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Sunday, 9 September 2012
Response on ENCODE reaction
61 comments:
- Eli Rodgers-Melnick said...
The ENCODE data will be an unparalleled resource for years to come - I don't think there's any doubt about that. I think the discussion of semantics among scientists is important, because our language is about conveying specifics, but I do hope that the articles in the popular press get people excited about science. Also, I'm betting that all this controversy will drum up some new ideas for how to analyze all the new data that's available.
- 9 September 2012 at 10:16
- SPARC said...
Note to self: one can be precise about definitions in paper or a scientific talk to scientists, but it's far harder via the medium of everyday press, even to the same audience.
IMHO the issue is not the precission of ENCODE's definition of "function" but rather about the fact that ENCODE ignored the well established and defined concept of Junk DNA. It's as if some geographer would define hills with height over base > 100m as mountains. This would transform the majority of the world's surface into mountains. It is obvious that this wouldn't make sense even if the given definition is very precise.
- 9 September 2012 at 23:31
- Laurence A. Moran said...
The ENCODE Consortium is promoting the idea that the human genome is chock full of a vast network of regulatory sequences.
This flies in the face of abundant evidence that most of our genome is junk. Why do you ignore that evidence?
And why would humans need so much more regulatory DNA than, say Drosophila? or pufferfish? These are not trivial questions. You are challenging a model of gene regulation that has been built up over several decades.
Do you really think that the ENCODE data supplies such extraordinary evidence in support of such an extraordinary claim?
I don't. Not even close.
- 10 September 2012 at 20:00
- Wade said...
So much hinges on the operational definition of "functional". The historic notion of "junk" DNA includes DNA that is non-functional. A great deal is being written about what is an what isn't functional, and a great deal of it appears to be fundamentally divorced from reality with respect evolutionary science. At the grossest level, there exists a cost to adding a base, or a million bases to a genome, but that cost is so negligible that invoking it is little more than an advertisement of ignorance. For much of the rest that is being declared "functional", a similar argument is trivially deduced, and yet, proponents are advocating those very definitions. For example, the mere fact that DNA is transcribed to RNA in a tissue specific manner says NOTHING about function. A functioning knowledge of the mechanisms of transcriptional regulation, and of mutagenesis actually predicts that we will have useless transcription in a regulated manner.
Ultimately, you seem to have promoted a definition of function that not only lacks a useful function, it is counter-productive.
- 12 September 2012 at 02:42
- themayan said...
You have T. Ryan Gregory complaining that function had already been known for years, yet on the other hand, complaining about the fact that a large amount of bio chemical function has been found. Which is it Gregory? Make up your mind! Of course what he refuses to admit, is that in the earlier years, the data that did indeed give hint to function, was largely ignored by the status quo, and now all those years of preaching the useless junk DNA paradigme to students and to the general public has now come back to bite them in the ass. Not to mention those all those sweet talking points given to ID theorist and creationist. No, we just couldn't have that! (Sarcasm emphasized)
As for Larry Moran challenging the findings of ENCODE. My question is, why cant he do this in peer review? If the counter evidence is there, as he insist it is, then he wouldn't even need funding. He could simply produce the data that already exist, but like Gregory, he chooses instead, to publicly ridicule and or marginalize the work of other very hard working researchers who have dedicated their precious time and effort into this project.
Again, it is easy to criticize from your a blog where your minions can shower you with praise and un-critical adulation. Do it the right way. Take it to the stage.
- 17 September 2012 at 06:05
- Bradley J. Fikes said...
I'm a science writer at a local paper in San Diego who blogged about this issue and tried to get it right.
Here's what I wrote: http://j.mp/dnajunk
- 20 September 2012 at 12:23
- Diogenes said...
TheMayan writes:
"You have T. Ryan Gregory complaining that function had already been known for years,"
"Function had already been known". Riight.
In what? In Junk DNA? In non-coding DNA? They were never the same thing. Most of your genome is still junk. TheMayan is going to distort T. Ryan Gregory's ideas, because themayan doesn't know squat about science. But it would be convenient if themayan were to quote T. Ryan Gregory in full, so that we can judge whether what Gregory wrote was accurate or inaccurate.
Creationists and IDers always quote-mine, so themayan's paraphrasing of Gregory is useless. Fork over the quote from Gregory himself.
Gregory correctly points out the guys who invented the Junk DNA hypothesis knew, way back in 1972, that much of it would be transcribed into RNA. They insisted though, that no organism-level function could constrain the DNA sequence of most of the human genome, and they were right.
The ENCODE consortium reported NO data indicating that most of the DNA sequence of the genome is constrained by an organism-level function. It's still junk.
TheMayan: "Of course what he refuses to admit, is that in the earlier years, the data that did indeed give hint to function, was largely ignored by the status quo..."
This is an old wives' tale; analogous to believing that your heart stops when you hiccup. Gregory disproved this false history by citing actual passages from scientists of the 70's and 80's.
Some dumb journalists and ID creationists write that "Junk DNA" inhibited research, but they have no evidence to back up. They refuse to even look at Gregory's citations.
ID creationists and dumb journalists need to make up a false history of science in order to get attention.
- 24 September 2012 at 12:04
- Diogenes said...
@Bradley Fikes:
Good job on your story. A much better story than the trash written in the NY Times, Wash Post, USA Today, The Guardian, The Independent, etc.
- 24 September 2012 at 12:06
- Diogenes said...
Birney: "For me, the driving concern was to avoid over-hyping the medical applications..."
Really? You mean like when you helped Nature produce a video cartoon in which ENCODE is presented as a mega-robot that destroys cancer and heart disease by punching it very hard?
Is that what you meant by avoiding over-hyping of medical applications? What, then, WOULD be hype by your definition? Immortality? Free nose jobs for ugly children? The ability to fly? What?
Birney: "With hindsight, we could have used different terminology to convey the concepts..."
True, you could have used accurate terminology.
Birney: "I do think we got our point to the general public: that there is a staggering amount of activity in the genome..."
No, no. You told the general public that there was 80% FUNCTION in the genome, FUNCTION not activity, and you told Ed Yong at Discover that would go to 100%. And almost all of the media interpreted function to mean "necessary", "needed", "essential". Was that accurate?
NPR reported John Stam as saying:
NPR: "Most of the human genome is out there mainly to control the genes," said John Stamatoyannopoulis, a geneticist at the University of Washington School of Medicine, who also participated in the project.
Was John Stam telling the truth or lying, Ewan?
This is from the Independent:
The Independent: "Scientists have once and for all swept away any notion of "junk DNA" by showing that that the vast majority of the human genome does after all have a vital function by regulating the genes that build and maintain the body."
Does the vast majority of the human genome have a vital function by regulating the genes, Ewan?
This is from the New York Times:
NY Times: "As scientists delved into the "junk" — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed."
Is 80% of human DNA active and needed, Ewan?
This is from the Washington Post:
Wash Post: "Indeed, the vast majority of human DNA seems to be involved in maintaining individuals' well being — a view radically at odds with what biologists have thought for the past three decades"
Is the vast majority of human DNA involved in maintaining individuals' well being, Ewan?
This is from USA Today:
USA Today: "International research teams have junked the notion of "junk" DNA, reporting that at least 80% of the human genetic blueprint contains gene switches, once thought useless, that control the genes that make us healthy or sick."
Is 80% of human DNA gene "switches" that control genes, Ewan?
Birney: "ENCODE also had the chance of making our results comprehensible to the general public..."
Ewan, did you succeed or fail?
- 24 September 2012 at 12:38
- T Ryan Gregory said...
