Sternberg Plasters Matheson

_{Salvador Cordova

June 13, 2010

Biology, Darwinism, Science}

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“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century…The failure to recognize the full implications of this-particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules-may well go down as one of the biggest mistakes in the history of molecular biology.”

—John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American

Steve Matheson, a teacher and Darwinist promoter at a religious school, repeats the biggest mistake in molecular biology. In contrast, Richard Sternberg, an evolutionary biologist at the Biologic Institute, defends objective analysis of the facts. See Sternberg’s defense of the facts against Matheson’s Darwinist ideology in the essay: Mathesons Intron Fairytale.

Comments

Jonathan Wells weighs in: Fact Free Science of Mathesonscordova_{June 15, 2010
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HT to Bradford at TelicThoughts for this gem by several authors http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030085
During RNA splicing, sequences (introns) in a pre-mRNA are excised and discarded, and the remaining sequences (exons) are joined to form the mature RNA. Splicing is regulated not only by the binding of the basic splicing machinery to splice sites located at the exon–intron boundaries, but also by the combined effects of various other splicing factors that bind to a multitude of sequence elements located both in the exons as well as the flanking introns. Instances of alternative splicing, where usage of splice site(s) is incomplete or different between tissues, cell types, or lineages, can be created by the interaction of sequence elements and tissue, cell type, and stage-specific splicing factors. To better understand constitutive and alternative pre-mRNA splicing, the authors describe a comparative genomics approach, using available mammalian genomes, to systematically identify splicing regulatory elements located in the introns proximal to exons. A quarter of the elements were tested experimentally, and most of them altered splicing in human cells. The authors also showed that that the intronic elements are close to tissue-specific alternative exons and are more likely to be located in specific positions in the introns, suggestive of potential regulatory function. These elements are also frequently found in tissue-specific genes, suggesting a coupling between expression and alternative splicing of these genes. Finally, the authors propose a strategy using the elements to identify the binding sites of several splicing factors.
scordova_{June 15, 2010
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Mattick points out here: http://ai.stanford.edu/~serafim/CS374_2006/papers/Mattick_NRG2004.pdf
The nematode worm Caenorhabditis elegans, the cellular ontogeny of which has been precisely mapped, has 1,179 and 1,090 distinct somatic cells (including those that undergo programmed cell death) in the male and female, respectively, each with a defined history and fate. Therefore, if we take the developmental trajectories and cell position into account, C. elegans has 103 different cell identities, even if many of these cells are functionally similar. By this reasoning, although the number of different cell types in mammals is often considered to lie in the order of hundreds, it is actually in the order of 1012 if their positional identity and specific ontogeny are considered.Humans have an estimated 1014 cells, mostly positioned in precise ways and with precise organization, shape and function, in skeletal architecture,musculature and organ type,many of which (such as the nose) show inherited idiosyncrasies. Even if the actual number of cells with distinct identities is discounted by a factor of 100 (on the basis that 99% of the cells are simply clonal expansions of a particular cell type in a particular location or under particular conditions (for example, fat,muscle or immune cells)), there are still 10^12 positionally different cell types.
a fact which he uses to argue
Although it is widely believed that intronic RNA is non-functional (simply being degraded and recycled after excision by splicing), there is another equally, if not more, plausible possibility — that introns are genetically active and that intronic RNA feeds genetic information into the regulatory network of the cell11,12. ncRNAs: a parallel digital regulatory system. If the possibility is entertained that introns are functional (actively transmitting genetic information through RNA molecules), then an entirely different type of regulation becomes possible, with an entirely different set of logical extensions and interesting predictions. First, it would mean that the genetic operating system of complex eukaryotes is fundamentally different and much more sophisticated than that of simple prokaryotes. Eukaryotic genes would express two types of information in parallel — proteins and (to borrow a term from neurobiology) EFFERENCE RNA SIGNALS that can communicate with other genes or gene products independently of the biochemical function of the encoded protein in the host transcript11–13. This leads to the deeper prediction that the emergence of a true parallel processing system was, in all likelihood, fundamental to the evolution and development of complex organisms11,12.
scordova_{June 15, 2010
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Mattick's analysis: The Role of Introns and Other Noncoding RNAs in the Development of Complex Organisms
Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.
I'd take Mattick research over Matheson illogical speculations.scordova_{June 14, 2010
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I’ve asked a simple question, which I think is clear, reasonable and highly relevant. I won’t ask it again. Nor am I interested in further discussion should you decline.
