Junk DNA: The original ‘onion test’ is a biological non-sequitur

_{Denyse O'Leary

October 10, 2011

'Junk DNA', Darwinism}

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Probably in response to Nick Matzke here and here, proposing among other things an onion test. A friend of UD News writes to say,

Those who employ “the onion test” should recall that the test — as originally formulated by geneticist T. Ryan Gregory — asks for a “universal function” for non-coding DNA. Is this a biologically reasonable question to ask? No. As Jonathan Wells writes, in The Myth of Junk DNA (pp. 85-86):

The “onion test,” according to Gregory, “is a simply reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?” [1]

Gregory directs his challenge to “anyone who thinks they have come up with a universal function for non-coding DNA.” Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is “a universal function” that applies both to mammals and to onions. Based on the evidence, scientists have proposed that non-protein-coding intronic DNA helps to regulate alternative splicing in brain cells, and that non-protein-coding repetitive DNA plays a role in placental development. Why should those scientists justify their proposals by referring to onions, which have neither brains nor placentas?

See also: Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”

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Comments

You know Nick your link on point 3 doesn't work, which is just as well since I am fairly certain that it is a sequence comparison instead of an actual demonstration of the almighty power of evolution, further down Your light dark colored moth example of preexisting information variation within kind is a friggin joke as to demonstrating the power of darwinism to create anything new. But hey Nick, I try to be a fair guy, so let's see if i can help you see what an actual SCIENTIFIC demonstration of Darwinian evolution might actually look like: The search for the 'Edge of Evolution'; What can neo-Darwinism really do???
Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species… (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) http://www.evolutionnews.org/2010/12/peer-reviewed_research_paper_o042191.html
Four decades worth of lab work is surveyed here:
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Michael Behe talks about the preceding paper in this following podcast:
Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00
How about the oft cited example for neo-Darwinism of antibiotic resistance?
List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding. http://www.trueorigin.org/bacteria01.asp
That doesn't seem to be helping! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action???
Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010 Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
Shoot that doesn't seem to be helping either! Perhaps we just got to give the almighty power of neo-Darwinism ‘room to breathe’? How about we ‘open the floodgates’ to the almighty power of Darwinian Evolution and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???
Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html
Now that just can’t be right!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!?! Hey I know what we can do! How about we see what happened when the ‘top five’ mutations from Lenski’s experiment were combined??? Surely now the Darwinian magic will start flowing!!!
Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations) Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually. http://www2.cnrs.fr/en/1867.htm?theme1=7
Now something is going terribly wrong here!!! Tell you what, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramped in the lab you know, and now let’s REALLY open the floodgates and let’s see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal??? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots, who believe in Intelligent Design, cower in terror!!!
A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.” http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge020071.html
Now, there is something terribly wrong here! After looking high and low and everywhere in between, we can’t seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can’t even find ANY power of neo-Darwinism whatsoever!!! It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!!!bornagain77_{October 11, 2011
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As to this lie, ahem, I mean comment of yours:
The very fact that protein sequences fit into a neat phylogenetic tree, with every amount of percentage difference between sequences, from 0 to 90%+, is evidence of this, and not just dismissible as “its only evidence of common ancestry”. * * (Note: and, to head off the usual ID bafflegab on tree congruence, observed congruence between different genes and proteins is always or almost always statistically very strong congruence. This is a universal problem with creationist/IDist arguments about congruence and incongruence in phylogenetic trees: the IDists have no concept of the fact, well-known in phylogenetics, that congruence and incongruence are quantatively measurable, and even the “incongruence” that biologists themselves often highlight is quite minor disagreement in a very tiny region of Possible Tree Space.
