficult to rationalise and the other easier to believe (to my simple mind).

    Does agreeing with AVS on some points make me a non-IDer?! No, of course not, but if we wish to be true scientists I think we have to accept some arguments do us little favours by over-interpreting data. It would be nice if the evolutionists could do the same, but hey, some of us scientists have to take the moral high-ground!!

    JD

  98. 98
    Dr JDD says:

    I find it a shame when we feel the need to throw around insults. Sorry, this is only my second post and I’m not sure of what value I can add but I feel a bit sad when things descend into insults (both sides) and it seems as though we forget the purpose of why we look into things, perhaps. There is also a danger with these discussions, that we are all so biased that we grasp onto any piece of information that supports (or we think supports) our views, and argue it until we are blue in the face. Secondly, we often as biased people will not accept anything the other side has to say.

    On that note, and please before you jump on me, remember I am a complete theist and one who rejects (macro) evolution (very much accept evolution on the “micro-scale” just not for arisal of new functional pathways and complex genes especially in a naturalistic setting) – I actually agree and see where AVS is coming from initially (I just wish his first post was a bit less patronising). In the context of the quotes, I think the argument Dr Wells makes here is somewhat weak. As AVS points out in his second post, the genetic information does in fact determine the final protein form by in large. Even things like carbohydrate modifications (not to mention palmitoylation, myristolation, prenylation, geranylgeranylation, ubiquitination, sumoylation, and all other manner of post-translational modifications of proteins) are in fact dictated by the amino acid motifs that allow these additions, which are in fact dictated by the DNA. Even the splicing is dictated by DNA code. So perhaps I would agree, the way this argument is portrayed does not make, in my scientific mind, the point that Dr Wells is trying to make.

     

    Personally, what I think ID-ists should be focusing on with respect to the complex nature of this is there for the taking though. For example, think about all these different post-translational modifications, such as lipid anchoring modifications which are in some cases, absolutely necessary to anchor a protein in a membrane for a particular orientation and to “see” its substrate correctly, and be useful as a protein. How did this arise? If the protein’s function is dependent upon these modifications, the original machinery and genetic code had to be in place when this gene came into existence. For example, the enzymes needed to attach this modification to the specific amino acid motif present on the protein. It is a network that again, seems somewhat irreducible and therefore makes its gradual appearance by evolution much more difficult to believe/explain. It points more to design (in my opinion)… (cont…)

  99. 99
    bornagain77 says:

    That the sequential information in DNA has only ‘tenuous’ (weak or very slight) influence over shape and form in the cell, and over the overall body plan, is made clear in part by the these following videos and articles. The following video gives a small glimpse of the astonishing process of DNA Replication, Wrapping and Mitosis:

    DNA – Replication, Wrapping & Mitosis
    https://vimeo.com/33882804

    Whatever it is in the cell directing such a highly choreographed ballet, during the process of DNA Replication, Wrapping and Mitosis, it simply is not reasonable to believe that the sequential information in the DNA is directing such a beautiful process. Especially considering the fact that basically the same highly choreographed process/ballet is happening in every cell of every organism on earth no matter what the sequential information in their DNA happens to be!

    In the following video Dr. Robert Carter speaks on the ‘multi-dimensional genome’.

    Multidimensional Genome – Dr. Robert Carter – video
    http://www.metacafe.com/watch/8905048/

    Specific to the topic at hand, at the 5:20 mark of the preceding video Dr. Robert Carter speaks about the ‘3rd Dimension’ (DNA Architecture) of information in the Genome in which genes with related physiological roles, though far apart sequentially on the DNA, are brought together. Here are a couple of articles making much the same point:

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
    http://www.sciencedaily.com/re.....142957.htm

    “Three-Dimensional Connections Across the Genome“ Keith Dunaway – ENCODE 2012
    Excerpt: These analyses portray a complex landscape of long-range gene-element connectivity across ranges of hundreds of kb to several Mb, including interactions among unrelated genes (Supplementary Figure Y1). Furthermore, in the 5C results, 50-60% of long-range interactions occurred in only one of the four cell lines, indicative of a high degree of tissue specificity for gene-element connectivity
    http://www.nature.com/encode/t.....the-genome

    Tissue-specific spatial organization of genomes – 2004
    Excerpt: Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence.
    Conclusion: Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues.
    http://genomebiology.com/content/5/7/R44

    Of related note:

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2.....ellig.html

    And remember until ENCODE 2012, many Darwinists had argued that upwards to 90 percent of the genome was junk. Even to this day, many Darwinists still argue that huge portions of the sequential information in the genome is junk.

    Another piece of evidence that the linear sequence of information on DNA only has tenuous influence over the structure and form of the cell (and over the body plan) is made clear by the quantum information in the cell.

    Quantum Information/Entanglement In DNA – short video
    http://www.metacafe.com/watch/5936605/

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

  100. 100
    bornagain77 says:

    The following paper deduces that the quantum information in the DNA is what gives DNA its characteristic twist:

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    That Quantum Information in the DNA, in regards to structure, is playing a much larger role than the sequential information in DNA is, is also made clear in the astonishing manner in which DNA is repaired:

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.

    NP-hard problem – Examples
    http://en.wikipedia.org/wiki/NP-hard#Examples

    Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013
    Excerpt: quantum computing is, “in some cases, really, really fast.”
    McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,,
    “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.”
    http://www.sciencedaily.com/re.....122828.htm

    Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA. That DNA has the inherent capacity for quantum computation is elucidated by Stuart Hameroff here:

    Is DNA a quantum computer? Stuart Hameroff
    Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,,
    http://www.quantumconsciousnes.....puter1.htm

    Moreover, the presence of such an elaborate DNA repair mechanism in the cell is itself a contradiction to evolutionary theory:

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    Another clue that brings clarity to the fact to the sequential information in DNA only has ‘tenuous’ influence over the structure of a cell, and the body plan of a organism, is made clear by the fact that a organism, though having the same collection of molecules immediately before and after death, starts to disintegrate in fairly short order upon death:

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,,Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

  101. 101
    bornagain77 says:

    I hold that the reason why a organism starts to disintegrate in fairly short order upon death is because the quantum information, which is ‘conserved’, is ‘missing’ from the organism and existing elsewhere in the universe:

    Quantum Entangled Consciousness (Permanence of Quantum Information) – Life After Death – Stuart Hameroff – video
    https://vimeo.com/39982578

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Of related note to quantum information in biology, not only is quantum information in the cell not reducible to the sequential information in the cell, but the sequential ‘classical’ information is found to be a subset of quantum information by the following method:

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    In fact, not only is quantum information in the cell not reducible to the sequential information in DNA, but all the energy and mass of an entire human body can ‘theoretically’ be reduced to quantum information and teleported elsewhere in the universe:

    Quantum Teleportation of a Human? – video
    https://vimeo.com/75163272

    Verse and Music:

    Luke 23:42–43
    And he said, “Jesus, remember me when you come into your kingdom.” And he said to him, “Truly, I say to you, today you will be with me in Paradise.”

    Evanescence – My Heart Is Broken
    http://www.vevo.com/watch/evan.....WV41100052

  102. 102
    Joe says:

    AVS @ 39:

    And it produces a different protein, Joe.

    LoL! That is what happens when you alter the amino acid sequence, duh.

    I’m not sure what your point was.

