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

_{Denyse O'Leary

March 31, 2014

Genetics, Intelligent Design}

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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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Comments

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.AVS_{March 31, 2014
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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.Upright BiPed_{March 31, 2014
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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/pmc/articles/PMC3472225/
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.com/2010/08/gene-myth-part-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
bornagain77_{March 31, 2014
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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 . . . "Jul3s_{March 31, 2014
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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/2011/04/understanding_ontogenetic_dept_1045581.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=rLl6wrqd1e0&list=SPHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&index=8 Darwin's Doubt narrated by Dr. Paul Giem - The Origin of Body Plans - video http://www.youtube.com/watch?list=PLHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&v=rLl6wrqd1e0&feature=player_detailpage#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/2013/12/a_listeners_gui079811.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.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.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
bornagain77_{March 31, 2014
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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.Joe_{March 31, 2014
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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.AVS_{March 31, 2014
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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?Dionisio_{March 31, 2014
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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?Joe_{March 31, 2014
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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, DionisioAVS_{March 31, 2014
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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 againJoe_{March 31, 2014
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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.Dionisio_{March 31, 2014
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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.AVS_{March 31, 2014
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From 12 years ago- Unraveling the DNA MythJoe_{March 31, 2014
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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.AVS_{March 31, 2014
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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!?Joe_{March 31, 2014
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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 ;-)Dionisio_{March 31, 2014
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AVS- Alternative gene splicing requires knowledge- what to edit out and what to splice back together. Just how does blind watchmaker evolution explain that?Joe_{March 31, 2014
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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.Dionisio_{March 31, 2014
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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.AVS_{March 31, 2014
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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.Dionisio_{March 31, 2014
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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.Dionisio_{March 31, 2014
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See above, Cant. Is that specific enough for you? Enough content for you upright?AVS_{March 31, 2014
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Wow, what BS this is.
Could you be just a tad more specific?cantor_{March 31, 2014
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Obviously, mooseknuckle, this guy has been talking in circles so much that he doesn't know which end is up anymore.AVS_{March 31, 2014
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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?Moose Dr_{March 31, 2014
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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.AVS_{March 31, 2014
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C'mon, AVS is a 14 year old. He still has water behind his ears. Don't be too hard on him.CentralScrutinizer_{March 31, 2014
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And another devastating "refutation" by AVS. How can ID withstand such from an anonymous ass?Joe_{March 31, 2014
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Perhaps its time for a content-free attack.Upright BiPed_{March 31, 2014
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