Yet contrary to your deceptive claim of 'quite minor disagreement in a very tiny region of Possible Tree Space'. The truth is;
Accidental origins: Where species come from - March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation - but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak." http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 Congruence Between Molecular and Morphological Phylogenies - Colin Patterson Excerpt: "As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology." http://www.arn.org/docs/odesign/od171/sampler171.htm Bones, molecules...or both? Excerpt: Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology. Can the two ever be reconciled?,,, When biologists talk of the 'evolution wars', they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging (between Darwinists) within systematics. http://www.nature.com/nature/journal/v406/n6793/full/406230a0.html The universal ancestor - Carl Woese Excerpt: No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. http://www.pnas.org/content/95/12/6854.full Evolution: Charles Darwin was wrong about the tree of life - 2009 Excerpt: "We have no evidence at all that the tree of life is a reality," Eric Bapteste, an evolutionary biologist http://www.guardian.co.uk/science/2009/jan/21/charles-darwin-evolution-species-tree-life Uprooting The Tree Of Life - W. Ford Doolittle Excerpt: as DNA sequences of complete genomes have become increasingly available, my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs. http://people.ibest.uidaho.edu/~bree/courses/2_Doolittle_2000.pdf Do orthologous gene phylogenies really support tree-thinking? Excerpt: We conclude that we simply cannot determine if a large portion of the genes have a common history.,,, CONCLUSION: Our phylogenetic analyses do not support tree-thinking. http://www.ncbi.nlm.nih.gov/pubmed/15913459 The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination, says Graham Lawton http://www.thedivineconspiracy.org/Z5221S.pdf Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html
bornagain77_{October 11, 2011
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Well Nick, as to:
There probably isn’t a single new protein fold between chimps and humans, for instance — based on what we know, all of mammalia or even vertebrates could have evolved without any new protein folds
And yet we find, at least, 1000 ORFan genes in humans alone that are not found in any other species. Completely unique ORFan genes that were thrown out of the human gene count, in one study, simply because the neo-Darwinists doing the study could not find the ORFan genes in any other species: This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 'ORFan' genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!
Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm
The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true. If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:
A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-5/#comment-358868
In fact it turns out that the authors of the 'kick the ORFans out in the street' paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
Comment by gpuccio on their analysis https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-4/#comment-358547
Moreover the 'anomaly' of unique ORFan genes is found in every new genome sequenced:
Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
As well, completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract
I would like to reiterate that Darwinian evolutionists cannot account for the origination of even one unique gene or protein, much less the over one thousand completely unique ORFan genes found deeply imbedded within the 20,000 genes of the human genome:
Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences." http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/
bornagain77_{October 11, 2011
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Nick, I'm seeing a lot of personal attacks and attempts at character assassination on ID proponents. Can you please cite any papers in support of your claims, especially pertaining to the claim that the Darwinian mechanism can produce copious amounts of complex, specified information? Thanks.bbigej_{October 11, 2011
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Nick, If you had explained it in previous threads we wouldn't be talking about it again.
I (well, the sources I cited) explained the origin of the snap trap *from* a glue trap with quantitative changes like changes in levels of mucilage secretion.
No. They. Did. Not. If the explanation is series of genetic changes which were selected, then it must actually include a pathway of specific genetic changes and describe how or why they were selected. At best you offer a handful of genetic differences and hope that we'll give you credit for pointing out the obvious - that two different plants are bound to have identifiable genetic differences. You insist that such processes effect the change, but then you are unable to explain the changes in the very terms of those processes. You revert to more vague descriptions of phenotypic change. I'm actually paying attention, so you can't fake it by telling me that you already told me. This is at the foundation of the theory, and you are plainly hiding from it.ScottAndrews_{October 11, 2011
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Really Nick??? REALLY??? Does this include ‘confirmation’ for THE PRIMARY, and most important, claim of neo-Darwinism that purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present???