    You sed that the amino acid sequence wasn’t altered. You were wrong, as usual.

    Try to make a point when you post and not just make single ambiguous statements that demonstrate your insecurities in talking about biology in such detail.

    Nice projection.

  103. 103
    Joe says:

    AVS is full of itself. It cannot demonstrate that blind watchmaker evolution produced alternative gene splicing. It doesn’t even know where to start such a demonstration.

    Yup, all science so far, AVS.

  104. 104
    Jehu says:

    AVS,

    You don’t get a pass on the information problems in Darwinism by waiving your hands around and saying “it’s a living system.”

    Since I actually do have a job, I can’t sit here all day and debate you point for point, but I have seen your type over the years and basically you are unable to comprehend the difference between a fact being false and a fact being used in an argument you disagree with. You believe that all facts must be used only to support your materialistic world view or else the person using the facts is a liar or a rube. In short, you are unable to objectively comprehend your own metaphysical biases and so you rage and rage against everyone that doesn’t agree with you, sputtering foolish nonsensical objections.

    Darwinism is over. Give up.

  105. 105
    scordova says:

    Dr JDD,

    No, AVS did not pick apart Wells claim, instead AVS put up a strawman. Wells was talking amino acid sequence not DNA sequence! AVS made a subtle misrepresentation insinuating that Wells was arguing a change in Exon sequence when Wells was talking about amino acid sequence.

    Yes they undergo alternative splicing, but the actual exons that become the protein coding mRNA retain completely retain their sequence.

    You were being far too generous to AVS for saying he picked Wells apart. AVS picked apart a statement Wells never made. In that respect, you’re get points docked for not recognizing a rhetorical gimmick and rushing to AVS defense prematurely.

    ID proponents should be criticized when they make misstatements, but in this case the AVS picked apart a statement Wells did not make.

    On that note, and please before you jump on me, remember I am a complete theist and one who rejects (macro) evolution (very much accept evolution on the “micro-scale” just not for arisal of new functional pathways and complex genes especially in a naturalistic setting) – I actually agree and see where AVS is coming from initially (I just wish his first post was a bit less patronising).

    You deserve to be jumped on. Someone obviously as knowledgeable and intelligent as you should have picked out that Wells was talking amino acid sequences in a protein and AVS was talking DNA sequences — they are not the same because:

    1. DNA sequences are made of DNA
    2. protein sequences are made of amino acids

    Yes they undergo alternative splicing, but the actual exons that become the protein coding mRNA retain completely retain their sequence.

    Where did Wells argue the Exons change? Strawman.

    Dr JDD:

    Even the splicing is dictated by DNA code.

    Not exactly. Environmental queues can affect the epigenome, and that may determine which splices to make. Example, in developmental biology we can either physically and or chemically affect the developmental paths. Wells used to do that with frogs. This necessarily affects how cells are developed which means different protein isoforms and alternative splices are made based on environmental queues. A more charitable reading would have perceived this was the sense in which Wells was talking.

    Thus DNA may dictate alternative splices, but what dictates when the DNA is to make an alternative splice in the first place? If the epigenome has a say, then the epigenome may have memory, and if the epigenome has memory its memory may or may not be heritable.

  106. 106
    Upright BiPed says:

    Dr JDD,

    I have been fortunate to catch both your first two comments on this forum. Truly, I hope you’ll see fit to continue to contribute.

    That said, AVS’s first point in his critique of Wells made the deliberately dishonest implication that Wells was saying something that Wells never said. Moreover, it was not what Wells actually said that AVS was objecting to (in fact he confirmed Well’s point). Instead it was his own dishonest implication that he used to launch his attack on Wells. This is the act of an intellectual coward.

    When I called AVS on it, he did not address the false implication, instead he packed on additional slurs – at which point, there was little reason to proceed.

  107. 107
    TSErik says:

    TSErik and Dionisio,

    Frankly, it’s becoming blatantly obvious that you’re having to endure vacuous insults and puffery from people who have little else to offer than cutting and pasting from who knows where.

    Certainly. And I admit I didn’t touch the original topic or the claims therein. I find it necessary to hold a mirror up to the nihilistic and antisocial drones. To cut open their parrot statements to reveal the absurdities that rattle around in their vacuous crania.

  108. 108
    scordova says:

    AVS said:

    the actual exons that become the protein coding mRNA retain completely retain their sequence.

    Did Wells say exons change sequence, or is that just your false insinuation that he said exons change their sequence?

  109. 109
    Dr JDD says:

    Hi,

    Perhaps I did not explain myself very well, or perhaps I was misunderstood – however I am happy to accept the former. Please do not see my reply as “rushing to the defence of AVS” as nothing could be further than the truth. I was not rushing, I was trying to provide a more balanced approach that is often lacking I feel. It appears to me that when we do not make the small concessions needed we give the impression we are extremists and not scientists.

    I do not think that the whole of Dr Wells quote above is wrong – far from it I wholeheartedly agree with the implications. However I do feel aspects of it are, as AVS says in SOME of his response (I am not defending AVS I am questioning some of the ways in which we respond) are due to perhaps the way it is phrased (in particular the carbohydrate addition).

    My post was intended to potentially raise the point that, for example, if a child does not understand something, and throws a tantrum do you respond by calling names and throwing a tantrum or do you as a mature adult, rise above it, explain the fallacy in their argument and not resort to name-calling? I fear that when we engage in an immature name-calling manner we open ourselves up to severe criticism.

    This is how I read it, in response to AVS’ first main post:

    1)      Yes alternative splicing is a genetic code determined thing i.e. splicing sites at intron-exon boundaries have specific sequences which allow them to be recognised and spliced. However Dr Wells is not talking about that, he is saying that other cues are in place, outside of the genetic code that determine which exons are transcribed into proteins. These environmental cues are not DNA events so they are outside the DNA code control (although they do rely on gene-encoded proteins to perform these events and other gene-encoded transcription factors)

    2)      Yes a carbohydrate addition can only occur at a glycosylation motif, which is genetically determined by the DNA code. However, if indeed the complex carbohydrate added to the protein that the DNA transcribed also contains information or its own “code” as studies suggest, this sugar code is independent of DNA code and has a purpose not dictated by an evolving genome as such (although you could argue that simply the presence of a glycosylation site dictates the presence of a sugar code so DNA has some role but this is a weak argument IMHO).

    3)      I agree with Dr Wells about the spatial distribution of proteins in particular on membranes and membrane trafficking/transport (in fact I did my PhD on this) and the lipid interactions and properties (especially if things such as lipid rafts do exist, for example) are complex processes that cannot be explained by DNA code, as Dr Wells elegantly summarises. So I would completely disagree with AVS here as (in his 2nd post) he only address protein:protein and protein:carbohydrate interactions and completely omits protein:lipid importances, which Dr Wells, IMO clearly alludes to.

    My personal opinion (which may well be wrong I will accept, and may change the more time I would spend on UD and get fed up of people talking to others like AVS does in such a dismissive, patronising way at times) would be that the most fruitful discussions address the issues directly. I was writing my original post in this thread having read through the first number of posts that seemed to change the direction, go off topic, and not answer AVS’ objections when I believe there are rational arguments against what he said, while he does make some (NOT ALL!) valid points. He just fails to take them where I believe Dr Wells intended them to go.