It's not complicated, Themayan. My complaint has three parts (and this isn't unique to ENCODE, it's so common as to be cliche in both the media and the primary literature).
First, there was never a time when non-coding DNA was *all* dismissed as "useless junk" such that functions were not considered. Quite the opposite -- functions were seriously considered for every new type of non-coding DNA when discovered. The early authors of the "junk DNA" concept explicitly mentioned possible functions for *some* non-coding DNA. Comings (1972) suggested 20% of the genome is actively used, for example.
Second, the concept of non-functional, non-coding DNA was not based on ignorance or giving up and just calling it "junk". There were (and still are) positive arguments for expecting much of the genome to be of little or no relevance to fitness. Mutational loads, variability in genome size, neutral evolution at the sequence level, 2/3 of the genome being transposable elements, etc. Several of these arguments have been around since the 1970s and they remain valid today.
Third, there is no evidence that a majority of the human genome is "functional" in any meaningful sense of that word. Of course some non-coding DNA is functional (regulatory regions, centromeres and telomeres, ribosomal RNA, etc.), but no one ever said otherwise. There are more examples coming up all the time, which is very interesting. But the total still hasn't even approached Comings's (1972) original figure of 20%. And even if some people are willing to interpret the current evidence as indicating that most DNA in the human genome will turn out to be functional, they still have to explain why a pufferfish does fine with only 1/10 as much whereas even the smallest salamander genome is 5x larger. This suggests that, even if 100% of the human genome is functional, a lot of eukaryotic DNA out there is not. That is, that the notion of non-functional, non-coding DNA remains valid. Claiming that humans are complex and so need more DNA is an expectation that was refuted in the 1950s. And, in any case, the human exceptionalism required to maintain the view that 100% functional in people but amount of non-coding DNA is irrelevant in pufferfishes and salamanders is biologically nonsensical.
There is nothing contradictory about these three arguments.
- 24 September 2012 at 13:08
- Diogenes said...
Well done. But theMayan will never answer.
- 24 September 2012 at 13:30
- Diogenes said...
@Ewan -
The definition of "function" that is relevant to the Junk DNA hypothesis is this: DNA sequence constrained by organism-level function (not some parasitic-level function, like the biochemical functions of transposons copying themselves.)
The definition of "junk" that is relevant to the Junk DNA hypothesis is this: DNA sequence NOT constrained by organism-level function.
I have two questions.
1. Ewan, do you agree that the above definition of "function" vs. "junk" is the definition relevant to the Junk DNA hypothesis as it was put forward by, say, Ohno in 1973? Yes or no?
2. Ewan, by the above definition of "function"-- the definition relevant to the Junk DNA hypothesis-- what fraction of the genome is known for sure to be "functional" based on ENCODE's data?
- 24 September 2012 at 13:34
- themayan said...
cont.....Again you you accused me of quote mining even though you later agree with what I said, an yet you went on to quote mine Ohno. Here is what Ohno actually concluded….."INASMUCH as the only requirement to be qualified as partitioning sequences is to be untranscribable and/or untranslatable. it is not likely that these sequences came into being as a result of positive selection. Our view is that they are the remains of natures experiments which failed. The earth is strewn with fossils remains of extinct species, is it a wonder that our genome too is filled with the remains of extinct genes?"
A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution
In the 1970s, the field of population genetics was dominated by analysis of the genetic polymorphism of populations using allozymes, with the aim of deciphering population structuring (LEWONTIN 1974). The entire emphasis was on the role of point mutations in coding regions as the primary source of evolutionary change. Despite the observations ofMCCLINTOCK (1950) that in maize some genetic factors [e.g., the Activator (Ac)/Dissociator (Ds)] that can control the cell color of kernels were able to change their locations within and between chromosomes and could control the expression of some genes [see FEDOROFF (1994) for a biography of B. MCCLINTOCK], and the demonstrated presence of mobile DNA elements in bacteria (SHAPIRO 1969), the possibility that TEs could influence genetic polymorphism, and therefore genetic diversity, was, for the most part, ignored.
Except for their use as potential genetic tools, the interest in molecular analyses of TEs faded between 1990 and 2000, and the population approach was not really understood……
- 24 September 2012 at 20:16
- themayan said...
I find it very interesting that you accuse me of quote mining when I mentioned that one of Gregory's complaint was that function was already known, when even you confirm this by mentioning the citations that Gregory has posted on his cite. Secondly, the amount of papers Gregory cites on junk DNA compared to other types of genomic studies during that same time frame, are scant to say the least. Go to Gregory's website and see how few papers you find in published just during the 80's alone. I am old enough to remember the 70's and 80's, and I remember as students we were told time and time again, that only 2% of the genome was active and the rest was useless vestigial junk. We were told this in schools, books, science channels on television, and radio and science magazines. If function was known by scientist, (and I have no reason to doubt it), then it was one of the best kept secrets, and or again was ignored by the same status quo.
It seemed that for the status quo, the junk DNA paradigm was instead used as a poster child for bad design….E.g. Kenneth Miller, "Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily"
Richard Dawkins, "The amount of DNA in organisms," Dawkins wrote in 1976, "is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the 'purpose' of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. 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."
Diogenes says….."Some dumb journalists and ID creationists write that "Junk DNA" inhibited research, but they have no evidence to back up. They refuse to even look at Gregory's citations"
"ID creationists and dumb journalists need to make up a false history of science in order to get attention"
Prof. John Mattick, recently claimed that, 'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology' [Genius of Junk (DNA), Catalyst, Thursday, 10 July 2003].
John Mattick is not a creationist or ID theorist.
The term is used mainly in popular science and in a colloquial way in scientific publications. "Scientific American" claims that its connotations may have slowed research into the biological functions of noncoding DNA.[32] Source Wikipedia and Scientific American, & I know neither to be creationist cites or orgs.
- 24 September 2012 at 20:17
- T Ryan Gregory said...
"...the possibility that TEs could influence genetic polymorphism, and therefore genetic diversity, was, for the most part, ignored."
Surely you jest.
It may very well be that your undergraduate instructors told you that junk DNA was all useless. It does not follow that researchers working on non-coding DNA dismissed the idea of function. That is what I have tried to show -- they published ideas on potential function all the time in the primary literature throughout the 1970s and 1980s. Every new type of non-coding DNA that was discovered (satellite DNA, LINEs, SINEs, ERVs, introns, and pseudogenes) had functions considered from the outset.
It also does not follow from whaty you heard in class or what you saw in Scientific American that the authors of the original junk DNA papers argued that all non-coding DNA is useless. Read Comings (1972), which is the first detailed treatment of the topic. Moreover, both the junk DNA and selfish DNA papers were met with strong resistance -- the prevailing view was that most genomic DNA must have a function or else it would have been deleted.
Ohno's version of "junk DNA" referred to pseudogenes, which is the context for the line you quoted. He did acknowledge non-sequence specific functions such as spacing among genes.
Of course, all of this is secondary to the fact that the ENCODE results do not, in fact, suggest anything like 80% "functional" non-coding DNA in the human genome under any biologically meaningful definition.
- 25 September 2012 at 06:37
- Diogenes said...
I am old enough to remember the 70's and 80's, and I remember as students we were told time and time again, that only 2% of the genome was active and the rest was useless vestigial junk. We were told this in schools, books, science channels on television, and radio and science magazines.
If that were true, then why do you have NO DOCUMENTARY EVIDENCE for your 2% number, not one citation in the peer-reviewed scientific literature asserting your 2% number-- and why do you ignore the huge amount of contrary evidence amassed and fully cited by Gregory?
Ryan Gregory cited Comings (1972) as writing the following:
Comings, 1972: These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn't mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA...
Then Comings lists some functions for junk DNA.