I'm attempting to answer, but I'll have a better idea of how to answer your question if you can tell me whether you think the following assertion by Matheson is a correct logical inference:
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
Translation: Matheson doesn't know that an intron has function, therefore in his mind if it is not yet known to have function it doesn't have function. Is that a logical deduction? Would we go about studying human physiology and say, "we don't know if the appendix has function, therefore the appendix is useless". If we were to do science by deeming something functionless because the function was not perceived, how could we ever expect to perceive it if indeed it is there. That's willful blindness. Notice, Matheson is not saying, "we don't yet know if it has function" rather he asserts:
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
He rules out possibility of function because it is not perceived. This is bad logic.
V: So, I’m still left wondering exactly where is the blunder that makes this reasoning so stupid.
I quoted it to you several times, or do you believe the following is evidence of Matheson's deep insight. :-)
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
C'mon V, are you going to defend that statement or call it for what it is. Are you going to claim, as Matheson suggests, that because a function has not been discovered for an intron, it has no function.
For example, you might say that his reasoning was “stupid” because these introns really do have a “function.”
NO! He is making a non-sequitur! The existence of function is independent of our knowledge of its existence. His conclusion:
"that leaves at least 189,000 introns without function."
Does not follow from the premise:
"Let’s say that a hundred introns in the human genome are known to have “important functional roles.”
This is illogical. This is like saying, "I don't know what function this part has in the space shuttle, therefore this part is useless." A human is arguably more complex than a space shuttle. How presumptuous then to assert something has no function merely because function hasn't been perceived yet. Lack of perceiving function in an intron is not the same as the intron having no functon. But that is Mathesonian reasoning, and he uses the same illogic with pufferfish!scordova_{June 14, 2010
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@scordova (#39) Scordova, I've asked a simple question, which I think is clear, reasonable and highly relevant. I won't ask it again. Nor am I interested in further discussion should you decline. However, if Matheson's reasoning really is that stupid, you should have no problem pointing exactly where the problem is, right? For example, you might say that his reasoning was "stupid" because these introns really do have a "function." But, Matheson has written much about the subject on his blog. To quote from the directly linked post, which was part two of a two part series on "Junk DNA"…
[...] nor have biologists ever assumed universal non-function of non-coding DNA in the first place.
You might suggest that Matheson was ignorant about the function of introns, not only in regard to Meyer's claim but in regards to Sternberg's post as well. However, this too was addressed here and here. So, I'm still left wondering exactly where is the blunder that makes this reasoning so stupid. While I'm under no illusion that you are somehow obliged to answer the question, your lack of response suggests that you're simply offended by the term "Junk DNA", despite the fact that ID is supposedly a scientific theory in that it makes no specific claim about who the designer is.veilsofmaya_{June 14, 2010
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Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
So do you agree that there is a specific error in his reasoning? Or are you going to defend his statement:
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
The inference he makes: "we know only a few functions for introns, therefore the rest do not have functions". Consider an engineering student assigned to evaluate a piece of hardware whose documentation is now lost. What if that student said, "we don't know the function, therefore it has none". Is that sort of reasoning worthy of a student the sciences?
v: Care to respond to the responses provided?
only if you respond to my question above. Has matheson made a wrong inference here:
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
If you agree he has made an error, on a scale of stupidity, how would you rate such logic.scordova_{June 14, 2010
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you know veilsofmaya, not to interrupt your ironing out over the precise meaning of Junk with sal, but I hope you can help me with this one particular problem that a lot of ID proponents can't get past,,, You see veilsofmaya the problem is that no neo-Darwinists has ever demonstrated that material processes can generate any functional information whatsoever!!! NOT EVEN ONE TIME!!! And yet the genome of the simplest organism on earth is vastly more complex in its programming complexity that any computer program ever written by man. I hope you can see my concern. You see you are sitting here arguing that what you mean by junk don't really mean what i mean by junk and yet this junk. however you want to look at it, is vastly superior to programs written by teams of our best engineers. All I can say is,,, Man that is some kind of junk you got there no matter what you want to call it!!! So if, after you take care of that important junk definition thing, you could get around to falsifying Abel's null hypothesis for information generation I would appreciate it: notes: "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" - David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009 To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: "Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration." A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis. http://www.mdpi.com/1422-0067/10/1/247/pdf Can We Falsify Any Of The Following Null Hypothesis (For Information Generation) 1) Mathematical Logic 2) Algorithmic Optimization 3) Cybernetic Programming 4) Computational Halting 5) Integrated Circuits 6) Organization (e.g. homeostatic optimization far from equilibrium) 7) Material Symbol Systems (e.g. genetics) 8) Any Goal Oriented bona fide system 9) Language 10) Formal function of any kind 11) Utilitarian work http://mdpi.com/1422-0067/10/1/247/ag First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009 Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. "At all three levels, we found M. pneumoniae was more complex than we expected," http://www.sciencedaily.com/releases/2009/11/091126173027.htm Simplest Microbes More Complex than Thought - Dec. 2009 Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes." http://www.creationsafaris.com/crev200912.htm#20091229a Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188 The Coding Found In DNA Surpasses Man's Ability To Code - Stephen Meyer - video http://www.metacafe.com/watch/4050638 Bill Gates, in recognizing the superiority found in Genetic Coding, compared to the best computer coding we now have, has now funded research into this area: Welcome to CoSBi - (Computational and Systems Biology) Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. http://www.cosbi.eu/index.php/component/content/article/171 DNA Optimized for Photostability Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. http://www.reasons.org/dna-soaks-suns-rays etc..etc..etc...bornagain77_{June 14, 2010
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@scordova (#32) My comment was referring to your suggestion that "propenesity to label anything that doesn’t code as junk, science and understanding have been hindered." was expected and had already been addressed elsewhere. Yet you chose to make the argument anyway. You changed the subject when you wrote; You wrote:
Finding utility in junkyard parts can be argued as evidence of innovation. So the label of “junk” is only prejudicial, it hardly argues against design.
So, I should assume [A] you object to the notion of “junk-DNA” in principal, because it's prejudicial? Again, it sounds like you're offended by the term, rather that confused about the context in which Matheson used it. Let me guess, God doesn't make "junk" and you couldn't possible imagine that the entirety of DNA wasn't specifically planned by God?
By Mathesons reasoning, the fact that a car may have a part that came from a junk yard some how disqualifies the rebuilt car from being designed?
It's unclear how you reached this conclusion or how this is relevant to your suggestion that using the term "junk-DNA" in conduction with non-coding DNA as has somehow harmed science. Care to respond to the responses provided?veilsofmaya_{June 14, 2010
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scordova, This isn't much of an improvement as you've simply reproduced the original quote and essentially made the same objection. You wrote I’m objecting to his inept line of reasoning: While I'm not trying to create a false dilemma, it seems you could only reach this conclusion by pointing out a specific error in his reasoning, rather than saying it's inept. Right? You wrote:
So according to Matheson, if a function has not been discovered in an intron, it is deemed functionless by default. Stupidity times 10! I’d expect more from a sceintist examing complex systems.
Are you suggesting that his reasoning breaks down, but in a way that none of the options I presented are relevant? If so, then kindly explain why his reasoning is "Stupidly times 10!" without appealing to any of them. For example, it seems obvious that context in which the term functionless was used is highly relevant in deterring if Matheson's reasoning was inept. Wouldn't you agree? But, again, Matheson's post included clear examples of what he meant by functionless. And he did so because he expected this sort of reaction from ID supporters. Could it be that you simply didn't want to disappoint him?veilsofmaya_{June 14, 2010
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Sal, here is what Sternberg says:
So let’s do the math. Again. I will make the task easy for everyone—even Moran and Matheson: Step 1. There are ~25,000 protein-coding genes in the human genome. Step 2. There are 190,000 introns/25,000 protein-coding genes = 7.6 introns/gene on average. Step 3. Ninety percent (possibly more) of gene transcripts undergo alternative splicing. Hence, 0.9 x 25,000 = 22,500 genes (actually, their RNAs) undergo alternative splicing. Therefore, 22,500 genes x 7.6 introns/gene = 171,000 introns involved in alternative splicing.
What else can this mean but that every one of the 7.6 introns in every gene that is subject to alternative splicing are themselves alternatively spliced? I think Sternberg is quite clear about this. Clear, and completely wrong.Arthur Hunt_{June 14, 2010
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v asked: Scordova, I’m having a difficult time understanding your responses given the numerous clarifications Matheson has presented. Are you… A. Objecting to the notion of “junk-DNA” in principal? B. Suggesting that Matheson is somehow ignorant of “functions” that “junk-DNA” has? C. Suggesting a lack of imagination on Matheson part? For examle, Matheson has already addressed [A] on multiple occasions, including a suggestion that the term “Junk-DNA” is a unfortunate choice of words
I'm objecting to his inept line of reasoning: Example of Matheson Reasoning:
Let’s say that a hundred introns in the human genome are known to have “important functional roles.” Oh fine, let’s make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
So according to Matheson, if a function has not been discovered in an intron, it is deemed functionless by default. Stupidity times 10! I'd expect more from a sceintist examing complex systems.scordova_{June 14, 2010
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Are we all in agreement with Sternberg and Wells when they claim that every intron in every human gene whose RNAs are subject to alternative splicing are themselves alternatively spliced?