    Perhaps I am a bit naïve and Utopian about all this but I believe if as ID’ers we really want to be taken seriously we cannot stoop to the level of name-calling and accepting rational points but engaging with people over them (even if they do not offer us the same luxury). Otherwise we set ourselves up to be labelled unreasonable and immature.

    Regards,

    JD (a bit naïve to trolls 😉 )
    PS – this was not aimed at all responders just a general comment from observing a few responses to this and other posts

  110. 110
    Upright BiPed says:

    Again Dr JDD, I hope you’ll find the time and continue to contribute.

  111. 111
    Eric Anderson says:

    JDD:

    Thanks for your comments. I hope you will continue to participate and comment.

    It is instructive to note, however, that Wells has provided a number of references for what he is describing (some cited in the OP). Meanwhile, the supposed takedown by AVS was characterized by bald assertions, strawmen, insults, and a lack of citations. He has not dealt with the substantive issues raised by Wells, but loudly proclaims that he is the only one who has addressed the science in this thread.

    In my view, it is a very open — and fascinating — question whether all information for an organism is specified in DNA. A growing number of researchers (not just Wells) are starting to suspect that there are additional layers of information in the cell beyond what is contained in DNA itself. This is a highly-interesting and cutting-edge question. Unfortunately, in his haste to trash anything on this site or anything by someone like Wells who deigns to question the evolutionary mantra, AVS has not only made mistakes about what Wells’ argument is, he has also essentially dismissed with the wave of a hand a very interesting and front-and-center research question that is receiving a lot of attention in the research community right now.

  112. 112
    Eric Anderson says:

    JDD:

    I was writing my comment #111 when you posted #109 and didn’t see it before I posted. Thanks again for your clarification and for sharing your thoughts.

  113. 113
    Moose Dr says:

    AVS, “I’m not an evolutionary biologist, but I do understand enough of it to know that it makes sense and puts biology in perspective.”

    Wow, a note of humility. AVS, I have three questions for you:
    1 – Do you believe that astrology is valid?
    (I presume you would say “No”).

    2 – Do you have a rich understanding of astrology?
    (I would presume you would say “No”. If you don’t say no, please explain the relationship between the phase of the moon and a person’s life path. I presume that you know that astrology is much more intricate than what “sign” you were born under.)

    3 – Do you believe that you have enough information about astrology to come to your conclusion in question #1?

  114. 114
    Querius says:

    JDD,

    Thanks so much for your cogent, insightful comments. As you have, my rejection of Darwinistic evolution is based on recognizing the prevalence of speculation over science, although you have a much deeper understanding of the biochemical issues than I have. What I picture is a sort of raisin bread—the raisins are observations with a high level of scientific confidence.

    In following the data, I wouldn’t mind if it led me to some form of evolution. But it currently doesn’t, and I think the paradigm that’s used for the context—the bread around the raisins—needs a major revision.

    Now I’m hungry for some toasted raisin bread. 😉

    Hope to see more posts from you.

    -Q

  115. 115
    Moose Dr says:

    Dr JDD, your post #109 is a breath of fresh air. Thanks.

  116. 116
    Upright BiPed says:

    I’d also note:

    How many ID proponents have their interest in ID hanging on what percentage of the information in the cell is entirely gene-based versus epigenetic?

    I’m willing to bet the number is virtually zero.

  117. 117
    Dr JDD says:

    Upright / Eric / Querius / Moose – many thanks for the generous welcome to UD. I sincerely hope I can in some small way occasionally add value to discussion.

    It is a breath of fresh air to be able to share common thought-processes that constantly come under fire on an almost daily basis coming from the science world (where most very intelligent scientists are in fact not even aware of many of these arguments against naturalistic evolution nor have given it thought given the axiom of atheistic evolution that has been largely established without question in the scientific community).

    I look forward to many more stimulating articles and discussions!

    JD

  118. 118
    News says:

    News note: Just been notified that Jonathan Wells has an article accepted for publication in a peer reviewed journal that tackles this question for an academic audience. We’ll doubtless be notified, and some of you may wish to comment in that venue.

  119. 119
    PaV says:

    Dr JDD:

    I feel this argument, or rather the evidence presented in quotes above can be easily picked apart like AVS is done. So I agree with him on those points (that even carbohydrate addition is down to the DNA as it is a specific sequence, etc.) but I interpret that as complexity of DNA outside the reach of a naturalistic evolution. It is not proof of either, it is merely adding complexity which makes one theory more difficult to rationalize and the other easier to believe (to my simple mind).

    Welcome JDD. At the end of your last post you seem to acknowledge an unfamiliarity with ‘trolls.’ In a certain sense, that’s what AVS is.

    You’re new to UD, and that’s great. But we who have been here for years have seen it all by now. That’s part of the reason we might seem (and be) edgy at times.

    When you wrote, “I interpret that as complexity of DNA outside the reach of a naturalistic evolution. It is not proof of either, it is merely adding complexity which makes one theory more difficult to rationalize and the other easier to believe . . .” you simply are stating the EXACT way we here at UD understand these things. AVS is a “Johnny-come-lately,” with this being the first we’ve seen (or heard) of him. We’ve had these kinds of arguments before with others like AVS, and we will have them again. And, unlike you, the arguments seem to mean nothing to the ‘other side.’ It does tend to make us a little impatient.

    What is so obvious—or should be so obvious to all—is the tremendous levels of complexity that are “integrated” together to effect cellular function . . . and LIFE! Exactly how long it’s going to take before the Darwinists “give up the ghost,” no one knows for sure. But what is crystal clear right now is that every advance of biological technology damages the likelihood of current ‘evolutionary’ thought to explain it, and, in the case of Darwinism, completely dismantles it.

    Welcome aboard.

    Now, as to some of the things AVS wrote:

    (a) He writes something like “all of these are subject to typical evolutionary mechanisms.”

    How nice. And what are those mechanisms? Positive/directional selection? Neutral Genetic Drift (NGD)? There’s another thread that’s up as we speak centering on how population geneticists now favor NGD over selection as the means by which evolution advances. In the face of the ‘layers’ of complexity we are talking about, how is this possible? It is inane to even begin to think that NGD could bring this about.

    But, now, traditional population genetics have been abandoned. Why? Because of genetic load. And that means that the amount of directional selection that can take place is now itself limited. Each layer contributes to more complexity and, hence, to greater genetic load. So, whence these ‘layers’ of complexity?

    (b) We are talking about the living world here in biology, while at the surface it may seem similar to the computer world, there are a vast amount of differences. The best way I can sum it up is the fact that biology is concerned with living things, to which there is no real comparison in the non-living world.

    And, yet, when it comes to “evolution,” computer models are built which, we are told, simulate what happens in real life. Most of what is used to prop up evolution is somehow tied to computer models.

    (c) Anyway here are some terms you can look up to get you on your path to knowledge:
    transcription factors, cell determination, cell differentiation, fate maps, ectoderm, endoderm, and mesoderm, gastrulation, mitosis, hox genes, and morphogens
    Wiki is a good resource, goodluck

    Besides the sneering quality these words drip with, this is a pathetic retort. You’re asked for an explanation, and you answer by saying to go look up the most basic structures of embryology.