Comings said 20% functional. Let's compare his prediction to the results of ENCODE.
Ewan Birney wrote: "However, on the other end of the scale – using very strict, classical definitions of "functional"... such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons... that number goes up to 9%...
...A conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20%."
So Comings predicted 20%, and Ewan Birney extrapolates to future experiments, not yet performed, will yield 20%.
I am old enough to remember the 80's, and I was never told any such thing about 2% of the genome being functional.
If your teachers told you that only 2% of the genome was functional, then it is your terrible school's fault for contradicting the scientific literature. That is your school's problem-- but you are blaming Ohno, Comings, Crick, Doolittle, Ohta et al.! Where is your documentary evidence?
Why are you ignoring Gregory's citations? Why do you ignore Birney's estimate that only 20%, at most (very optimistically), of your genome is functional. Why do you ignore the scientific evidence?
- 25 September 2012 at 06:46
- Diogenes said...
@The Mayan:
Prof. John Mattick, recently claimed that, 'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology' [Genius of Junk (DNA), Catalyst, Thursday, 10 July 2003].
I cannot judge Mattick's meaning in context, because I don't have the original. It is universally true that creationists take quotes out of context, sifting through vast piles of literature to find one quote with a different meaning out of context than its original meaning. Thus, I cannot fully disagree with Mattick's meaning in context.
However, Mattick's quote, at least its apparent meaning taken out of context, is obviously dead wrong, and contradicted by the history of the last 50 years of research in molecular biology, which has been largely focused on finding functions in non-coding DNA.
No molecular biologists nor geneticist ever equated Junk = non-coding DNA; that is a scurrilous lie promoted by ID creationists and newspapers desperate for sensational stories.
Do we need to remind you of the history of science?
Nobel Prize for Jacques Monod and co-workers, 1965, for finding functions in non-coding DNA (regulatory elements).
Nobel Prize for Barbara McClintock in 1983 for her discovery of new functions in non-coding RNA (mobile genetic elements.)
Nobel Prize for Tom Cech and Sidney Altman in 1989, for discovery of catalytic functions resulting from non-coding DNA (catalytic RNA= ribozymes).
Nobel Prize for Jack Szostak and co-workers in 2009, for research in 1980's on function in non-coding DNA (telomeres).
The structure of tRNA was known by 1964, crystal structure solved in 1974. tRNA is made from non-coding RNA.
The ribosome was known to be largely nucleic acid in the 1950's, general molecular structure known since the early 1970s, by the 1980's it was known the ribosome was a ribozyme-- based on functions residing in non-coding DNA.
Explain to me how scientists did not pay enough attention to function in non-coding DNA?
Is there a single base pair of non-coding DNA that had a novel function discovered by any creationist or ID proponent-- any? Even one base pair? No. Not one.
- 25 September 2012 at 07:55
- T Ryan Gregory said...
Also, Nobel Prize in 1993 to Richard J. Roberts, Phillip A. Sharp for discovering introns.
- 25 September 2012 at 08:42
- Diogenes said...
"Scientific American" claims that its connotations may have slowed research into the biological functions of noncoding DNA.[32] Source Wikipedia.
Thanks for citing me. I wrote that sentence in the Wikipedia entry. Since you trust as reliable the sentences I wrote in Wikipedia, why am I unreliable when I say most of your genome is still junk?
Since you trust Scientific American as a reliable source (I DO NOT), maybe you'd like to read this debunking of the ENCODE hype at Scientific American:
Scientific American: "A similar kind of 'theory of everything' hype surrounded the [Human Genome Project] but in the case of the [ENCODE Project] the hype has been ratcheted several fold... And science journalists who should know better (in Science, BBC, NY Times, The Guardian, Discover Magazine) made things worse by conflating junk, non-protein-coding and regulatory DNA...
So even bona fide junk DNA is not neutral and is still subject to evolutionary scrutiny – but neither does every single element map to a specific function. We know this partly because genome size varies very widely across species whereas the coding capacity is much less variable (the "C-value paradox"), partly because removal of some of these regions does not affect viability in several animal models, including mice. It's this point that [the ENCODE Project] almost deliberately obfuscated by trumpeting (or letting be trumpeted) that 'junk DNA has been debunked', ushering in 'a view at odds with what biologists have thought for the past three decades.' ...The EP results are important and will be very useful – but they're not paradigm shifters... and should not pretend to be."
[Athena Andreadis, Scientific American, http://blogs.scientificamerican.com/guest-blog/2012/09/17/junk-dna-junky-pr/]
I don't trust Scientific American very much-- but you consider it as a reliable source, and you do so by citing a sentence in Wikipedia that I wrote.
- 25 September 2012 at 09:05
- themayan said...
I have already spoken about issue of what scientist knew and what we as students were taught, and which in many cases is still being taught. A couple of weeks ago I gave you an example of PZ Myers in a room full of biology majors who said many things including ridiculing those who claim the genome contains massive amounts of information, and then goes on to insinuate that those who are trying to associate function within non protein coding regions of DNA, are simply biologist who are looking for job security. Why is there no anger on your part towards guys like this. How can you build interest among young people by ridiculing those who are trying to advance science?
Rummaging About in the Genetic Junkyard Skepticon 4 PZ Myers
This is why ignoring is a type of ignorance in itself, and how it can, and has slowed down scientific progress, and let me just use one more example below.
Everyone knows of the Barbara Mcclintock story and how junk DNA was ignored long before the term "junk DNA" even existed.
Yes, Mcclintock was a respected science of her day, this is true, but what is also true, is that her specific work on maze and transposable genetic elements was largely ignored, only to later be redeemed in 1983 decades after her initial work. Think of all those decades lost when we could have been researching instead of condemning others because their finding did not fit or conform to our own personal world views or biases. Yes that right, even scientist can have and be bias. And again it would be pretty embarrassing to finally admit after all these years that maybe the word junk should not be used anymore in light of histories lessons. Maybe the term 'no known function' would be a safer and more accurate term. However here below is my response to yours.
"Surely you jest"
No sir. Not in this case."Where it is said that she defiantly and deliberately challenged the paradigme view of the gene"
Barbara McClintock: Pioneering Geneticist (Unlocking the Secrets of Science) [Library Binding]
Kathleen Tracy (Author)From all her experiments with maize (Indian corn), Barbara discovered that there were movable elements inside each gene, which she called "transposable elements." Because her revolutionary ideas challenged a cemented belief among mainstream geneticists that genes were fixed in place, her research was rejected. She was deeply stunned and bitterly disappointed at the close-mindedness of the scientific community.
Digital Archives Cold Spring Harbor
McClintock's studies and observations of mutation in kernels of maize (corn), led to her discovery of transposable genetic elements. Although the scientific community largely ignored her concepts, advances in molecular and microbial genetics ultimately proved her findings correct. She is now credited as the discoverer of transposable—or "jumping"—genes, a discovery which is at the very root of much of today's research in genetic engineering.
http://en.citizendium.org/wiki/Barbara_McClintockHer work on controlling elements and gene regulation was conceptually difficult and was not immediately understood or accepted by her contemporaries; she described the reception of her research as "puzzlement, even hostility".[7] Nevertheless, McClintock continued to develop her ideas on controlling elements. She published a paper inGenetics in 1953 where she presented all her statistical data and undertook lecture tours to universities throughout the 1950s to speak about her work. She continued to investigate the problem and identified a new element that she called Suppressor-mutator (Spm), which, although similar to Ac/Ds displays more complex behavior. Based on the reactions of other scientists to her work, McClintock felt she risked alienating the scientific mainstream, and from 1953 stopped publishing accounts of her research on controlling elements.