We've had, like, a million threads on the origin of new genes. They typically go like this: someone says "evolution can't explain how 'purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present'! I explain how gene duplication + mutation + selection can generate new genes with new functions, which is new information on any reasonable definition of "information". I also give lots of references. Pretty soon the IDists beat a hasty retreat to the origin of life and forget that their original claim was that evolution couldn't produce ANY new information. Re: Luskin -- his argument is so poor he couldn't even convince a longtime Telic Thoughts blogger. See guts's reply, and my reply, here, since Luskin bravely closed the DI thread: http://telicthoughts.com/casey-luskin-vs-kimura/ My reply to Luskin, which I'll quote here http://telicthoughts.com/casey-luskin-vs-kimura/#comment-277428
nickmatzke Says: September 29th, 2011 at 2:16 am Hmm, Luskin wrote a big reply and then closed comments, which sadly I noticed only after composing a reply. I'll post it here. Casey — very briefly as I am in London and will not spend too much time on this - 1. One of the points of Meyer's book was that his argument was different than Behe's and Dembski's, and added something to them. He says this several times, that he's not just rehashing their arguments. But, when you are defending the book, you retreat to IC-like arguments. So what was the point of the book and all of the subsequent rhetoric? We might as well have just ignored Meyer's book and should have just kept arguing about whether the IC argument works, since the "information" argument can't stand on its own without IC supporting it. As it stands, while playing defense you've walked Meyer's argument all the way back to "evolution can't produce new protein folds", which is dramatically less bold than claiming that evolution can't produce new genes and new information (which was what the main message of Meyer's book and all the propaganda surrounding it was — go back and read the promotional materials and the original taunts from the ID side, before you guys started playing defense and claiming that the book wasn't about intelligence being required to produce information). There probably isn't a single new protein fold between chimps and humans, for instance — based on what we know, all of mammalia or even vertebrates could have evolved without any new protein folds 2. Similarly, you keep going back to calculations based on the ASSUMPTION that IF it takes some moderately large number of mutations before some selectable function is achieved, THEN the expected waiting time for such events to occur is way to long occur in the history of the earth. But this is an unproven and unlikely "if". I'm sure you disagree, but that's the point — all of the probability calculations are just a smokescreen, because the key factor determining whether or not the ID critique of evolution has any merit is whether or not the ASSUMPTION that multiple mutations are required to produce anything interesting is correct. Assessing this requires not more smokescreen calculations, but a fair assessment of whether or not it really in fact looks like multiple independent changes would ever be required to produce the kinds of changes that have occurred in biological history. My experience is that (a) this question is usually ignored by you guys, who just brazenly assume it is so and then proceed to snow your audience with calculations, and (b) whenever some case is investigated in detail, the features (sequences, proteins, whatever) that are supposed to be "required for function" are typically (1) not all universally required and/or (2) are known to be present, often widespread, in systems without the function. This has happened with the flagellum, the immune system, the wing, the malaria pfcrt resistance gene, etc. etc. Plus, over here in real biology, we know of lots of generic, basic facts that indicate that gradual, step-by-step paths through sequence space are a reasonable thing to believe in. The fact that a protein can have the same structure & function with essentially no sequence similarity is one piece of evidence. The very fact that protein sequences fit into a neat phylogenetic tree, with every amount of percentage difference between sequences, from 0 to 90%+, is evidence of this, and not just dismissible as "its only evidence of common ancestry". * * (Note: and, to head off the usual ID bafflegab on tree congruence, observed congruence between different genes and proteins is always or almost always statistically very strong congruence. This is a universal problem with creationist/IDist arguments about congruence and incongruence in phylogenetic trees: the IDists have no concept of the fact, well-known in phylogenetics, that congruence and incongruence are quantatively measurable, and even the "incongruence" that biologists themselves often highlight is quite minor disagreement in a very tiny region of Possible Tree Space. Another piece of evidence is that you can do histograms of the distance between homologous genes and get a nice bell curve, exactly what you expect if the differences between sequence pairs are due to gradual divergence through many independent point mutation events: http://www.talkorigins.org/faq... 3. Re: Sdic – I linked to a detailed graphic from a paper, I guess you missed that, here it is again: http://pandasthumb.org/archive... Please give us the equivalently detailed ID explanation of Sdic — doesn't matter if it's just a hypothesis, what would a "detailed ID explanation" of Sdic even look like? They become absurd as soon as you start proposing them in concrete fashion. 