    You fail to “see the forest for the trees.” The ID argument is one of unexplainable levels of complexity. That there are all these various inputs to sequence information requires us to believe that the information stored in DNA must be information that is ‘computable’ with a whole series of other codes, or modes of processing. Is it permissible—that it, can logic sustain the hypothesis—to believe that this unimaginable level of complexity slowly arose out of natural forces themselves?

    Darwinists love to mock IDists by saying our view is simply: “God did it.” Your view, I’m afraid, is simply: “DNA does it.” Now if you could only explain where all the information contained in DNA came from, this would be an acceptable answer.

    Oh, yeah, I remember: “Typical evolutionary mechanisms can explain it all.” So, I guess it isn’t “DNA does it all,” but “NGD and selection” does it all. Would you like to explain how it does this, or should I just accept this on faith?

  120. 120
    PaV says:

    Dr JDD:

    (where most very intelligent scientists are in fact not even aware of many of these arguments against naturalistic evolution nor have given it thought given the axiom of atheistic evolution that has been largely established without question in the scientific community).

    This is exactly right. I have a degree in Biology that is well dated. However, I remember taking chordate morphology and thinking: when will they explain the so-called “missing links”? It never happened. And I thought, “Oh well, maybe they explain that in some other class.”

    And on I went, assuming a kind of, as you say ‘theistic evolution’ per Darwinian mechanisms. Then I read the Origin of Species in an old book shop. Oh, my! “Difficulties on the Theory”! I should say. Then Behe’s “Darwin’s Black Box” and Denton’s “A Theory in Crisis.” I decided to go looking for an answer. Surely it had to be out there. It was never to be found. Then you go to the blogosphere thinking they will have an answer to your questions and objections. No. Instead they simply belittle you and cast scorn on you. Then you know there is no answer or else they would have provided it instead of the scorn.

    I think the vast majority of scientists simply accept what the evolutionary biologists tell them, supposing the entire time that if pushed, these scientists could buttress their claims. EVS is probably one of those scientists. They’re simply unaware that the “emperor has no clothes.”

  121. 121
    AVS says:

    Scordova, since you are the only UDer that I know to have some intelligence, I will respond to you and most likely you only. My problem with Mr. Wells is not only what he says, but how he says it. Not only is his assertion about alternative splicing wrong, but he words it vaguely, most likely on purpose. In that first sentence he is trying to bolster his claim that protein sequences are not fully specified by DNA sequence. He makes it seem as if alternative splicing is changing the primary sequence of the protein so that it no longer exactly matches what would be predicted from the corresponding coding segments of DNA. This is completely false. You can take the exon straight from the DNA, and compare its translation to the corresponding segment in the expressed protein, and the two would match perfectly.

  122. 122
    AVS says:

    JDD, its nice to see someone reasonable on here for once. Thank you.
    Erik, when you’re ready to talk about biology you can try to refute my original points. I won’t hold my breath.

  123. 123
    scordova says:

    From wiki:

    Protein Splicing

    Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (called exteins) on both sides. The splicing junction of the precursor protein is mainly a cysteine or a serine, which are amino acids containing a nucleophilic side chain.

    This slide compare protein splicing to RNA splicing:

    http://tools.neb.com/inbase/intro.php#T

    More:

    http://tools.neb.com/inbase/intro.php#A

  124. 124
    AVS says:

    You do realize that the amino acid sequence after, protein splicing, still exactly matches what would be predicted from the corresponding coding segments of DNA, right? As far as this conversation is concerned there is no difference between splicing before or after translation, the final gene product still matches what was originally encoded in the DNA for each extein. Splicing does not change the primary sequence of the protein so that it no longer exactly matches what would be predicted from the corresponding coding segments of DNA.

  125. 125
    AVS says:

    Also, the splicing event is signaled by a stretch of amino acids in the precursor protein which are encoded by none other than the original DNA sequence. This means the information for protein splicing, as well as the information that signals sugar modification that I mentioned before, is encoded by the DNA itself.

  126. 126
    Mung says:

    AVS:

    Yet another person who tells me I have no idea what I am talking about, and yet I am the only person to actually demonstrate any knowledge of biology in the 60 comments above this one. It’s quite comical.

    You don’t know what life is and you don’t know that causes life, and you don’t know that you don’t know what you don’t know. Now that’s comical.

  127. 127
    Upright BiPed says:

    A friendly note to UD participants…

    AVS is here because he’s been caught in a ridiculous and dishonest representation of what Wells has said. He has been specific, and the text is right here on this very thread. It’s not going anywhere.

    So how do you deal with a stupid lie when you don’t have the character to recant it? You tell it again, of course. You gather up some different words and a different angle and say it all over again – just like he did in 121.

    So AVS is now back, thrown out a couple of kisses, and if that doesn’t work, he’s surely ready to incite someone (anyone) to get back in it with him so he can tell his whole thing again.

    Why not just let him stand in it this time? He’s definitely a thumper – so he’s not going anywhere. Let him have his famous indignant last words. Allow him to fool himself he can change the dishonest attack he’s already laid down.

  128. 128
    AVS says:

    Did you have anything to add to the conversation or are you just trolling too?

  129. 129
    AVS says:

    If my attack is dishonest, surely someone should be able to prove me wrong, no?

  130. 130
    scordova says:

    From wiki Posttranslational Modification of Proteins.

    I guess that means what happens to proteins after the ribosomes using the mRNA from DNA has made them. 🙂

    After translation, the posttranslational modification of amino acids extends the range of functions of the protein by attaching it to other biochemical functional groups (such as acetate, phosphate, various lipids and carbohydrates), changing the chemical nature of an amino acid (e.g. citrullination), or making structural changes (e.g. formation of disulfide bridges).

    Also, enzymes may remove amino acids from the amino end of the protein, or cut the peptide chain in the middle. For instance, the peptide hormone insulin is cut twice after disulfide bonds are formed, and a propeptide is removed from the middle of the chain; the resulting protein consists of two polypeptide chains connected by disulfide bonds. Also, most nascent polypeptides start with the amino acid methionine because the “start” codon on mRNA also codes for this amino acid. This amino acid is usually taken off during post-translational modification.

  131. 131
    AVS says:

    Scordova, you’re late to the game so I’ll cut you some slack. I guess you haven’t noticed but an important part of my original argument was that the modification of proteins, whether it’s by enzymes that add sugars, phosphates, or lipids, or enzymes that splice or cleave the protein, or it’s enzymes that alternatively splice the mRNA, or enzymes that are helping transport the protein, every single one of these enzymes recognize a specific amino acid sequence on the protein or mRNA strand. And as I hope you know, the protein and mRNA strands are all controlled by the DNA.

  132. 132
    Joe says:

    AVS:

    In that first sentence he is trying to bolster his claim that protein sequences are not fully specified by DNA sequence.

    Liar- or moron. He is talking about the final 3-dimentional shape- its spatial structure, is not determined by the DNA sequence that codes for it:

    We have rigorous experimental evidence that DNA does not even code completely for proteins; in most cases the final forms of proteins are not fully specified by DNA sequences.

    That is because with longer chains chaperones are required or the functional shape is never realized.

    Look AVS, if you can’t even get the first part right perhaps you should just leave and come back when you are all grown up.

  133. 133
    Joe says:

    AVS:

    You do realize that the amino acid sequence after, protein splicing, still exactly matches what would be predicted from the corresponding coding segments of DNA, right?