- 25 September 2012 at 19:09
- themayan said...
As for Diogenes.....Your initial complaint was.."Some dumb journalists and ID creationists write that "Junk DNA" inhibited research, but they have no evidence to back up"
After I cite a couple of sources to back up my claim including Wikipedia.
You then respond by saying..... "Thanks for citing me. I wrote that sentence in the Wikipedia entry"
Diogenes, are you a dumb journalist or creationist? Otherwise you statement makes little sense.
You then go on to ask me why I questioned your credibility?....
"Since you trust as reliable the sentences I wrote in Wikipedia, why am I unreliable when I say most of your genome is still junk?"
I'm not even sure how to respond to this example of a blatant contradiction. And by the way, Wiki articles require sources other wise they are rejected or in other cases, they are published, but with a 'citation needed caveat'
As for Matick's statement 'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology'
Nowhere did he say that there wasn't any past research going on concerning this subject. Again his point was sciences failure to recognize the implications of the non-coding DNA" as in the status quo. As he is also a member of the science community, and did not exclude himself as a member, I can only assume that he may also be partly to blame, but this particular point is moot.
- 25 September 2012 at 20:42
- themayan said...
T. Ryan Gregory
One more example, and these are not my words below but the words of favorite of mine, and I'm sure yours too, J. Wells, and all kidding aside, before you attack the messenger, consider the substance as it relates to what I said before.
In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain "DNAs whose only 'function' is survival within genomes," and that "the search for other explanations may prove, if not intellectually sterile, ultimately futile." In the same issue of Nature(284:604), Leslie Orgel and Francis Crick wrote that "much DNA in higher organisms is little better than junk," and its accumulation in the course of evolution "can be compared to the spread of a not-too-harmful parasite within its host." Since it is unlikely that such DNA has a function, Orgel and Crick concluded, "it would be folly in such cases to hunt obsessively for one."
Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. "It is a remarkable fact," he wrote, "that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes." In particular, pseudogenes "are genes that once did something useful but have now been sidelined and are never transcribed or translated." Dawkins concluded: "What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene... unless he was deliberately setting out to fool us."
But if most of our DNA is functional, as the ENCODE results suggest, then the "junk DNA" argument against ID collapses.
So the four bloggers listed above are doing everything they can to discredit the ENCODE project's estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is "pervasively transcribed," suggesting functionality. The 2012 results, based on 1,640 datasets, documented that "the vast majority (80.4%) of the human genome" is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body.
Clearly, we have a lot more to learn about our genome -- but not if we start by assuming that most of it is junk.
- 25 September 2012 at 21:31
- Misc said...
These Darwin Junk DNA thugs are Psychotic.
- 26 September 2012 at 00:28
- Diogenes said...
But if most of our DNA is functional, as the ENCODE results suggest
What nonsense! Multiple ENCODE scientists admitted that their results do not debunk the Junk DNA hypothesis, and they've shown that only a small fraction of the genome is functional.
Just the other day, ENCODE researcher Max Libbrecht wrote:
"Max Libbrecht from ENCODE and the ENCODE AMA on reddit here... I thought I'd put in that I essentially agree with this article: ENCODE did not debunk the idea of "junk" DNA, contrary to many news outlets. Here is one summary of the true results and their misinterpretation -- there are many others:
http://selab.janelia.org/people/eddys/blog/?p=683" [Source: Mike White's blog]
Max above approvingly cited a blog post by Cryptogenomicon, which is a devastating smackdown of the hype regarding the "Death of Junk DNA." Read Cryptogenomicon before you comment again.
Ewan Birney wrote on this very blog: "...using very strict, classical definitions of "functional"...we see a cumulative occupation of 8% of the genome. With the exons... that number goes up to 9%."
Michael Eisen, a scientist consultant for ENCODE, wrote a devastating and widely quoted critique where he disputes the Press Release claim that ENCODE dispoved Junk DNA:
Eisen: "So it is more than just intellectually lazy to start the story of ENCODE this way. It is dishonest – nobody can credibly claim this to be a finding of ENCODE. ...And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn't need to be overturned. ...The pullquote from the [ENCODE] press release is that the human genome is a "massive control panel with millions of switches regulating the activity of our genes". ...But as even the authors admit, only some fraction of these sequence will actually turn out to be involved in gene regulation. So it is simply false to claim that the papers have identified millions of switches." [Michael Eisen's blog]
I listed quotes from many other ENCODE scientists admitting that they did not disprove the Junk DNA hypothesis at Mike White's blog.
TheMayan: "But if most of our DNA is functional, as the ENCODE results suggest, then the "junk DNA" argument against ID collapses."
On the contrary, the existence of just one viral DNA insertion (8% of the genome) or transposon (about a million of those, 45% of the genome) demolishes Intelligent Design.
- 26 September 2012 at 09:53
- T Ryan Gregory said...
I think you are missing the point of the quotes from the selfish DNA papers. You also seem to miss the point of the papers as well, and what it implies about the state of assumptions regarding non-coding DNA in the early 1980s.
As to the first, the important points are that we should not "hunt obsessively" for functions at the organism level if there is a plausible explanation at the subgenomic level (i.e., that the element is parasitic). Not, "we should never consider function". That "we should not keep looking for function after function after function in a sequence, assuming that there absolutely must be one."
Read the rest of the papers. Especially parts like this:
"It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another."
Two things need to be understood about these papers. One, they were written in response to the prevailing tendency to "look obsessively for function". This was the genomic counterpart to Gould and Lewontin (1979) about adaptationism in studying morphological and behavioural traits. If this were not the prevailing assumption, then these two papers would not have been necessary -- let alone published in Nature.
Moreover, these papers were met with strong resistance. See, e.g.,
Doolittle, W.F. 1982. Selfish DNA after fourteen months. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 3-28. Academic Press, New York.
- 26 September 2012 at 10:07
- Diogenes said...
These Darwin Junk DNA thugs are Psychotic.
Misc, do you have anything to support your point besides ad hominem attacks and hysterical blurts?
If you had any evidence to support your claim, you would have presented it. No, instead, you just used ad hominems, thus showing you had no evidence to support your emotional blurts.
As for your use of the phrase "Psychotic"-- I return to my previous point: Intelligent Design creationism is not a competitor to Darwinism. It is a competitor to Freudian psychoanalysis.
ID creationists spend all their time trying to figure out why scientists like evidence so much, a behavior that creationists consider a mental disorder.
ID creationists put us on the couch:
"Tell me more about your mother. Perhaps that will explain this disorder of yours-- your caring about scientific evidence and data and experiments! No normal Christian does that!"
- 26 September 2012 at 10:09
- Diogenes said...
In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is "pervasively transcribed," suggesting functionality. The 2012 results, based on 1,640 datasets, documented that "the vast majority (80.4%) of the human genome" is biochemically functional in at least one cell type.
What nonsense! The fact 76% of the genome is transcribed into RNA, often at very low levels, has nothing to do with the Junk DNA hypothesis. Now ID has a problem with junk RNA on top of your massive problem with junk DNA. No intelligently designed system would have 76% transcription when most of that RNA just gets degraded.
David Comings, in the FIRST published use of the term 'junk DNA', wrote:
Comings, 1972: "The observation that up to 25% of the genome of fetal mice is transcribed into rapidly labeled RNA, despite the fact that probably less than half this much of the genome serves a useful function, indicates that much of the junk DNA must be transcribed... There are several possible reasons why it is transcribed..."
Comings then goes on to list several potential functions for Junk DNA.
So Comings in 1972 wrote "much of the junk DNA must be transcribed."