4. Origin of the Sdic promotoer. This gets us back to point #2 — IDists/creationists have this instinctual feeling that various sequence features that they see must be "highly specific" and "hard to evolve" — but that's all it is, subjective gut instinct, usually put forward camouflaged with irrelevant calculations and with a complete lack of the kind of responsible review of the literature you would have to do to even begin to make such claims. Over in actual biology, what is known is that promoter sequences are typically short, they occur throughout genomes and many of them aren't even being used, and they occur at random at high frequency even in randomly-generated sequence. ID/creationist instinctual feelings about scientific matters do no a rigorous argument make. 5. Re: detecting selection. You aren't getting what a selective sweep is. It's not the fact that everyone has the same allele — that applies to most of the human genome, for instance. It's the amount of polymorphism when you compare two or more homologous chromosomes. A gene under selection will sweep through the population, but adjacent sequence will be dragged along with it. At the end of the sweep, the whole region around the selected gene will have very low diversity across the population. The shape of the curve depends on the rate of crossing over and the strength of selection. Diversity gradually returns over time, depending on the mutation rate. It's not like this stuff is obscure, there are armies of population geneticists that work on just this stuff. The quote you keep using/abusing about the problems with computational detection of selection is about a rather different thing — trawling through entire genomes with a computer in an attempt to pick out evidence of selective sweeps, biases in nonsynonymous substitutions, etc. Because such projects are running millions of statistical tests, and there is random noise in any stochastic process such as mutation, crossing over, etc., and effects like population expansion and contraction can influence all this, it is trickier to be confident that every positive result picked up in one of these fishing expeditions is a real case of selection. Probably a lot of it is, but one has to estimate the rate of false positives etc. It's rather different when, a priori, you have a reason to think that a specific spot in the genome is of interest and may have been effected by selection — for instance, when an obvious new gene is found that is the fusion of two adjacent genes, as in Sdic, which is found in one species but not close relatives. In that context, seeing a classic signature of a selective sweep is highly suggestive. This isn't even abstract-theory-which-creationists-can-deny-because- theory-is-hard-and-they'd -rather-not think-about it. When they looked at the peppered moth genome and found the allele that causes dark bodies, guess what they found in the surrounding region of the chromosome? That's right, significant diversity dip, classic evidence of recent selective sweep. Bam. Even at Telic Thoughts they were surprised at your missing the boat on this point, Casey: http://telicthoughts.com/casey... It leads to the interesting question — if an ID commentator is unfamiliar with basic introductory material in a scientific field, yet nevertheless is engaged in announcing to the world that the entire field is bunk, why should scientists take ID seriously? There is other stuff that could be said but I'd rather go to Kew Gardens. Cheers, Nick Comment by nickmatzke — September 29, 2011 @ 2:16 am
NickMatzke_UD_{October 11, 2011
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Nick, I thought we were talking about the evolution of a snap-trap from a glue trap. Why are you retreating to a variation in mucilage? It is both possible and likely. It’s also possible and likely that a variation might result in a rodent having longer forelimbs. That does not explain bats. When pressed to explain your extrapolation you retreat defensively to a safer position. That’s fine. If you want to say that evolution can increase or decrease the amount of mucilage on a leaf, so be it. We can leave it there and now we both agree on what type of changes evolution can produce.
Hmm, I guess you didn't read my previous posts on the other threads after all. If you agree that evolution can do things like change mucilage secretion levels, then the argument about the origin of the snap trap is over, because I (well, the sources I cited) explained the origin of the snap trap *from* a glue trap with quantitative changes like changes in levels of mucilage secretion. Pretty please, go back and read that stuff, we had several threads on it, I can't sit around typing out the origin of the Venus Flytrap over and over and over again.NickMatzke_UD_{October 11, 2011
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Nick Matzke:
Saying that epigenetics determines genome size is a contradiction in terms — epigenetics is what happens on top of the genome, e.g. methylation. If the genome size changes, that’s genetics, straight-up.
If the genome size changes due to factors beyond itself and the organism it occupies, then that's epigenetics, straight-up. Or, as Dr Spetner put it in "Not By Chance"- "built-in responses to environmental cues".Joseph_{October 11, 2011
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Nick, I thought we were talking about the evolution of a snap-trap from a glue trap. Why are you retreating to a variation in mucilage? It is both possible and likely. It's also possible and likely that a variation might result in a rodent having longer forelimbs. That does not explain bats. When pressed to explain your extrapolation you retreat defensively to a safer position. That's fine. If you want to say that evolution can increase or decrease the amount of mucilage on a leaf, so be it. We can leave it there and now we both agree on what type of changes evolution can produce.ScottAndrews_{October 11, 2011
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Nick matzke:
So, you really think that it’s unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf?
Nice equivocation, Nick. It's as if you really believe your ignoirance is some sort of refutation. ID is not anti-evolution, Nick, so when you say:
So, you really think that it’s unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf?
What "evolution" are you talking about? Are you talking about: A) Front-loaded evolution B) Intelligent Design evolution C) Blind Watchmaker evolution
Why should anyone believe this is unlikely? It’s a simple change in degree, and typically such changes are just a matter of upregulating or downregulating a pathway, which is just a matter of altering the binding strength of a promoter or some such.