    So what? No one is saying otherwise.

    AVS tilting at windmills and losing. Very entertaining.

  134. 134
    Joe says:

    AVS:

    And as I hope you know, the protein and mRNA strands are all controlled by the DNA.

    So the DNA controls alternative gene splicing and mRNA processing? Is it some kind of telepathy?

  135. 135
    AVS says:

    The sentence you have bolded is his claim, and the following sentences, the first of which is about alternative splicing which I was referring to at that time, are the evidence he uses to back this claim. Please do not take what I say out of context.

  136. 136
    AVS says:

    Telepathy? No Joe, it’s sequence specific binding and it’s how this little thing called biochemistry works. I wouldn’t expect you to now anything about that though.

  137. 137
    AVS says:

    I guess I’ll demonstrate my intellectual honesty for you all and let you guys know that the cellular process you are looking for is called RNA editing. This is the only process that you can truly say “changes the sequence” of the final, expressed amino acid chain. And even this process is regulated by complementary base-pairing to the mRNA strand, which requires specific sequences in the original DNA strand.

  138. 138
    Joe says:

    AVS- Alternative splicing does change the sequence- the introns and perhaps some exons are taken out. He is talking about the DNA sequence is different from the processed mRNA sequence:

    After transcription, most multi-exon eukaryotic genes undergo alternative splicing, which changes the sequence.

    AFTER TRANSCRIPTION, NOT TRANSLATION.

    So why are you talking about amino acid sequences? It’s as if you are just a poseur.

  139. 139
    Joe says:

    AVS:

    No Joe, it’s sequence specific binding and it’s how this little thing called biochemistry works.

    LoL! DNA is inert. It doesn’t do anything if left alone. And sequence specific binding doesn’t mean blind processes did it nor that if you get all the right chemicals together that it all just starts happening.

    So no, AVS, you are just a bluffer with nothing but you to back you up.

  140. 140
    Joe says:

    AVS:

    I guess I’ll demonstrate my intellectual honesty for you all and let you guys know that the cellular process you are looking for is called RNA editing.

    Wells talks about RNA editing in the OP. So thank you for demonstrating your dishonesty. You are one sick troll, AVS.

    Thanks for the laughs…

  141. 141
    AVS says:

    Thank you for proving the point I made about his wording being ambiguous. both Scordova and I seem to think he is referring to the amino acid sequence, not the mRNA.

    I never claimed any of these processes are carried out by DNA directly, but the processes I have mentioned are all completely dependent on the initial DNA sequence, in either the the form of mRNA or amino acid sequence due to the fact that they rely completely on sequence-specific binding.

  142. 142
    AVS says:

    Ah yes, he did. My mistake, I knew I’d heard about it recently. Anyways, let me know when you guys can refute anything I have said. See ya.

  143. 143
    Joe says:

    AVS:

    Thank you for proving the point I made about his wording being ambiguous. both Scordova and I seem to think he is referring to the amino acid sequence, not the mRNA.

    LoL! It is only “ambiguous” if you don’t understand biology. Most likely Sal just got caught up in your BS.

    It was very clear to me. Go figure.

  144. 144
    Joe says:

    AVS- There isn’t anything you said that refutes Wells. Meaning there isn’t anything you said that needs addressing except to correct, as I have been doing.

  145. 145
    AVS says:

    Yeah, because you understand biology, right Joe? Good one.
    And why don’t you ask scordova himself then? It’ll probably be the first time he agrees with me.
    Everything I have said completely refutes Wells’ dishonest presentation of biological processes. The fact that you think you have corrected me in much of anything is laughable. On the troll scale, you’re not far from our old pal Erik. If you think of something intelligent to say, let me know. I won’t hold my breath.

  146. 146
    Moose Dr says:

    AVS, “you’d realize I was saying that it puts you at a disadvantage in thinking about biology. Computer engineering lends itself better to a different way of thinking than biology does, just as math and chemistry lend themselves to different ways of thinking.”

    There is a bit of truth hidden in that statement. However, these “different ways of thinking” should compliment each other, not clash with each other. In the other fields of science, all of them, you find that coming at the question from a different perspective compliments rather than questions.

    Mathematicians (think Hoyle or Dembski) don’t like the theory. Engineers don’t like the theory (they love biology because it contains incredible feats of engineering.) Us software developers don’t like the theory. The theory only makes sense to people who fantasize that the impossible can be achieved if there is enough time.

    Please understand what a software engineer is, we are logic engineers. Developing computer software is assembling a rack of logical pathways. Developing computer software that works requires that the logic be flawless and complete. Evolutionary biology, by your reasoning, cannot be properly understood with logic. I agree that evolutionary biology cannot be understood with logic — because it is illogical.

    BTW AVS, I don’t believe that you have answered the questions I posed to you in #113.

  147. 147
    AVS says:

    Well I’m glad we could finally agree on something..somewhat. Unfortunately, the fact of the matter is that to understand biology at a high level, you need a high degree of training in the field. You can’t just take a computer scientist and ask them to analyze a scientific paper out of the journal of biological chemistry. Most of the people who claim to “not like that theory” don’t have much of a background in biology to begin with. The individuals behind the ID movement with a background in biology know exactly how to take advantage of it. They craft their arguments around what science hasn’t figured out yet and blow any shortcomings they can find out of proportion. They know their audience well and cater to them, preying on the scientific illiteracy and lack of knowledge in biology of the majority of them.
    The evidence behind evolution has been accumulating for decades and no matter how much you guys scream “darwinism is bankrupt,” the truth is its being taught more and more, at least at the college level, slowly gaining a stronger and stronger foothold in the public. It doesn’t seem like you guys are doing much I’m sorry to say.

  148. 148
    Jehu says:

    AVS

    In that first sentence he is trying to bolster his claim that protein sequences are not fully specified by DNA sequence.

    His claim is accurate. Alternative splicing is determined in part by epigenetic inputs, hence protein sequences are not fully specified by DNA. That is not exactly a big win for ID, but whatever I am not the one making the objection.

  149. 149
    Jehu says:

    BTW, Darwinism is intellectually bankrupt.

  150. 150
    Jehu says:

    BTW, Darwinism is intellectually bankrupt.

  151. 151
    Jehu says:

    Sorry computer lag resulted in a double post.

  152. 152
    AVS says:

    Do I really have to repeat myself again? While it was interesting to learn that we think epigenetics has a role in splicing, the fact still remains that the amino acid sequence of the final gene product is still exactly what would be predicted from the corresponding nucleotide sequence in the DNA. Like I said, RNA editing is the only process that supports his claim and it is not only rare but largely has no effect on the ultimate primary sequence.

    And like I said, you can call it “bankrupt” all you want, but I have seen with my own eyes, the increase in mentioning of both abiogenesis and evolution in university-level basic biology classes.

  153. 153
    Dionisio says:

    Proverbs 12:15

    The way of a fool is right in his own eyes, but a wise man listens to advice.

    Proverbs 13:20

    Whoever walks with the wise becomes wise, but the companion of fools will suffer harm.

    Proverbs 14:7

    Leave the presence of a fool, for there you do not meet words of knowledge.

    Proverbs 15:2

    The tongue of the wise commends knowledge, but the mouths of fools pour out folly.

    Proverbs 15:14

    The heart of him who has understanding seeks knowledge, but the mouths of fools feed on folly.