Art, I don't agree that is their claim, that is your characterization of what they said. We'll have to hear it from them before I agree. Salscordova_{June 14, 2010
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Matheson: And I hope it's a little clearer what I mean when I say that introns aren't known to be functional. Sternberg was wrong to assume that I would share his view of what it means for something to have "function," and he was doubly wrong to think that I would predict that introns don't sometimes – even often – contain elements that serve functional roles. Junkyards, after all, contain lots of stuff that can serve a function. (My previous attempt to illustrate this concept employed Yugos. Check it out. Todd Wood liked it too.)
Sounds more like someone embarassed to admit his error after being called on it. :-)scordova_{June 14, 2010
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v wrote:
It seems you’ve made an argument that was both predicted and addressed in Matheson’s response. See the article he referenced here.
To quote Matheson:
Matheson writes: Junkyards, after all, contain lots of stuff that can serve a function
Finding utility in junkyard parts can be argued as evidence of innovation. So the label of "junk" is only prejudicial, it hardly argues against design. By Mathesons reasoning, the fact that a car may have a part that came from a junk yard some how disqualifies the rebuilt car from being desinged? The label of "junk" is only prejudicial, and even if it were junk, it hardly refutes the design hypothesis. There is something beautiful to be said about turning what is bad into something good, or does Matheson want to argue God recreating something that was bad into something is evidence God is not as smart as Matheson? :-) NOTE: I'm not saying the DNA is junk, I'm saying, even it you labeled it as such, it doesn't refute the design hypothesis.scordova_{June 14, 2010
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veils; the c-value paradox is most assuredly NOT resolved within the materialistic framework, despite your very forgiving attitude towards the Darwinian materialistic foundation in science. This is because information is presupposed to "emerge" from a material basis; the non-correlation of genome size to the apparent complexity witnessed in life is a "surprise" since the material basis of the genome is suppose to have a fairly linear correlation to the information "emerging" from it, whereas in Intelligent Design the genome size is first presupposed to be directly dependent of functional optimality, as was amply illustrated by Sal here: "Junk DNA" is found to have purpose in an astonishing way in this following paper: 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/2009/04/shoddy_engineering_or_intellig.html#more It is clear from this study, by itself, that your presupposition of "paint cans and junk cars" is vastly to simplistic.bornagain77_{June 14, 2010
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@ bornagain77 You wrote:
Thus the finding of enormously varying genome sizes is actually a failed prediction of evolutionary theory
You're referring to the C-paradox, which was resolved via the discovery that some of an organism's genome is non-coding. That is, areas are not directly involved in coding. What remains is the C-value enigma, which reflects our lack of understanding of non-coding DNA in a number of areas… - How prevalent is non-coding DNA in other biological organisms? - Where does non-coding DNA come from and what determines it's transfer (or lack there of) over time? - What other functions might non-coding DNA have in other areas? - Why doe the amount of non-coding DNA vary greatly between organisms? However, none of these questions negate Matheson's point. To repeat, what "function" are these 127 billon bases performing in a Lungfish that are not being performed in a Human Being? We can ask the same about the 129+ billion bases not found in a Pufferfish. @uoflcard You wrote:
i.e., argument from ignorance.
But then wrote:
I’m still waiting for the evidence or model that makes it remotely reasonable to expect law and chance, devoid of intelligence, to create functional, complex, specified information, at least within the probabilistic resources of the history of the known Universe.
Should I assume you're just as open to the idea that the possible "functions" of non-coding DNA could resolve many if not all of the supposedly insurmountable problems you've just mentioned? @scordova (#24) You wrote:
Maybe the prejudicial view of pufferfish genomes is preventing exploration of the real function of the DNA.
It seems you've made an argument that was both predicted and addressed in Matheson's response. See the article he referenced here.veilsofmaya_{June 14, 2010
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@scordova (#19) Scordova, I'm having a difficult time understanding your responses given the numerous clarifications Matheson has presented. Are you… A. Objecting to the notion of "junk-DNA" in principal? B. Suggesting that Matheson is somehow ignorant of "functions" that "junk-DNA" has? C. Suggesting a lack of imagination on Matheson part? For examle, Matheson has already addressed [A] on multiple occasions, including a suggestion that the term "Junk-DNA" is a unfortunate choice of words. But even then, a few of the items in my home would qualify as "junk", despite the fact that they may perform their original purpose and their value is purely sentimental. To other people, these items are "junk." However, I in no way object or to nor am I offended by the use of the word because I understand the context in which is it's used. To quote Matheson's translation of Sternberg's post….
Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.
Given the generous number of clarifications presented, could it be that your simply find the term "junk" offensive? In regards to [B], Matheson clearly addressed this issue in his reply which I'll defer to rather than quote here. In other words, you seem to be presenting arguments which Matheson has already addressed, which again makes me think you're simply offended by the use of term, despite multiple clarifications.veilsofmaya_{June 14, 2010
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Further note on Junk DNA: Darwinists clinging to the Junk DNA paradigm is against reason and more importantly is also now shown to be against current experimental evidence: Arriving At Intelligence Through The Corridors Of Reason (Part II) - April 2010 Excerpt: In fact the term ‘junk DNA’ is now seen by many an expert as somewhat of a misnomer since much of what was originally categorized as such has turned out to be pivotal for DNA stability and the regulation of gene expression. In his book Nature’s Probability And Probability’s Nature author Donald Johnson has done us all a service by bringing these points to the fore. He further notes that since junk DNA would put an unnecessary energetic burden on cells during the process of replication, it stands to reason that it would more likely be eliminated through selective pressures. That is, if the Darwinian account of life is to be believed. “It would make sense” Johnson writes “that those useless nucleotides would be removed from the genome long before they had a chance to form something with a selective advantage….there would be no advantage in directing energy to useless structures”. https://uncommondescent.com/intelligent-design/arriving-at-intelligence-through-the-corridors-of-reason-part-ii/ These following studies back up this assertion: Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/content/vp471464014664w8/ Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - May 2010 Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2bornagain77_{June 14, 2010
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If Matheson, Hunt, Moran and company entertain any doubts that the Junk DNA mindset had anything whatsoever to do with unraveling the "second code", here is the proof that the team totally disregarded neo_Darwinian thinking: Researchers Crack 'Splicing Code,' Solve a Mystery Underlying Biological Complexity - May 2010 Excerpt: Frey and Blencowe attribute the success of their project to the close collaboration between their team of talented computational and experimental biologists. "Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," Frey said. http://www.sciencedaily.com/releases/2010/05/100505133252.htmbornagain77_{June 14, 2010
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Off-topic, This researcher puts technological innovations into nested hierarchies. http://www.iir.hit-u.ac.jp/iir-w3/file/OLDfunk_HP%20nested.pdfCollin_{June 14, 2010
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Here is Dr. Sternberg on ERV's Refutation Of Endogenous Retrovirus - Richard Sternberg PhD. - video http://www.metacafe.com/watch/4094119/refutation_of_endogenous_retrovirus_richard_sternberg_phd/ further notes: No Such Thing As 'Junk RNA,' Say Researchers - Oct. 2009 Excerpt: Tiny strands of RNA previously dismissed as cellular junk are actually very stable molecules that may play significant roles in cellular processes, http://www.sciencedaily.com/releases/2009/10/091013105809.htm Excerpt Of Conclusion: When examined in detail, the full pseudogene dataset we collected does not lend itself to a reasonable neo-Darwinian interpretation. http://creation.com/images/pdfs/tj/j21_3/j21_3_118-127.pdf Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said, speaking of the gene regulation was a straightforward, linear process of gene coding for regulator protein that controls transcription. “Biology’s new glimpse at a universe of non-coding DNA – what used to be called ‘junk’ DNA – has been fascinating and befuddling.” If it’s junk, why would the human body decode 74% to 93& of it? The plethora of small RNAs produced by these non-coding regions, and how they interact with each other and with DNA, was completely unexpected when the project began.,,, http://www.creationsafaris.com/crev201004.htm#20100405a All Proposed Elements Of Junk DNA have been Found To Have High Level Function - assorted studies http://docs.google.com/View?id=dc8z67wz_25gqm4zzfdbornagain77_{June 14, 2010
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Just because DNA doesn't code for something, are we justified in presuming it's junk? INTEL chips on computers large amounts of casing that have no apparent computational use. In fact the casing looks excessively large. It seems to provide no structural benefit. They don't provide any memory or information (coding if you will). Do we deem it useless "junk" since it doesn't code for anything? NO. If functions as a heat sink and radiator, and prevents the chip melting! But junk advocate Darwinsits like Matheson resort to about the same level of twisted reasoning regarding DNA. Just because DNA doesn't code for something, they presume it's junk! That would be about as stupid as saying because the heat sink in a computer chip doesn't provide any computation, it is junk. I provided examples where DNA is used for other purposes than coding. The repetitive nature of the DNA in certain cases is essential for functioning, but because of the propenesity to label anything that doesn't code as junk, science and understanding have been hindered. Maybe the prejudicial view of pufferfish genomes is preventing exploration of the real function of the DNA.scordova_{June 14, 2010
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Matheson:
Consider the green pufferfish. It’s a pretty interesting creature: it puffs itself up to intimidate predators. More ominously, it sports a fearsome venom called tetrodotoxin that is much beloved of neuroscientists for its ability to block sodium channels (and thus nerve conduction). And consider the marbled lungfish. It has some notably peculiar traits, most obviously the ability to breathe air. Just a couple of fish. The genome of the green pufferfish contains about 340 million bases. That’s a lot of bases, but the pufferfish genome is about a tenth the size of the human genome. The genome of the marbled lungfish contains about 130 billion bases. That’s about 40 times the size of the human genome. That means that the lungfish genome is almost 400 times the size of the pufferfish genome. If you don’t see why this is a huge problem for anyone who objects to the notion of non-functional DNA (and lots of it), then you should really lay off the Kool-Aid.
i.e., argument from ignorance. I understand the apparent problem, but I also know that this same statement could have a couple of the facts replaced and it would be identical to a typical statement a couple decades ago, which are now becoming more and more fallacious with each molecular biology discovery, it seems. With what it seems that we don't know about regulation and expression on the molecular level in biology, the less convincing this argument is to me. I'm still waiting for the evidence or model that makes it remotely reasonable to expect law and chance, devoid of intelligence, to create functional, complex, specified information, at least within the probabilistic resources of the history of the known Universe. Until then, functional "junk" DNA, marvelous engineering wonders in biology that trump anything humans have created, consciousness, etc. are simply circumstantial evidence, comparatively. It seems that if one is determined to believe in naturalism, they could dream up stories that could possibly fill those voids, but there is no cheating statistics.uoflcard_{June 14, 2010
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Sal, I really like those references: Let's not forget the paper that Dr. Sternberg referenced: Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data Excerpt: “Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues,” Frey and his co-authors wrote. “The method assembles a code that can predict how a transcript will be spliced in different tissues.” http://www.genomeweb.com/informatics/canadian-team-develops-alternative-splicing-code-mouse-tissue-data Thus the fairly stunning success at which they were able to predict alternative splicing in different tissues was directly dependent of presupposing the intron sequences to be functional. Whereas Matheson would not have even have been "in the ballpark" for trying to figure out the alternative splicing code since he so drastically presupposes non-functionality for intron sequences.bornagain77_{June 14, 2010
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Example 2, "junk" DNA used as qudruplex "organelles": Guy Walks Into a Bar and Thinks He's a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity
At this break, three things happen. The bartender receives my nod that I want another drink and then, after he places it before me, I inquire as to whether he can play anything by Ethel Ennis — I now want to listen to something languorous, music that will soothe the feeling of ennui that has come over me. Next, or simultaneously, my sparring partner makes one of two moves. Either he places his book into his hand-woven Inca-nesque bag and leaves without so much as a farewell, or he decides to tarry a bit longer and says, “You have no answer for ITSs, do you?” ITSs…interstitial telomeric sequences…the chromosome scars, the pieces of junk DNA he was lecturing me about earlier. As you know, telomeres are the ends of chromosomes. In many species, including chimps and humans, the DNA sequences that are found at these genomic tips are tandem repetitions of TTAGGG. That’s right…TTAGGGTTAGGGTTAGGG…over and over and over again. A notable exception to this rule is the fruit fly, an organism that in this regard has provided the junk DNA notion no succor, since its telomeres have complex combinations of three different retrotransposons instead of those six-basepair units. What is important to note, though, is that telomeric sequences are essential to the cell, and it seems that hardly a week does not pass without some new role being discovered for these elements. How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique “suborganelle” — for the lack of better term — at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations. I try to outline all the functions of telomeric repeats, but my friend tells me that I am getting off the subject. He wants to me to focus on the ITSs, the tracks of the hexamer TTAGGG that reside within chromosome arms or around the centromere, not at the ends. I tell him that I was just coming to that topic. The story, you see, is that in the lineage leading up (or down, I forget which) to chimps and humans, a fusion of chromosome ends occurred — two telomeres became stuck together, the DNA was stitched together, and now we find the remnants of this event on the inside of chromosomes. And to be fair, I concede at this point that the 2q13 ITS site shared by chimps and humans can be considered a synapomorphy, a five-dollar cladistic term meaning a genetic marker that the two species share. As this is said, it is apparent that the countenance of my acquaintance lightens a bit only to darken a second later. For I follow up by saying that of all the known ITSs, and there are many in the genomes of chimps and humans, as well as mice and rats and cows…, the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates (Farré M, Ponsà M, Bosch M. 2009. "Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates," Cytogenetic and Genome Research 124(2): 128-131.). In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed. Exasperated with my stubbornness, the caffeine from innumerable herbal teas having only enhanced his tension, he rises from the bar and asks: “How, then, do you account for such ITSs in the first place…everyone knows they are out-of-place junk.” I tell him that I do have an answer but that first I must be excused for a moment. While making my way back to the bar, I mentally rehearse so as to be as succinct as possible. My rejoinders are, simply, that ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered — literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots. And just as I begin to reflect on where the references are in my bag that supports those points I notice…he is gone.