You, TheMayan, in 2012 write: 'our DNA is "pervasively transcribed,"' and on this basis, you claim Junk DNA is disproven.
No, this confirms Comings' statement in 1972 that "much of the junk DNA must be transcribed."
Do you understand how you know nothing, nothing, about genetics or about the Junk DNA hypothesis, and have failed at basic logic?
- 26 September 2012 at 10:19
- Misc said...
@ Diogenes
Yes, YOU are delusional and Psychotic as evident in your continual berating comments here and elsewhere. Also, where is the blog you promised on how Shapiro is "Scared to death of you"? What a joke!! And I never said anything about ID, Creationism or Christianity, another delusional projection from you.
- 26 September 2012 at 10:42
- Diogenes said...
@Misc #1: I never said anything about ID, Creationism or Christianity...
@Misc #2: These Darwin Junk DNA thugs
No one but creationists use "Darwin" as an adjective, to describe molecular biologists!
- 26 September 2012 at 12:16
- Misc said...
@ Diogenes
Where is your blog on Shapiro being 'scared to death' of you?
- 26 September 2012 at 12:27
- Diogenes said...
Where is your blog on Shapiro being 'scared to death' of you?
Now that's a fair question. True, I've been a bit lax posting at my blog. I have a big post I'm working on about ENCODE, and I hope to post tonight or tomorrow. Then I'll go after Shapiro. That might not be till next week.
Do you see when Max Libbrecht of ENCODE showed up at Mike White's blog to say the critics are right-- ENCODE didn't disprove Junk DNA?
- 26 September 2012 at 12:40
- Misc said...
@ Diogenes,
Perhaps you are a bit lax because you are too busy at the Christian post telling people you are a theist to prop up your arguments. Also, whether ENCODE disproved Junk DNA or not is a matter of opinion. I will say this however, it's not looking too good for the Junk DNA groupies..
- 26 September 2012 at 12:48
- Misc said...
Also, since you bring up ID, you have some unfinished business over at UD ..> http://www.uncommondescent.com/intelligent-design/ub-sets-it-out-step-by-step/#comment-434621
- 26 September 2012 at 12:52
- themayan said...
Diogenes, the only reason why I'm responding to your many assortments of selected quote mining for the simple reason that I feel inaccuracies must be challenged and cited. First off lets start with this your 'Encode says what?' citation.
The first clue should have been the first line.....
"So I read in the newspaper this week that the ENCODE project has disproven the idea of junk DNA. I sure wish I'd gotten the memo, because this week a collaboration of labs led by myself, Arian Smit, and Jerzy Jurka just released a new data resource that annotates nearly 50% of the human genome as transposable element-derived, and transposon-derived repetitive sequence is the poster child for what we colloquially call "junk DNA".
He is speaking of the popular press as in "newspaper" and He cited newspapers and not ENCODE's own release (and this is important to take note of) Secondly when he mentions that his lab just released study on 50% of the human genome being transposable element, etc. He is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk. As many already know, important function has been found in transposons.
Transposons, or Jumping Genes: Not Junk DNA?
By: Leslie Pray, Ph.D. © 2008 Nature Education
Again Barbera Mcclintock whose work was ignored for decades until she was finally redeemed decades later was the first to discover these elements, but I digress.
He goes on to say..."The newspapers went on to say that ENCODE has revolutionized our understanding of noncoding DNA by showing that far from being junk, noncoding DNA contains lots of genetic regulatory switches. Well, that's also odd, because another part of my lab is (like a lot of other labs in biology these days) studying the regulation of genes in a model animal's brain (the fruit fly Drosophila). We and everyone else in biology have known for fifty years that genes are controlled by regulatory elements in noncoding DNA. (Well, I've only known for thirty years, not fifty, I admit — only since Mrs. Dell'Antonio kicked me out of high school biology class and gave me a molecular genetics textbook to read by myself."
Here again, he is speaking of the newspapers release but doesn't cite fault for reason you insisted, his problem seems to be with reporting that this is something new, when he goes on to say we have known this for fifty years.
He continues and says......"Now, with all respect to my journalist friends, I've learned not to believe everything I read in the newspapers. I figured I'd better read the actual ENCODE papers. This is going to take a while. I've only read the main Nature paper carefully so far (there's 30+ of them, apparently, across multiple journals). But it's already clear that at least the main ENCODE paper doesn't say anything like what the newspapers say"
Yes this is the wise thing to do. Read the actual data.
I'm not going to go into everything he says other than he raises some questions, but thats what scientist are supposed to do, and when he speaks of that actual ENCODE release this is as critical as he gets.....
"ENCODE calls a piece of DNA "functional" if it reproducibly binds to a DNA-binding protein, is reproducibly marked by a specific chromatin modification, or if it is transcribed. OK. That's a fine, measurable operational definition. (One might wonder, why not just call "DNA replication" a function too, and define 100% of the genome as biochemically functional, but of course, as Ewan Birney (the ENCODE czar) would tell you, I would never be that petty. No sir.) I am quite impressed by the care that the ENCODE team has taken to define "reproducibility", and to process their datasets systematically"
- 26 September 2012 at 13:52
- themayan said...
Diogenes Let me point one other thing out concerning selected quote mining tactics.
Example... Eisen: So it is more than just intellectually lazy to start the story of ENCODE this way. It is dishonest – nobody can credibly claim this to be a finding of ENCODE. ...And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn't need to be overturned. ...The pullquote from the [ENCODE] press release is that the human genome is a "massive control panel with millions of switches regulating the activity of our genes".
This is how Larry Moran puts it concerning Eisen...."Here's the interesting thing. Many of us are upset about the press releases and the PR because we don't think the ENCODE data disproves junk DNA. Michael Eisen's perspective is entirely different. He's upset because, according to him, junk DNA was discredited years ago" "Eisen is wrong, junk DNA is alive and well. In fact almost 90% of our genome is junk"
Besides criticizing quote mining tactics, the bigger point I'm making, is that even seasoned scientist and scholars are getting confused and stumbling over who said what, and what does junk really mean? Again, I say in response to ENCODES eulogy, not just rest in peace, but good riddance to this outdated paradigme. When speaking of parts of the genome we dont yet fully understand, lets be wiser and learn our lesson from history and replace this term, and instead use the term 'no known function'
- 26 September 2012 at 14:14
- themayan said...
Gregory, as I said before, although I disagree with many of your assessments, and your portrayal of past historic events within there full context. I do respect your contributions to science, and I think its only fair to tell you that one of the reasons I posted that last response, was because you were one of the names mentioned in the article. You can read full article at...
I'm also curious to know if you watched the PZ Myers lecture I cited, and if you did, do you agree with his presentation?
- 27 September 2012 at 05:00
- Diogenes said...
Perhaps you are a bit lax because you are too busy at the Christian post telling people you are a theist to prop up your arguments.
I have never been to the Christian post.
Is there another guy there calling himself Diogenes?
- 27 September 2012 at 06:37
- Misc said...
- This comment has been removed by the author.
- 27 September 2012 at 07:05
- Misc said...
Funny, you only reply to me and not themyan. No, there isn't anyone on CP calling themselves Diogenes, because you are under your real name, but you already knew that.
- 27 September 2012 at 07:10
- T Ryan Gregory said...
Thank you for the kind comments. I think we may be talking about two different aspects of past history. There may have been a period where people were often taught that non-coding DNA is all useless. It may have been a common view in the media. I haven't looked into this side of things in detail, as it's much more difficult to quantify. (I did, however, have an assistant go through genetics textbooks back 30 years at one time, so I could look into that info again sometime).