    Proverbs 16:22

    Good sense is a fountain of life to him who has it, but the instruction of fools is folly.

    Proverbs 17:10

    A rebuke goes deeper into a man of understanding than a hundred blows into a fool.

    Proverbs 18:2

    A fool takes no pleasure in understanding, but only in expressing his opinion.

    Proverbs 20:3

    It is an honor for a man to keep aloof from strife, but every fool will be quarreling.

    Proverbs 23:9

    Do not speak in the hearing of a fool, for he will despise the good sense of your words.

    Proverbs 26:11

    Like a dog that returns to his vomit is a fool who repeats his folly.

    Proverbs 29:9

    If a wise man has an argument with a fool, the fool only rages and laughs, and there is no quiet.

    Proverbs 29:11

    A fool gives full vent to his spirit, but a wise man quietly holds it back.

    Proverbs 26:4

    Answer not a fool according to his folly, lest you be like him yourself.

    Proverbs 26:5

    Answer a fool according to his folly, lest he be wise in his own eyes.

    Taken together the latter two verses illustrate the point that no proverb is intended to cover every possible situation. The apparent contradiction in the two proverbs indicates that proverbs must be appropriately applied. One situation demands that we avoid playing the fool’s game by giving an answer, while another demands that we expose the folly so that the fool is not considered wise.

  154. 154
    Joe says:

    AVS- Obviously I understand biology better than you do. At least I knew what transcription entails.

    Everything I have said completely refutes Wells’ dishonest presentation of biological processes.

    Liar. You don’t even understand what Wells said.

    The fact that you think you have corrected me in much of anything is laughable.

    The evidence says I have corrected you.

    the fact still remains that the amino acid sequence of the final gene product is still exactly what would be predicted from the corresponding nucleotide sequence in the DNA

    So what? No one is saying anything different. Are you really that dishonest or stupid?

  155. 155
    Jehu says:

    AVS

    While it was interesting to learn that we think epigenetics has a role in splicing, the fact still remains that the amino acid sequence of the final gene product is still exactly what would be predicted from the corresponding nucleotide sequence in the DNA.

    That is simply not true. DSCAM, for example, can express over 38,000 different proteins depending on alternative splicing. Epigenetic inputs influence alternative splicing, therefore the resulting protein cannot be predicted from the DNA alone.

  156. 156
    AVS says:

    Yes it most certainly is true. Put an amino acid sequence of the whichever final protein is made, up to the corresponding exon in the DNA. The sequence predicted from the DNA will exactly match that of the actual amino acid sequence. Like I’ve said three times now, RNA editing is the only process that supports Wells’ claim and it not only occurs rarely, but it rarely changes the final fold of the protein.

  157. 157
    Joe says:

    Jehu, AVS has been backed into a corner and now he is relegated to flailing away. He has no idea what Wells claims He has been caught misrepresenting Wells and now he just spewing meaningless drivel.

    Typical but still pathetic.

  158. 158
    Jehu says:

    AVS

    Put an amino acid sequence of the whichever final protein is made, up to the corresponding exon in the DNA. The sequence predicted from the DNA will exactly match that of the actual amino acid sequence.

    So what? The point of alternative splicing is whether or not an exon is included in the mRNA or not. Alternative splicing is influenced by epigenetic inputs.

  159. 159
    AVS says:

    So what??? Wells’ argument is that alternative splicing results in a difference in the amino acid sequence and what would be expected from the DNA coding regions. This is completely false, except in the case of RNA editing. Joe has already proven my point that Wells’ wording is ambiguous anyway. Could you let him know that the sequence Wells refers to in the alternative splicing sentence is most likely the amino acid sequence, by the way.

  160. 160
    Andre says:

    Well epigenetics is non Darwinian and thus the only reason, AVS rejects it, you can’t mess with the Jesus of materialism (Darwin), atheists will have none of that, you see it would compromise their belief system….

  161. 161
    AVS says:

    I love how you guys toss the phrase “darwinian” around. If you guys ever want to be taken seriously , you should refer to it as “the theory of evolution.” And epigenetics does not refute the theory of evolution, it has become a part of it.

  162. 162
    Andre says:

    AVS

    Firstly, is there such a thing as evolution and I would say yes like most other ID people, is there such a thing as Darwinian evolution and the answer is no. Darwin’s theory is mostly stolen from other people, that’s a free lesson for you. Darwin was a crazy, delusional angry at God racist.

    Evolution is true but it ain’t Darwinian.

  163. 163
    Andre says:

    AVS

    Perhaps you could spare some time and read Lamarck’s work and then some Alfred Russel Wallace so you can understand better what ID people like me understand about evolution.

    The Darwinian blind luck did it just does not hold with the evidence, Wallace and Lamarck observations and theories however does.

  164. 164
    AVS says:

    Again, I love how you guys refer to things as darwinian. Outside of your kool-aid drinking circles, here in the world of science, it’s “the theory of evolution” and it has stemmed from the ideas put together in Darwin’s book. One of the first things often taught in evolution classes is the, “evolution” of the idea itself, starting with Linneaus’ classification system in the 1700’s. Darwin may not have been the only person to think of evolution, but he was the first to think of it clearly and amass the evidence needed to support his new hypothesis.

  165. 165
    Andre says:

    AVS

    If you think epigenetics has become part of Darwin’s pseudo scientific ramblings then it’s abundantly clear you don’t really know much about the subject in-spite of your recurring and often vehement claims about your proficiency on the subject.

    Stultus Est Sicut Stultus Facit

  166. 166
    AVS says:

    Are you serious Andre? Lamarck has been proven to be almost completely wrong about the mechanisms of evolution over the last 200 years. A giraffe that stretches its neck out to reach higher leaves does not have offspring with a longer neck. Only changes in the heritable material are passed to offspring. And Wallace had virtually the same idea that Darwin did, he actually spurned the publishing of Darwin’s work.

  167. 167
    AVS says:

    Andre, you can join Joe and BA on the sideline now, you have nothing intelligent to say and have demonstrated that you have no idea what you are talking about.

  168. 168
    Andre says:

    O Brother, why do I even bother?

    Get schooled friend come back when you’ve learnt something. Start here….

    https://www.youtube.com/watch?v=tdhQWkTl1PQ

  169. 169
    AVS says:

    Ah yes, and the illiterate tells the educated to “get schooled.” Enjoy life in the slow lane Andre.

  170. 170
    Andre says:

    AVS

    Lets have some fun….. Now how do you measure that you are somehow more “schooled” than me? Please do tell?

  171. 171
    Andre says:

    AVS

    I will quote you….

    “But anyways I can picture a scenario where genes do not need to be spliced, but a relatively simple protein evolves that is capable of modifying RNA at low levels, producing a new protein with a slightly different function that may benefit an organism. You’re problem is that you think these huge complex protein complexes we see in eukaryotes today had to all come about at once. No one is claiming this happened.”

    Do you see the problem with your words above? Read it to yourself aloud and report back what you’ve found please?

  172. 172
    RodW says:

    I can see I’ve been posting on the wrong thread! Joe brought up this topic and this is what I posted over there:

    Joe said,

    See also Why Is A Fly Not A Horse? Dr Sermonti is a geneticist.

    Jonathan Wells is a developmental biologist and he also disagrees with you.