scordova_{June 14, 2010
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If you don’t see why this is a huge problem for anyone who objects to the notion of non-functional DNA (and lots of it), then you should really lay off the Kool-Aid.
THe problem is that just because Matheson can't perceive the function he presumes there is no function. Utter stupidity! DNA is not only for coding! Just because it is not obviously utilized for coding does not mean it has no use. The use may yet be discovered. Examples 1: non-coding DNA for lenses Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye
We often hear from Darwinians that the biological world is replete with examples of shoddy engineering, or, as they prefer to put it, bad design. One such case of really poor construction is the inverted retina of the vertebrate eye. As we all know, the retina of our eyes is configured all wrong because the cells that gather photons, the rod photoreceptors, are behind two other tissue layers. Light first strikes the ganglion cells and then passes by or through the bipolar cells before reaching the rod photoreceptors. Surely, a child could have arranged the system better — so they tell us. The problem with this story of supposed unintelligent design is that it is long on anthropomorphisms and short on evidence. Consider nocturnal mammals. Night vision for, say, a mouse is no small feat. Light intensities during night can be a million times less than those of the day, so the rod cells must be optimized — yes, optimized — to capture even the few stray photons that strike them. Given the backwards organization of the mouse’s retina, how is this scavenging of light accomplished? Part of the solution is that the ganglion and bipolar cell layers are thinner in mammals that are nocturnal. But other optimizations must also occur. Enter the cell nucleus and “junk” DNA. Only around 1.5 percent of mammalian DNA encodes proteins. Since it has become lore to equate protein-coding regions of the genome with “genes” and “information,” the remaining approximately 98.5 percent of DNA has been dismissed as junk. Yet, for what is purported to be mere genetic gibberish, it is strikingly ordered along the length of the chromosome. Like the barcodes on consumer items that we are all familiar with, each chromosome has a particular banding pattern. This pattern reflects how different types of DNA sequences are linearly distributed. The “core” of a mammalian chromosome, the centromere, and the genomic segments that frame it largely consist of long tracks of species-specific repetitive elements — these areas give rise to “C-bands” after a chemical stain has been applied. Then, alternating along the chromosome arms are two other kinds of bands that appear after different staining procedures. One called “R-bands” is rich in protein-coding genes and a particular class of retrotransposon called SINEs (for Short Interspersed Nuclear Elements). SINE sequence families are restricted to certain taxonomic groups. The other is termed “G-bands” and it has a high concentration of another class of retrotransposon called LINEs (for Long Interspersed Nuclear Elements), that can also be used to distinguish between species. Finally, the ends of the chromosome, telomeres, are comprised of a completely different set of repetitive DNA sequences. In general, C-bands and G-bands are complexed with proteins and RNAs to give a more compact organization called heterochromatin, whereas R-bands have a more open conformation referred to as euchromatin. Why bother with such details? Well, each of these chromosome bands has a preferred location in the cell nucleus. Open any good textbook on mammalian anatomy and you will note that cell types can often be distinguished by the shape and size of the nucleus, as well as the positions of euchromatin and heterochromatin in that organelle. Nevertheless, most cell nuclei follow a general rule where euchromatin is located in the interior, in various compartments that are dense with transcription factories, RNA processing machinery, and many other components. Heterochromatin, on the other hand, is found mainly around the periphery of the nucleus. A striking exception to this principle is found in the nuclei of rod cells in nocturnal mammals. Reporting in the journal Cell, Irina Solovei and coworkers have just discovered that, in contrast to the nucleus organization seen in ganglion and bipolar cells of the retina, a remarkable inversion of chromosome band localities occurs in the rod photoreceptors of mammals with night vision (Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. "Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution." Cell 137(2): 356-368). First, the C-bands of all the chromosomes including the centromere coalesce in the center of the nucleus to produce a dense chromocenter. Keep in mind that the DNA backbone of this chromocenter in different mammals is repetitive and highly species-specific. Second, a shell of LINE-rich G-band sequences surrounds the C-bands. Finally, the R-bands including all examined