Then you should have no problem going into a lab and conducting experiments to demonstrate your claim. In the absence of that you don't have any science.Joseph_{October 11, 2011
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As well Nick, it might interest you to know, (Actually it will probably be severely 'inconvenient' for you to know, since you fight so hard against the truth), that proof for non-locality, (beyond space and time causation), of 'material' reality was recently extended past the 'spooky action at a distance' effects of quantum entanglement (A. Aspect), to the 'material' particles themselves! i.e. Now, a transcendent 'non-local' (beyond space and time) cause must be supplied to explain the existence of 'material' particles in this universe in the first place:
'Quantum Magic' Without Any 'Spooky Action at a Distance' - June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically.,,, Asher Peres, a pioneer of quantum information theory, once remarked jokingly in a letter to a colleague (Dagmar Bruß): Entanglement is a trick 'quantum magicians' use to produce phenomena that cannot be imitated by 'classical magicians'. When two particles are entangled, measurements performed on one of them immediately affect the other, no matter how far apart the particles are. What if, in an experiment, one considers a system that does not allow for entanglement? Will the quantum magicians still have an advantage over the classical magicians? Quantum physics beyond magic This is the question the team of quantum physicists led by Anton Zeilinger from the Faculty of Physics at the University of Vienna and from the IQOQI of the Austrian Academy of Sciences addressed in their experiment. The physicists used a "qutrit" -- a quantum system consisting of a single photon that can assume three distinguishable states. "We were able to demonstrate experimentally that quantum mechanical measurements cannot be interpreted in a classical way even when no entanglement is involved," Radek Lapkiewicz explains. The findings relate to the theoretical predictions by John Stewart Bell, Simon B. Kochen, and Ernst Specker. Quantum world versus everyday life Quantum physics is in stark contrast with what we perceive and experience in our everyday lives and what we understand as "classical physics." http://www.sciencedaily.com/releases/2011/06/110624111942.htm Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: "In the beginning was the Word." Professor Anton Zeilinger - a leading expert in quantum teleportation and quantum information: http://www.metanexus.net/Magazine/ArticleDetail/tabid/68/id/8638/Default.aspx
Further notes: The following describes how quantum entanglement is related to functional information:
Quantum Entanglement and Information Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. http://plato.stanford.edu/entries/qt-entangle/
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
Quantum Teleportation Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state. http://www.cco.caltech.edu/~qoptics/teleport.html
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian worldview of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!
Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts
Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!! verse and music:
John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. Casting Crowns - The Word Is Alive http://www.metacafe.com/watch/5197438/ Flyleaf - All Around Me http://www.youtube.com/watch?v=xN0FFK8JSYE
bornagain77_{October 11, 2011
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Nick you state:
Evolution, on the other hand, is confirmed by evidence almost every place you look, if you take a fair and thorough look at the primary evidence
Really Nick??? REALLY??? Does this include 'confirmation' for THE PRIMARY, and most important, claim of neo-Darwinism that purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present??? Seems to me your grand claims for such irrefutable proof for neo-Darwinism, from the 'primary evidence', were just recently shown to be non-existent!!!:
Leading Darwin Defender Admits Darwinism's Most "Detailed Explanation" of a Gene Doesn't Even Tell What Function's Being Selected - Casey Luskin - October 5, 2011 Excerpt: ...You (Nick Matzke) just admitted that the most "detailed explanation" for the evolution of a gene represents a case where: *they don't even know the precise function of the gene, *and thus don't know what exactly what function was being selected, *and thus don't know if there are steps that require multiple mutations to produce an advantage, *and thus haven't even begun to show that the gene can evolve in a step-by-step fashion, *and thus don't know that there are sufficient probabilistic resources to produce the gene by gene duplication+mutation+selection. In effect, you have just admitted that Darwinian explanations for the origin of genes are incredibly detail-poor. http://www.evolutionnews.org/2011/10/leading_darwin_defender_admits051551.html
Nick, how quickly you seem to forget this so as to move on the ever important onion argument? :) That episode with Casey Luskin is fairly embarrassing in itself as to shooting down your very own credibility for any claims you might make in the future (a boy crying wolf if you will),,,, yet you also stated this;
People messing with science, in the teeth of the facts, is what bothers me.
Really Nick??? REALLY??? I actually have such anger towards neo-Darwinian atheists for 'messing with science'! Moreover, It might interest you to know that, 'science' would not even be possible if neo-Darwinism were true! Thus if you truly loved science, as you claim you do, then you would in fact be angry with atheistic neo-Darwinists for perverting it so severely to their own personal agenda:
Should You Trust the Monkey Mind? - Joe Carter Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties. http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind What is the Evolutionary Argument Against Naturalism? ('inconsistent identity' of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) - video http://www.youtube.com/watch?v=5yNg4MJgTFw Can atheists trust their own minds? - William Lane Craig On Alvin Plantinga's Evolutionary Argument Against Naturalism - video http://www.youtube.com/watch?v=byN38dyZb-k "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881 “Atheism turns out to be too simple. If the whole universe has no meaning, we should never have found out that it has no meaning...” CS Lewis – Mere Christianity “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
This following site is a easy to use, and understand, interactive website that takes the user through what is termed 'Presuppositional apologetics'. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.