    I think the vast majority of biologists would agree with me that the genetic information ultimately determines the form of an organism ( with a few caveats)
    I’m not familiar with what Sermonti says on the matter. I only know his arguments that the leaf and stick-mimic insect fossil record was evidence against evolution.
    Was the quote that genes only influence form from Wells or Denton? In any case, if the major source of information on form is not genetic information where does it come from?
    Has this other form of information ever been demonstrated? How is it different from genetic information?

  173. 173
    AVS says:

    The fact that you are on here trying to talk about evolution, despite you obviously having no real knowledge on the subject tells me your are an idiot.

  174. 174
    AVS says:

    “Mutate a fruit fly embryo in every possible way, and observe only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.”
    Seriously what does that even mean?
    The fact you guys think that is even an intelligent statement just goes to show how clueless you are, were you expecting an “alien” fly?

  175. 175
    Andre says:

    AVS

    Is that just a general observation or have you addressed me?

    So how about your measurements on being more schooled than me? Can I have it then?

    Since you are not forth coming in any answers let us start with;

    “But anyways I can picture a scenario where”

    You know AVS I can picture a scenario where Megan Fox falls in love with me, but that does not mean it actually happened……

    “but a relatively simple protein evolves that is capable of modifying RNA at low levels, producing a new protein with a slightly different function that may benefit an organism”

    Extraordinary claims require extraordinary evidence do you have some to verify this claim?

    “You’re problem is that you think these huge complex protein complexes we see in eukaryotes today had to all come about at once. No one is claiming this happened.”

    In light of this, can I ask you what good is half a lung? Half a brain? Half an anus? Half a penis?

    Here is your problem, you have to much faith in your imagination.

  176. 176
    AVS says:

    That comment was specifically for you Andre.
    Not only is there evidence for the evolution of splicing mechanisms, but it has been shown that some RNA sequences can splice themselves.
    Half a lung is always better than no lung, just as half a brain is better than no brain. I really wish you had at least a half a brain Andre.

  177. 177
    Andre says:

    AVS

    Not only has a village lost its idiot the circus is missing it’s clown…

    http://www.alternativeinsight.com/Lamarck.html

    knock yourself out…

  178. 178
    Andre says:

    AVS

    If you did not know, and I know you did not, both Lamarck and Wallace argued that evolution is a directed process, aka, designed. Both these gentleman have been vindicated….

    http://www.voicesfromoxford.or.....iology/184

    Noe please if you have a single ounce of integrity, please do the right thing and apologize, then go learn what you have missed all these years. It’s an amazing journey I promise you.

  179. 179
    Joe says:

    AVS the only theory of evolution came from Darwin.

    Wells’ argument is that alternative splicing results in a difference in the amino acid sequence and what would be expected from the DNA coding regions.

    That is NOT what he says. You are a moron

  180. 180
    AVS says:

    Andre, you question my use of wiki and then send me a link from a random website? Good one bud.
    Epigenetics is the closest thing to support for lamarck and it consists of heritable modifications made to DNA structure made largely during development. You should really try to learn about biology from sources other than what you friends here at UD are peddling.

  181. 181
    Joe says:

    RodW:

    I think the vast majority of biologists would agree with me that the genetic information ultimately determines the form of an organism

    Until they come up with supporting evidence or some way to test that claim, no one cares what they agree with. It ain’t science.

    In any case, if the major source of information on form is not genetic information where does it come from?

    Other parts of the cell including its cytoskeleton and membrane.

    Has this other form of information ever been demonstrated?

    Yes.

    How is it different from genetic information?

    It isn’t genetic

  182. 182
    AVS says:

    Yes, we know Joe, you think he’s referring to the mRNA sequence. And yet scordova, your own pal, disagrees with you and agrees with me.

  183. 183
    AVS says:

    “Other parts of the cell including its cytoskeleton and membrane.”
    Care to explain this in your own words Joe?

  184. 184
    Joe says:

    AVS spews:

    Yes, we know Joe, you think he’s referring to the mRNA sequence.

    Nope, I don’t think tat. Just read what he says, moron. And I don’t care what Sal says. That doesn’t change the fact that Wells was referring to TRANSCRIPTION which does NOT involve amino acid sequences.

    So stop being a dishonest ass for once in your life.

  185. 185
    AVS says:

    Joe, this is what you said yesterday:
    “He is talking about the DNA sequence is different from the processed mRNA sequence”
    You just completely contradicted yourself, congrats. You are a blubbering troll with no knowledge in the field of biology. Have a nice life.

  186. 186
    Joe says:

    Other parts of the cell including its cytoskeleton and membrane.

    AVS:

    Care to explain this in your own words Joe?

    Are you admitting ignorance of developmental biology? Sweet.

    Well, for one, the cytoskeleton contains micro-tubules that allow proteins to get where they are needed where they are needed.

  187. 187
    Andre says:

    AVS

    It sights proper references and highlights the differences between Darwinian evolution and Lamarckian evolution, its important to know that they are two opposing views. Epigenetics are NOT part of your Darwin based view, to say that it is makes you liar….

  188. 188
    Joe says:

    AVS- you are a liar and a moron. How did I contradict myself?

  189. 189
    Jehu says:

    AVS

    Wells’ argument is that alternative splicing results in a difference in the amino acid sequence and [sic] what would be expected from the DNA coding regions.

    No, Wells’ argument is that the final forms of proteins are often not fully specified by the DNA. Which is true because alternative splicing is influenced by epigenetic inputs.

  190. 190
    Andre says:

    Which brings us full circle AVS…..

    Darwin was wrong and Lamarck was right…..

  191. 191
    Jehu says:

    BTW, AVS, alternative splicing is not rare, it occurs in well over 90% of human genes.

  192. 192
    RodW says:

    Joe said,

    In any case, if the major source of information on form is not genetic information where does it come from?

    Other parts of the cell including its cytoskeleton and membrane.

    I’d say this is correct, the cytoskeleton and membrane do store information in a sense and pass that down to subsequent generations. There are many other such sources of information…one could even say the cell itself is a source. DNA doesnt specify how to make a cell or organism from scratch, it only specifies how maintain a cell or grow an organism within the context of a living cell or zygote.
    But I think Wells dismisses the role of DNA too easily. The cytoskeleton may store information but the actin and tubulin proteins that make up the cytoskeleton are coded for in the DNA. The proteins that interact with them and allow the cytoskeleton to store info are also coded in the DNA of course..and all of these are turned on and off by regulatory elements coded in the DNA.
    Heres another example of what your talking about: An alligator egg is developing. Where is the information that will determine whether its a male or female? Its not in the DNA, its the outside air temperature that will determine it. The only way you could predict boy alligator versus girl would be to know the air temp! Of course, its molecular machinery within the developing embryo, coded for by the DNA, that responds to the air temperature and directs the developing embryo to a particular fate

  193. 193
    Dionisio says:

    Polish astronomer Kopernik (allegedly a believer in God) and Italian astronomer Galileo (also allegedly a believer in God) were convinced by the strong evidences they observed, so they went against the widely and firmly established Aristotelian thinking of their times. The rest is known history.

    Can history repeat itself?

  194. 194
    kairosfocus says:

    D: The alleged can readily be set aside in both cases, especially that of the good Canon. KF

  195. 195
    AVS says:

    I never said alternative splicing was rare, Jehu.