What I am talking about is what was actually being said in the primary literature. In that case, it is abundantly clear that there was no widespread dismissal of possible functions for non-coding DNA among the researchers working in the field. I have not been quoting selectively, either -- I looked at the papers that first described each type of non-coding DNA elements, for example, or review papers from the period, or news stories in Science and Nature from that time. All of them show that function was a common expectation, or at least a serious question, throughout the supposed period of dismissal.
If your profs got it wrong, that's a shame. If the media got it wrong, that's not so surprising. Same thing still happens all the time -- see, e.g., ENCODE.
- 27 September 2012 at 07:55
- T Ryan Gregory said...
In terms of PZ Myers, or ID proponents, I personally don't think non-functional junk DNA is all that relevant to the fight from either side. Why should "intelligent design" assume that nothing is non-functional? Our own intelligently designed artifacts often have crap in them. Who would argue that the computer code for Windows is flawless and without non-functional, redundant, sloppy, or otherwise unnecessary bits? I have never seen a clear articulation of the reason that ID predicts no non-functional DNA (other than the obvious "God don't make no junk" -- and even then, why not?).
- 27 September 2012 at 08:02
- themayan said...
Well then Dr Gregory let me try to make this more clear. Maybe its my fault in failing to comunicate properly. The question doesn't seem to be that scientist didn't have a clue that we would someday find function.
This point is moot. The question is the amount of function, and the sheer complexity that the human genome project first revealed and how ENCODE is trying to decode this vast amount information. I have heard some scientist say that the amount of data left people with their jaws dropping from the initial sequencing alone.
As I said before, if you read Matticks statement, he is not necessarily denying that there was zero research or interest. In my opinion he is referring to sciences failure to recognize the full importance of junk DNA. There are many scientist today who have said and are still saying that much of what we have discovered was once thought to be useless junk DNA, but this is not necessarily an either or black or white argument. Both our assessment can be true at the same time.
Again, it is the amount of data that was unexpected, i.e. the amount of junk DNA that turned out not to be useless junk after all. They cant all be wrong. Francis Collins and many others including some I already cited have also said the same, and this is not just a matter of un-enlightened teachers or popular science magazines. As I said before, very influential scientist like Dawkins, Miller and many others tried for many years to use junk DNA as a poster child for bad design and spoke of how useless junk was better predicted by the neo Darwinian model.
As for ID, I'm not sure this is the proper forum to get into a debate concerning intelligent design, but on another forum, if you have the time, sure why not? The real point concerning the questioned I asked about PZ Myers, was a very specific one. It had to do with the specific lecture I cited, and the question was, if you agreed with his presentation? Do you think it is appropriate to down play the role of ncDNA and tell students, those who are looking for function are only doing it for job security? How can telling these young future scientist to not concern themselves with researching possible function, or publicly ridiculing and trying to humiliate those that do, a good thing? Its a fair question. I'm not really sure If I can make my concerns anymore clear.
- 27 September 2012 at 09:10
- T Ryan Gregory said...
Mattick is wrong about the state of research on the topic at that time. I'm not sure how else *I* can make *my* point any clearer.
I am not sure I have seen PZ Myers's lecture. He's not a genome biologist, and he is predominantly focused on atheism and defending evolution from creationists, so I don't know that I would consider that a definitive source for information on genomic research.
- 27 September 2012 at 12:30
- Diogenes said...
"No, there isn't anyone on CP [Christian Post] calling themselves Diogenes, because you are under your real name, but you already knew that."
Ah ha. I am under my real name... at the Christian Post... where I have never gone. But where I, you assert... pretend to be a theist.
Tell me more about me, insane person. Am I handsome? Am I male?
Do I defeat you in debates over there, like I do here? Does that make you angry? Does your mother here you screaming at me from your room in her basement?
Do go on. Tell me everything you know about me. Everything. (No one interfere. This will be fascinating.)
- 27 September 2012 at 22:36
- Diogenes said...
He is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk.
NO. ABSOLUTELY NOT. Junk DNA never meant non-coding DNA. That is a lie promoted by ID creationists and Muggle newspapers.
No geneticist nor molecular biologists ever equated non-coding DNA= Junk.
Cryptogenomicon says that scientists have know for a long time that there is function in NON-CODING DNA. What do you think that means? Do you think that means that scientists have know for a long time that there is function in Junk DNA? If that's what you think.... sheesh.
No geneticist nor molecular biologists ever equated non-coding DNA= Junk. If you think non-coding DNA= Junk, no wonder you're confused.
- 27 September 2012 at 22:55
- Diogenes said...
Your quote mining of Cryptogenomicon is fantastically dishonest and selective.
You are an incredibly dishonest human being. You are just incredible.
Here is what Cryptogenomicon says:
"Noncoding DNA is part junk, part regulatory, part unknown...
"noncoding" DNA is not synonymous with "junk" DNA..."
Here is what YOU say Cryptogenomicon says:
"He is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk."
NO. NO NO NO. No molecular biologist nor geneticist ever equated non-coding DNA = Junk.
Here again is what Cryptogenomicon says:
"Noncoding DNA is part junk, part regulatory, part unknown...
"noncoding" DNA is not synonymous with "junk" DNA..."
Are a pathological liar?
Or do you just have zero reading comprehension?
Do I have to repeat this 100 times, would that help, assuming your reading comprehension is 1 percent level?
- 27 September 2012 at 23:04
- Diogenes said...
@TheMayan: "He is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk."
NO. Cryptogenomicon says:
Cryptogenomicon: "The "junk DNA" question is about how much DNA has essentially no direct impact on the organism's phenotype – roughly, what DNA could I remove (if I had the technology) and still get the same organism."
That is certainly not non-coding DNA!
There is no way anyone can really interpret that to mean non-coding DNA = Junk, the way you do.
You say: "He is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk."
NO. Cryptogenomicon says:
"There's likely to be other nonfunctional DNA "junk" too..."
How, how could he be more clear?
He says "nonfunctional DNA junk". But you say that he "simply means ncDNA and not necessarily useless junk."
Do you think "useless" is different from "nonfunctional"? Or what, what, are you going on about?
- 27 September 2012 at 23:27
- Diogenes said...
Why are you so selectively quoting from Cryptogenomicon? You must be very selective indeed to tiptoe around his unambiguous statements.
Here is what Cryptogenomicon says:
"The human genome has a lot of junk DNA... the genome is mostly nonfunctional...
...the main ENCODE paper cites neither Orgel/Crick [1980] or Sapienza/Doolittle [1980]; what this means is, regardless of what we read in the newspapers, ENCODE is not actually trying to interpret their data in light of the current thinking about junk DNA...
...most reasonable people (ok, I) would say at this point that the human genome is mostly junk...
...The newspapers add, "therefore it's not junk", but that's a critically incorrect logical leap... But as far as questions of "junk DNA" are concerned, ENCODE's definition isn't relevant at all."
Why do you not mention those unambiguous statements?
He defines "Junk" quite precisely and it's NOT non-coding DNA as you claim!
Again, this is the article that Max Libbrecht of ENCODE cited approvingly three times-- twice at Reddit, once at Mike White's blog.
- 27 September 2012 at 23:31
- Diogenes said...
@TheMayan: "He [Cryptogenomicon] is using the term junk DNA in its "colloquial" sense which can simply means ncDNA and not necessarily useless junk. As many already know, important function has been found in transposons."
I am tired of dishonest ID creationists using innuendo and insinuation to IMPLY that most nucleotides in most transposons have been shown to be functional.
To the extent that your sentence has meaning, it is a lie-- although to be fair, you are using vague waffle words, to just insinuate that most nucleotides in most transposons have been shown to be functional.