Proof That God Exists - easy to use interactive website http://www.proofthatgodexists.org/index.php
Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:
Dr. Bruce Gordon - The Absurdity Of The Multiverse & Materialism in General - video http://www.metacafe.com/watch/5318486/ John Lennox - Science Is Impossible Without God - Quotes - video remix http://www.metacafe.com/watch/6287271/
further notes:
Materialism compared to Theism within the scientific method: http://docs.google.com/Doc?docid=dc8z67wz_5fwz42dg9 Christianity Gave Birth To Each Scientific Discipline - Dr. Henry Fritz Schaefer - video http://vimeo.com/16523153
bornagain77_{October 11, 2011
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Nick: "And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side." Nick, this is good to know, and thank you for clarifying your position. At least you're in good company! "Evolution, on the other hand, is confirmed by evidence almost every place you look . . ." This statement, however, is possible only by the rhetorical trick of conflating wildly different meanings of "evolution," from the obvious and well-supported to the outrageous and wildly-speculative. Once a person escapes from the intellectual trap of thinking that "evolution" is a single process that operates across the whole of reality, the evidence for "evolution" looks a whole lot more modest.Eric Anderson_{October 10, 2011
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Do you really need me to cite you saying that glue traps evolved into snap-traps by a series of incremental, selected variations? If you don’t think you said that, just tell me. This is your central dogma, and one of the primary reasons why critical thinkers ridicule darwinism. Having asserted it, why would you ever think the demands for evidence would stop unless you produced it, yielded, or just gave up and went away?
So, you really think that it's unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf? That's where we left the discussion on the last CP thread. Why should anyone believe this is unlikely? It's a simple change in degree, and typically such changes are just a matter of upregulating or downregulating a pathway, which is just a matter of altering the binding strength of a promoter or some such.NickMatzke_UD_{October 10, 2011
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Nick Matzke you deliver priceless commenting gold to have on display here. Please do not stop schooling us ID/creasionist.butifnot_{October 10, 2011
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Nick, It might interest you to know that I find you to be one of the most religious, intellectually dishonest, atheistic neo-Darwinists I’ve ever met!!! And I’ve met my fair share!!!
LOL -- then you ought to be able to find plenty of times where I've argued for atheism. I bet you can't find *any*. It's not something I do -- I am actually pretty profoundly disinterested in theism vs. atheism. I doubt it's resolvable on objective evidence. Evolution, on the other hand, is confirmed by evidence almost every place you look, if you take a fair and through look at the primary evidence, and don't rely on misinterpretations of news stories, wishful thinking based on superficial study, etc. People messing with science, in the teeth of the facts, is what bothers me.NickMatzke_UD_{October 10, 2011
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Onions have lotsa DNA, therefore, all of biology of have been one massive fluke. The evidence is overwhelming...bbigej_{October 10, 2011
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Nick, It might interest you to know that I find you to be one of the most religious, intellectually dishonest, atheistic neo-Darwinists I've ever met!!! And I've met my fair share!!! In fact it is such shamelessly intellectually dishonesty on the part of religious atheists such as yourself who have made my faith in the truthfulness of the claims of Christianity that much stronger!!! Before I met people like you I pretty much thought everyone was basically fair minded. But I've certainly learnd differently! And for that I thank you, even though I certainly fear for the fate of your soul for trying to lead people away from the truth of God with such shameless, and persistent, deception!!! notes:
coast to coast – Blind since birth – Vicki’s Near Death Experience http://www.youtube.com/watch?v=e65KhcCS5-Y Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This 'anomaly' is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).) http://findarticles.com/p/articles/mi_m2320/is_1_64/ai_65076875/
It is also very interesting to point out that the 'light at the end of the tunnel', reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as an observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video which was made by two Australian University Physics Professors with a supercomputer.)