    Joe, talking to you is exactly like trying to explain a biological principle to someone with absolutely no science background. This is exactly what happened to me today, and I thought in my head as the conversation went on “this is exactly how the conversations at UD go.” No matter what comes out of my mouth, you are going to remain in a state of confusion. You are completely clueless when it comes to science, especially biology. For this reason, I will not even attempt to try to talk about biology any further with you.

  196. 196
    AVS says:

    “Darwin was wrong and lamarck was right”
    Wow that’s a pretty bold statement there Andre. In fact it’s another statement that completely proves you have no idea what you are talking about. While I am fine with arguing that epigenetics may support lamarckian evolution, it only represents a small portion of what is going on. The majority of evolution occurs at the level of DNA initially, as “darwinism” suggests. Andre, read my post to Joe, you’re in the same boat as him. You may actually be slightly more intelligent than him, but that’s not saying much.

  197. 197
    Joe says:

    AVS- Shut up. You have proven to be a moron and a poseur. You are also a liar and misrepresent Wells. I have forgotten more about science than you will ever know- and I don’t forget.

    You are a pathetic excuse for a human.

  198. 198
    Joe says:

    RodW,

    How can we test the claim that organisms are the sum of their genome?

    Rodent’s bizarre traits deepen mystery of genetics, evolution:

    The study focuses on 60 species within the vole genus Microtus, which has evolved in the last 500,000 to 2 million years. This means voles are evolving 60-100 times faster than the average vertebrate in terms of creating different species. Within the genus (the level of taxonomic classification above species), the number of chromosomes in voles ranges from 17-64. DeWoody said that this is an unusual finding, since species within a single genus often have the same chromosome number.

    Among the vole’s other bizarre genetic traits:

    •In one species, the X chromosome, one of the two sex-determining chromosomes (the other being the Y), contains about 20 percent of the entire genome. Sex chromosomes normally contain much less genetic information.

    •In another species, females possess large portions of the Y (male) chromosome.

    •In yet another species, males and females have different chromosome numbers, which is uncommon in animals.

    A final “counterintuitive oddity” is that despite genetic variation, all voles look alike, said DeWoody’s former graduate student and study co-author Deb Triant.

    “All voles look very similar, and many species are completely indistinguishable,” DeWoody said.

    In one particular instance, DeWoody was unable to differentiate between two species even after close examination and analysis of their cranial structure; only genetic tests could reveal the difference.

    Nevertheless, voles are perfectly adept at recognizing those of their own species.

    Yup after all this “evolution” a vole is still a vole.

  199. 199
    Dionisio says:

    kairosfocus @ 194

    D: The alleged can readily be set aside in both cases, especially that of the good Canon. KF

    Yes, that’s a good point. I accept the correction. Thank you.

  200. 200
    Jehu says:

    Anyway AVS, alternative splicing is influenced by epigenetic factors and changes the ultimate protein, hence the protein is not fully specified by the DNA. Alternative splicing is not rare and occurs in over 90% of human genes. In at least one case, alternative splicing can result in over 38,000 different proteins from a single gene.

  201. 201
    AVS says:

    My issue is with the statement “protein is not fully specified by DNA.” The amino acid sequence is completely specified by the DNA, you can take the amino acid sequence, and 99% of the time it will exactly match the predicted sequence from the corresponding DNA exon. RNA editing accounts for the 1% that doesn’t. The majority of alternative splicing also functions through the recognition of the nucleotide sequence by spliceosome proteins and bound RNA. This means that the majority of splicing also functions by sequence specificity; sequences directly taken from DNA.

  202. 202
    Jehu says:

    The issue is not whether the amino acid sequence matches the corresponding exon but which exons are expressed in the ultimate protein.

  203. 203
    AVS says:

    No. It doesn’t matter which exons are expressed as far as this conversation is concerned, what matters is the sequence of the DNA and the amino acid sequence that comes from it. They will always match. Not only is Wells wrong but even more unforgivable is how vague his claim are. He words things poorly and in a way that seems to support his position. Wells’ audience is largely scientifically illiterate and lacking any knowledge in biology so I would expect him to spell every detail out. Instead he makes ambiguous claims (as Joe has already demonstrated) in order to paint a picture of “scientific support.”

  204. 204
    Joe says:

    AVS:

    My issue is with the statement “protein is not fully specified by DNA.”

    It isn’t

    amino acid sequence is completely specified by the DNA

    ‘The amino acid sequence doesn’t make the protein.

    And no, Wells did NOT make any ambiguous statements. AVS is just too stupid to be able to comprehend what Wells said.

    AVS is a moron and a liar.

  205. 205
    AVS says:

    It’s already been demonstrated that his statement was ambiguous. By you no less, Joe. Thank you for making yourself look like a complete imbecile. Take care now and have fun peddling this pseudoscience bullshit of yours.

  206. 206
    Joe says:

    AVS, you are a liar and a moron. Wells statement is not ambiguous. But thanks for showing us all you can do is accuse others of your faults.

    And the only pseudoscience bullshit is coming from your hole.

  207. 207
    bornagain77 says:

    Joe, you might appreciate this:

    New level of genetic diversity in human RNA sequences uncovered – May 2011
    Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person’s genetic material.”
    http://www.physorg.com/news/20.....ences.html

  208. 208
    Jehu says:

    AVS, you completely wrong. Wells is talking about alternative splicing, which edits mRNA with respect to exons. Alternative splicing is influenced by epigenetic factors. Hence, the DNA doesn’t specify the ultimate protein. Of course exons included in the final protein will have the anticipated amino acid sequence but other exons may not be expressed at all. Which exons will be expressed cannot be predicted from the DNA alone because … wait for it … alternative splicing is influenced by epigenetic factors.

  209. 209
    DATCG says:

    Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

    “This indicates that the complexity of the mammalian genome, especially the transcriptome, cannot be interpreted merely according to the central dogma of molecular biology “DNA-RNA-protein.”

  210. 210
    DATCG says:

    Epigenetics: The sins of the father

    In relation to new discoveries and Epigenetics…
    “‘It’s a huge black box,’ Lane says”

    Controversial…

    The subject remains controversial, in part because it harks back to the discredited theories of Jean-Baptiste Lamarck, a nineteenth-century French biologist who proposed that organisms pass down acquired traits to future generations. To many modern biologists, that’s “scary-sounding”, says Oliver Rando, a molecular biologist at the University of Massachusetts Medical School in Worcester, whose work suggests that such inheritance does indeed happen in animals3. If it is true, he says, “Why hasn’t this been obvious to all the brilliant researchers in the past hundred years of genetics?”.

  211. 211
    DATCG says:

    So-Called “Junk” DNA influence on facial form developmental process…

    Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest

    “Beyond providing a direct link between the signaling environment and the transcriptional machinery controlling NC function, the importance of identifying such ligand in the future is underscored by observations that human craniofacial development is particularly sensitive to environmental changes resulting from fetal exposure (Lammer et al., 1985).”

    Wiki…

    Neural Crest – cells are a transient, multipotent, migratory cell population unique to vertebrates that gives rise to a diverse cell lineage including melanocytes, craniofacial cartilage and bone, smooth muscle, peripheral and enteric neurons and glia.[1]

    Just the beginning of discovery in Epigenetics and the Epigenome.

  212. 212

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