If you actually came out and really said that, then you would be a liar. But admittedly, you don't say that outright. You say:
@TheMayan: "As many already know, important function has been found in transposons."
Like all ID creationists, you write sentences without articles or quantities or numbers in front of the nouns. Thus your sentence says "function has been found", with no articles or quantities or numbers in front of the noun "function." Thus you insinuate without saying that most nucleotides in most transposons have been shown to be functional.
Cunning. This is a very common ID creationist writing style, to deceive by insinuation, without outright lying. It's practiced; ID creationists are drilled on it.
There are million transposons. They make up 45 percent of your genome, about 1.4 BILLION nucleotides. The experiments you cite show that 10 nucleotides, and 10 nucleotides there, have been co-opted as regulatory elements to control genes.
A few transposon genes are used at the organismic level-- less than a dozen out of one million transposons.
So if we count by nucleotides within transposons, only a fraction of a fraction of all nucleotides within transposons have been shown to be functional.
But you use insinuation to claim them all for "function"! Cunning. You have learned from Jonathan Wells and Casey Luskin, all right.
- 27 September 2012 at 23:43
- Diogenes said...
Regarding your assessment that Larry Moran and Michael Eisen appear to contradict each other:
They don't contradict. It was a misunderstanding, later resolved. They are in agreement about Junk DNA.
Michael Eisen wrote a post in which he said that newspapers claim ENCODE just proved non-coding DNA has a function. But Eisen objected, basically saying that scientists already knew non-coding DNA had a function.
However, his choice of words was confusing. Larry Moran thought that Eisen was saying scientists know there's no Junk DNA, so Moran wrote a post called What in the World is Michael Eisen Talking About?
Your quote from Larry comes from that first post: "Here's the interesting thing. Many of us are upset about the press releases and the PR because we don't think the ENCODE data disproves junk DNA. Michael Eisen's perspective is entirely different. He's upset because, according to him, junk DNA was discredited years ago"
Moran was wrong in interpreting Eisen's point. Eisen meant that scientists have always known non-coding DNA can have function, but Moran thought he meant there is no Junk DNA.
This confusion was cleared up shortly thereafter. Eisen later wrote another post where he expressed himself clearly.
Eisen: "Given that such a large fraction of the genome is biochemically active... it is simply impossible for such a large number of molecular traits to have been driven to fixation by selection – argues strongly that most biochemical events do not contribute significantly to fitness... ... it is all but impossible that we would still exist if every new molecular event had a strong phenotypic effect.
This, of course, does not mean that all these molecular events do nothing... But we are generally interested in different types of function – things that did arise through natural selection, are maintained by purifying selection, and whose disruption will cause a disease or other significant phenotype... here, I think we should once again take our cue from Kimura... meaning that adaptive change had to be demonstrated, not assumed. We need to apply the same logic to molecular interactions." [Source]
Moran later approvingly cited Eisen's later post.
To sum up, they're in agreement on three points:
1. Non-coding DNA is NOT junk DNA.
2. Scientists have known for a long time that non-coding DNA has many functions.
3. There is positive evidence that most of your genome is Junk, meaning it cannot have organism-level function that constrains the DNA sequence.
- 28 September 2012 at 00:44
- Diogenes said...
"There are many scientist today who have said and are still saying that much of what we have discovered was once thought to be useless junk DNA"
No, not many; a few scientists, but many journalists.
And, as Gregory would tell you, neither the journalists nor the scientists who say "Long dismissed as junk..." ever have citations to old-times scientists saying (for example) that regulatory elements were all junk, or that all non-coding DNA were junk, etc.
As Gregory has said: beware unsourced citations. Beware phrases like "Long dismissed as junk..."
In the phrase "Long dismissed as junk..." the verb is in passive tense. Passive tense verbs allow the speaker to NOT identify who, precisely, did the dismissing. Who dismissed all non-coding DNA as junk? Who dismissed regulatory elements as junk, or RNA genes as junk?
If you say "Long dismissed as junk..." the passive tense verb absolves you of the responsibility to cite a source that did the dismissing.
If you used an active tense verb, you would have to name names and give citations. "Prof. Smith dismissed non-coding DNA as junk..." No, if you said that, Prof. Smith would object.
Beware unsourced citations and passive tense verbs.
- 28 September 2012 at 00:56
- Misc said...
@ Dio;
What is your take on Creation activists? As for me posting your real name, why bother, because of course you will deny it, but we both know who you are on CP, you are the one whom calls people *liars* on a regular basis. Hey, perhaps if you post as Igor or L Moreau no one will notice..
- 28 September 2012 at 01:32
- Diogenes said...
Misc thinks I comment at Christian Post, posing there as a theist, but he will not reveal to me my "real name."
Misc: "As for me posting your real name, why bother, because of course you will deny it, but we both know who you are on CP, you are the one whom calls people *liars* on a regular basis"
So, you will not reveal to me my real name. Oh, drat. So what bad things do you think I would do with that information, if you revealed to me my real name?
And you think I am that person, because... he calls you a liar. And I too call you a liar.
Just wondering... Do you get that a lot?
Also. Do many people call you insane? If so, is everyone who calls you that also me?
Do you see me everywhere now? Out your basement window?
When your neighbor's dog tells you to do bad, bad things, do you think that's me too?
- 28 September 2012 at 13:32
- snoopy said...
- This comment has been removed by the author.
- 28 September 2012 at 16:21
- Misc said...
Hey Igor, I mean L Moreau, I mean, Diogenes,
Why didn't you answer my question on what your take is on 'Creation Activists'?
And yeah, I'm not revealing your real name because of course you will lie and say it isn't you, just like Igor and L Moreau are not you. You're a joke and fortunately a no body in the world of Science, except a Larry Moran groupie kicking and screaming on a sinking ship.
BTW, you never called me a liar on CP, but you do on a regular basis with many other people there, not to mention here, reddit, Larry's blog (there you did call me a liar), HP blogs and the list goes on and on.
Hey, why don't go back to UD and finish what you started, oh yeah,, you ran off with your tail between your legs after you made a complete ass of yourself.
Later looser..
- 28 September 2012 at 16:25
- The whole truth said...
Ewan, will you please respond to all the questions that have been asked of you?
- 29 September 2012 at 01:19
- Diogenes said...
Misc: Later looser..
Misc, if you do not start spelling your ad hominems correctly, you will loose this debate as you always loose.
Misc asserts that I comment at Christian Post under my "real name" which he will not reveal to me, because if I knew my real name, I might, I don't know, get superpowers or something. He's vague on why he won't tell me my "real name." At Christian Post, of all places.
Misc: Hey Igor, I mean L Moreau, I mean, Diogenes...
And yeah, I'm not revealing your real name because of course you will lie and say it isn't you, just like Igor and L Moreau are not you.
What other names do you call me by? Genghis Khan? Cthulhu? Pazuzu? Voldemort?
When you hear a voice at night telling you you're worthless, do you think that's me too?
Wikipedia: The Fregoli delusion, or the delusion of doubles, is a rare disorder in which a person holds a delusional belief that different people are in fact a single person who changes appearance or is in disguise. The syndrome may be related to a brain lesion and is often of a paranoid nature with the delusional person believing themselves persecuted by the person they believe is in disguise.
Does it comfort you to believe that when you are made to look foolish everywhere on the internet, there's only one person behind that?
I suppose it is comforting believing that only one person is vastly smarter than you. Alas, the truth is that there are many.
- 1 October 2012 at 23:38
- Misc said...
@ Diogenes
I posted two replies addressing your BS on Moran's blog, but it appears he is now moderating and not sure if it will get through. If it doesn't, not wasting anymore time on a Psycho such as yourself.