Traveling At The Speed Of Light - Optical Effects - video http://www.metacafe.com/watch/5733303/
Here is the interactive website, with link to the relativistic math at the bottom of the page, related to the preceding video;
Seeing Relativity http://www.anu.edu.au/Physics/Searle/
Here are some 'typical' Near Death Experiences from Judeo-Christian cultures
The NDE and the Tunnel - Kevin Williams' research conclusions Excerpt: I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn't walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn't really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different - the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.(Barbara Springer) Near Death Experience – The Tunnel, The Light, The Life Review – video http://www.metacafe.com/watch/4200200/
further note:
Science and Theism: Concord, not Conflict* – Robert C. Koons IV. The Dependency of Science Upon Theism (Page 21) Excerpt: Far from undermining the credibility of theism, the remarkable success of science in modern times is a remarkable confirmation of the truth of theism. It was from the perspective of Judeo-Christian theism—and from the perspective alone—that it was predictable that science would have succeeded as it has. Without the faith in the rational intelligibility of the world and the divine vocation of human beings to master it, modern science would never have been possible, and, even today, the continued rationality of the enterprise of science depends on convictions that can be reasonably grounded only in theistic metaphysics. http://www.robkoons.net/media/69b0dd04a9d2fc6dffff80b3ffffd524.pdf
bornagain77_{October 10, 2011
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Perhaps someone should start a Please Be Nice to Me I Only Came To Ridicule You But I Get Sad When You Ask Difficult Questions thread. Perhaps the simple question won't haunt you there.ScottAndrews_{October 10, 2011
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Sorry, Nick. It's just that you're so busy and I thought I'd catch you while you have time. Somehow the time always flies away talking about onions and there's never time to address the central question of how you can know that incremental genetic variations are selected to produce significant diversity in living things when you have not determined or even bothered to imagine a detailed pathway. You know, that one critical piece of information that either validates the theory or leaves it blowing in the wind. Do you really need me to cite you saying that glue traps evolved into snap-traps by a series of incremental, selected variations? If you don't think you said that, just tell me. This is your central dogma, and one of the primary reasons why critical thinkers ridicule darwinism. Having asserted it, why would you ever think the demands for evidence would stop unless you produced it, yielded, or just gave up and went away?ScottAndrews_{October 10, 2011
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Nick this is OT, but in case your interested, Holly Ordway, a former atheist, is interviewed by Apologetics315 here; http://www.youtube.com/watch?v=uA4pho7QfVw
Wow, trying to convert me? And here I thought this ID stuff was just about science, not apologetics. Listening to this while running a program -- she started out being an English Ph.D. by hating Christians, then found out her nice fencing coach was one. This doesn't really speak to me, as I don't hate Christians. I was raised religious but am not particularly now, although I'm not anti-religious either. But, would you like know the biggest thing than made me agnostic about religion? Creationists and their continual, unabated, shameless, eternally uncorrected shenanigans. Once you've seen creationists distort scientific evidence, distort the views of scientists, etc., once you've seen them refuse to correct such mistakes in themselves and others, once you've seen them do this on an industrial and institutional scale, all the while insulting hardworking scientists and blaming them for pretty much every bad thing that has ever happened, it's hard to not be more than little skeptical of their critical thinking abilities, intellectual honesty (not in the sense of lying, but in the sense of doing "due diligence" before opening one's big fat mouth about some technical topic), and the rest. If creationists/IDists want to evangelize people like me, they should start correcting each other's mistakes before I do, they should start criticizing widespread but indefensible creationist views (like young-earthism), and they should start making arguments that are not shot down by a few minutes on Wikipedia and Google Scholar.NickMatzke_UD_{October 10, 2011
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Re: carnivorous plants, "information", etc. -- start a new post if you want to talk about off-topic stuff, there is no point to discussing a million things at once. And, it would be nice if you quoted my previous remarks on those topics and explained why they are wrong, rather than just inviting me to rehash the same basic case I've made several times already.NickMatzke_UD_{October 10, 2011
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Got it, Nick, the genome sizes of onions are an effect of their population size. That would explain why raspberries have a genome about 8% the size of ours. Or does it? And that would explain the difference in genome sizes within onions of the same population. Or does it?
Dude, you are just being angry, not making any sense. Raspberries could well have a larger historical population size than humans. You also have to factor in generation time, growth rate, number of offspring per generation, etc. It seems that fast-growing, fast-reproducing critters tend to have smaller genomes. And it's just a hypothesis in any case. Might be wrong, but it's dang well better than "Let's just brazenly assume everything is functional, despite all the evidence against this idea, and let's call all the scientists who are aware of the evidence idiots while we're at it."
And that would explain the difference in genome sizes within onions of the same population. Or does it?