protein-coding genes are placed next to the nuclear envelope. The nucleus of this cell type is also smaller so as to make the pattern more compact. This ordered movement of billions of basepairs according to their “barcode status” begins in the rod photoreceptor cells at birth, at least in the mouse, and continues for weeks and months. Why the elaborate repositioning of so much “junk” DNA in the rod cells of nocturnal mammals? The answer is optics. A central cluster of chromocenters surrounded by a layer of LINE-dense heterochromatin enables the nucleus to be a converging lens for photons, so that the latter can pass without hindrance to the rod outer segments that sense light. In other words, the genome regions with the highest refractive index — undoubtedly enhanced by the proteins bound to the repetitive DNA — are concentrated in the interior, followed by the sequences with the next highest level of refractivity, to prevent against the scattering of light. The 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 — that the data only point to the lack of design and suboptimality — remind them of the rod cell nuclei of the humble mouse.
scordova_{June 14, 2010
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veils @ 16, lets get into the whole c-value enigma a little bit here: C-value enigma Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical; http://en.wikipedia.org/wiki/C-value_enigma Thus the finding of enormously varying genome sizes is actually a failed prediction of evolutionary theory since the materialistic presuppositions, under-girding neo-Darwinism, predicted there to be a correlation between genome sizes and macroscopic complexity of the species. That neo-Darwinists would try to twist this failed prediction of materialism around to argue that it supports the ludicrous claim of Junk DNA, despite the finding of large scale functionality in so called "junk" regions, is another prime example of a theory that is completely divorced from any empirical falsification whatsoever.bornagain77_{June 14, 2010
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well veils it seems Matheson's whole argument, once you get past the "poor Richard" platitudes of condescension against anything related to ID, rest on the assumption that neo-Drawinists never really meant that "Junk DNA" in fact junk. Well contrary to Matheson's disbelief and your support of that disbelief: Junk DNA Predictions By Evolutionists Selfish DNA: the ultimate parasite. Orgel LE, Crick FH. The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype. http://www.ncbi.nlm.nih.gov/pubmed/7366731 Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional. The slow, painful death of junk DNA: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work....Junk DNA is a necessary mathematical extrapolation...Without Junk DNA, evolution runs into insurmountable mathematical difficulties. http://creation.com/junk-dna-slow-death Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, "they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?" In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are "largely genetic 'junk'": Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk” Soon thereafter, the 1995 edition of Voet & Voet's Biochemistry textbook explained that "a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome..." Will Darwinists try to Rewrite the History of Junk-DNA? In 1996, leading origin of life theorist Christian de Duve wrote: "The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA." (Richard Dawkins makes similar pronouncements that DNA is junk in an article after 1998) http://www.evolutionnews.org/2007/06/will_darwinists_try_to_pull_a.html Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that: "The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it." The Unseen Genome, Gems Among the Junk: “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003) http://www.evolutionnews.org/bornagain77_{June 14, 2010
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@gpuccio (#7) From Matheson's reply.
Consider the green pufferfish. It's a pretty interesting creature: it puffs itself up to intimidate predators. More ominously, it sports a fearsome venom called tetrodotoxin that is much beloved of neuroscientists for its ability to block sodium channels (and thus nerve conduction). And consider the marbled lungfish. It has some notably peculiar traits, most obviously the ability to breathe air. Just a couple of fish. The genome of the green pufferfish contains about 340 million bases. That's a lot of bases, but the pufferfish genome is about a tenth the size of the human genome. The genome of the marbled lungfish contains about 130 billion bases. That's about 40 times the size of the human genome. That means that the lungfish genome is almost 400 times the size of the pufferfish genome. If you don't see why this is a huge problem for anyone who objects to the notion of non-functional DNA (and lots of it), then you should really lay off the Kool-Aid.
veilsofmaya_{June 14, 2010
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