The onions with different genome sizes are not in the same population, they are different species. Take a deep breath and think before you write, dude!NickMatzke_UD_{October 10, 2011
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Nick, if Mr Andrews hasn't worn you out, I could always use another refresher course on the rise of information.Upright BiPed_{October 10, 2011
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Better audio to music video:
The Police – Spirits in the Material World http://www.youtube.com/watch?v=cDs9zbiumDc
bornagain77_{October 10, 2011
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Got it, Nick, the genome sizes of onions are an effect of their population size. That would explain why raspberries have a genome about 8% the size of ours. Or does it? And that would explain the difference in genome sizes within onions of the same population. Or does it? If you ever have time to explain it to me, don't. Use it to describe to me the incremental genetic steps, both the variation and selection, leading from a glue trap to a flypaper trap. Sadly you've used up all your precious time telling me what you don't know about onions and once again you have none left to illustrate how the cornerstone of biology works. Come up with that and with your newfound credibility I'll just take your word for all the rest.ScottAndrews_{October 10, 2011
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Well Nick, perhaps we should just go a little deeper into exactly what kind of epigenetic information we are dealing with; A few comments as to 'non-local' epigenetic information: Though when many people speak of epigenetic information they are mainly focused on information flow in the cell that is not DNA centric in its basis, such as the many examples of epigenetic information flow Dr. Shapiro lists on page 22 of this following paper: ,,,
Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009 http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
,,,There is a particular type of extra ‘epigenetic’ information in life, that is not listed in Dr. Shapiro’s paper, that is very important for people to consider. To give a little background on this ‘extra’ epigenetic information, Dr. Stephen Meyer comments at the end of this following video,,,
Stephen Meyer – Functional Proteins And Information For Body Plans – video http://www.metacafe.com/watch/4050681/ ‘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 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)
So exactly where does this mysterious information, that Dr. Meyer illustrates the necessity of, that controls the overall ‘biological form’ of a organism, actually reside if not in DNA coding??? I think a very strong case can be made that it is ‘non-local’, beyond space and time, quantum information, which is not reducible to a material basis (A. Aspect), that is what is actually in control of, and orchestrating, the biological forms of organisms to be in the particular ‘3D shapes’ we find them in.,,, To show the plausibility of this, first we find that DNA itself would not even have its necessary helical shape/structure if it were not for ‘non-local’ quantum information/entanglement holding it in that particular shape;
Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/
As well, DNA is shown to do ‘chemically impossible’ things here, thus, once again, demonstrating 'non-local' information's overarching control of '3-D form' in molecular structures:
Does DNA Have Telepathic Properties?-A Galaxy Insight Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html
As well, At the 6:05 minute mark, of this following video, cells are witnessed as they pull themselves together, from a distance, to form 'flawless' blood vessels. The commentator on the video refers to the 'at a distance' action of the cells as a 'miracle';
Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 Psalm 139:13-14 For you created my inmost being; you knit me together in my mother's womb, I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
Next we also find that non-local, beyond space and time, quantum information/entanglement is also necessary for dictating the final shape that proteins will take upon protein folding;
Quantum states in proteins and protein assemblies: The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf
Another very interesting piece of evidence, that 'non-local’ quantum information/entanglement is dictating the shape of a organism, comes forth when we realize that the ‘4-Dimensional shape’ of a organism fairly quickly disintegrates to 3-dimensional thermodynamic equilibrium upon the death of the organism:
“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 The Unbearable Wholeness of Beings – Steve Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
As well it is very interesting to note that this quantum information/entanglement, which will assuredly be 'totally missing’ from the organism, once the organism disintegrates to complete thermodynamic equilibrium, is shown to be ‘conserved’. i.e. This transcendent non-local quantum information, though missing from the dead, and now disintegrated, organism must reside somewhere 'in the universe':
Quantum no-deleting theorem Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist. http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence
It is clear that a very strong case is now evident, that ‘non-local’ quantum information/entanglement is in fact the ‘highest level’ of epigentic information in organisms, and that it is this non-local, beyond space and time, epigentic information that is, in fact, ‘shaping’ 4 dimensional creatures in this 3-Dimensional world!!! Music:
The Police - Spirits in the Material World http://www.youtube.com/watch?v=-LtN7evu-eI Matthew 16:26 What good will it be for a man if he gains the whole world, yet forfeits his soul? Or what can a man give in exchange for his soul?
bornagain77_{October 10, 2011
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Nick, I did read it. You can't have it both ways. It's junk. It has no function. It does have a function, but one that doesn't technically count as a function. The more you carry on about what you think you might know about genes, their purpose or lack of it, the more it underscores that most of of it over your head. I don't mean that as bad as it sounds, because you clearly know a great deal. I know what it sounds when someone tries to sound even smarter by stating what they don't know. It sounds like this:
The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others, or whether genome size is just a byproduct of e.g. population size, where extra DNA is always deleterious, but very mildly so, such that only in very large populations with rapid generation time is selection strong enough to favor the very weakly beneficial deletions.
Notice how you admit to not knowing why there is a difference in genome size (no problem there) but then lay it on pretty thick as you suggest that you've got it narrowed down to two distinct possibilities while leaving the door open for other unnamed 'higher-level factors.' Most people only need a few words to say they have no idea, and then I trust them more when they say they do know something. I had a friend who talked like you. I can hear it a mile away.ScottAndrews_{October 10, 2011
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For this stuff to make any sense to you, you would have to understand the influence of population size on selection/drift balance, I don't have time to explain it, maybe someone else will.NickMatzke_UD_{October 10, 2011
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That's right! Quit tossing around words starting with "e" that mean just about anything and everything! (Except "everything.")ScottAndrews_{October 10, 2011
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