"What other names do you call me by? Genghis Khan? Cthulhu? Pazuzu? Voldemort"
Nope, just Igor and L Morea as you were too chicken to face Shapiro on his confrontation about you, and you kept whining all over the place he banned you, which he did not. BTW, he just did a similar assessment on your ideology zealot friend Kwok, wonder why he wasn't 'banned'
To put my suspicions to rest about CP, why don't you tell me your first name? This person's communication style is strikingly similar to yours, such as calling people liars left and right, using the phrase 'Waaaaahhhh' and an over the top hate for ID, to name a few.
So go ahead, set the record straight and can check around to see if your telling the truth...
- 2 October 2012 at 10:37
- Diogenes said...
you were too chicken to face Shapiro on his confrontation about you
Shut your lie-hole, psychopath. I wrote a bunch of comments at Shapiro's blog and they were all deleted.
I must conclude Shapiro is terrified of me, because it would explain why he deletes ALL my comments.
Why doesn't Shapiro go over to my blog and comment? What's he afraid of? Go tell your cowardly wuss Shapiro to attack me at my blog, or any blog where I can't be banned.
Why doesn't he show up again at Mike White's blog? Because at Mike Whit'e blog, I kicked his tail cherry red and he ran away. Gutless Shapiro will never return.
I wouldn't delete his comments, but he deletes mine. That's because I'm not afraid of him; he's terrified of me.
Shapiro wrote an entire blog post that consisted of no scientific evidence, no data, nada, just ad hominem attacks on me. He's got nothing.
and you kept whining all over the place he banned you, which he did not
How do you know? Present the evidence he did not ban me, or shut your lie-hole.
Igor and L Morea
You think I am them and many other people because so many people on the Internet are vastly smarter than you and defeat you in debates.
You don't know any science, and at no point have you posted any comment with any scientific evidence. All you do are ad hominem attacks, like your cowardly Ken doll, that ignorant gutless Shapiro.
It makes you feel better to imagine everyone smarter than you is the same person, but they're not. There are many, many, many people smarter than you who defeat you in debates.
- 2 October 2012 at 11:03
- Misc said...
"I must conclude Shapiro is terrified of me, because it would explain why he deletes ALL my comments"
Riiight, here is a direct quote by him:
03:50 PM on 09/21/2012
"Diogenes is upset that I quoted his words that were posted on my blog. He claims that he has been blocked from posting further comments here. I have not seen any of them"
> http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html
(Isn't it ironic that both L Morea and Igor's only 'fan' is you, and when I (rjop) called L Morea out, he never showed up again but immediately after we see Igor show up, funny that)
We then have Shapiro's statement to your friend Kwok:
01:48 PM on 09/30/2012
"Don't worry about having your posts rejected as abusive. Since I singled out your comments for the blog, you are entitled to have your say"
Sorry, I will take his word over yours any day.
"I must conclude Shapiro is terrified of me"
So says the person who appears to suffer from delusions of grandeur. Next I suppose you will say Ewan is 'terrified' of you.
Also, you didn't answer my question on what your first name is, why do you think this is so?
- 2 October 2012 at 11:44
- Misc said...
- This comment has been removed by the author.
- 2 October 2012 at 12:11


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Web Stories
2004 Nobel winner to discuss future of physics, April 29
Posted April 22, 2005; 01:37 p.m.
Nobel laureate David Gross, the Thomas Jones Professor of Mathematical Physics Emeritus, will speak on "The Future of Physics" at 8 p.m. Friday, April 29, in A02 McDonnell Hall.
Gross won the 2004 Nobel Prize in physics with Frank Wilczek, who earned his Ph.D. from the University in 1975, for a discovery they made while working together at Princeton. They were recognized along with David Politzer for their fundamental insights concerning the force that holds the parts of an atomic nucleus together.
Now director of the Kavli Institute of Theoretical Physics at the University of California-Santa Barbara, Gross was a faculty member at Princeton from 1969 to 1997. He received a MacArthur Foundation Fellowship in 1987 and the Dirac Medal in 1988.
In his talk, designated as the 30th Donald Ross Hamilton Lecture, Gross will discuss 25 questions that might guide physics -- in the broadest sense -- over the next 25 years.
The lecture is sponsored by the Department of Physics.

subset: commoncrawl


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This Friday coming (11-11-12) the regional "NWTF-Women in the Outdoors" is having a gala fund raising dinner called "Camo and Pearls" in Orange Park, FL, part of the festivities is the choosing of a "2012 Miss Camo and Pearls". They asked my daughter to "do up" the crown thingy for the winner, so....., she came up with the one below. I thought it was kind of cool. Thanks for taking a look.
Oh, and she came up with a new ear-ring design using the tips of wing feathers I'll post those below too.


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Here is one currently on ebay.
Here is one currently on ebay.
"You know I love the guy but I swear he writes like freaking Yoda."-Dean Winchester
R12:2-Be Transformed
It looks like 4 reasons to NOT buy Transformers if you ask me. Only you guys who are regular enthusiasts know what Alternators and MPEs are, and how they far outweigh anything else in terms of quality. I can make exceptions for the Classics, but their proportions to each other are pretty 'off.' Also, they need to quit painting Prime white and calling him Ultra Magnus. The latter character needs a completely redesigned mold to make him look like the classic G1 character that Magnus was (and poseable at that). I've never seen one good Magnus toy, as a matter of fact. The G1 with non-poseable body armor wasn't worth it either, but the look for display was cool and the car carrier functional.
Oh well. No one understands...
BAD Pts Need: R5-C7 lf leg (x2), , R4-P44 right leg BAD Pts Offered For Trade: PM me - I have lots of parts now including BG-J38!. New Kyle Katarn is also available.
it was a worthwhile repaint to me, because he also came with another jet. together they should've been $30 according the pricepoint of each of the original versions, but instead it was $20, and therefore literally a greater deal than the sum of it's parts.
Nachos are the right of all sentient beings.
The guns... They've stopped!
- Dan Akroyd, Star Wars Episode IV - A New Hope
Okay... So I just read a rumor that War Within Grimlock is finally in the works.
So, the War Within Titanium Series looks like this so far:
Optimus Prime (out of production)
Thundercracker (out of production, but still available on hts.com)
Jetfire (out of production, but still available on hts.com)
Starscream (current)
The Fallen (current or forthcoming)
Megatron (forthcoming)
Wikipedia (of all places) also lists forthcoming Ultra Magnus, Sunstorm, and Skywarp (though I don't recall any but Skywarp actually appearing in the comic).
So if I were to decide to get these, the only one who's somewhat tough to find now is Prime, right? I'm not missing anybody on my list, in other words, correct?
That's my jacket!
MPE 06 is SKYWARP!
He'll have a new headsculpt too! No pictures are yet available. But they are also increasing the amount of metal parts in the mold that MPE Starscream did not have, thereby possibly even making it more palitable for Hasbro to import.
Very nice.
BAD Pts Need: R5-C7 lf leg (x2), , R4-P44 right leg BAD Pts Offered For Trade: PM me - I have lots of parts now including BG-J38!. New Kyle Katarn is also available.
That's awesome news! Any word on who will have this exclusive? (Please say Target. I've had much better luck with Target exclusives over the past year than Wal-Mart exclusives.)
Also, anyone know the story on this? I found that on hasbro.com/transformers, but when I click on it, it just takes me to the Transformers listings on hasbrotoyshop.com. Is there a code you have to enter? And does anyone know what these magnets are? I'm guessing the insignias based on the image, but that's not necessarily a given.
That's my jacket!
Chux, i believe JT has those magnets so he should be able to shed more light on them. i think they're just the Autobot and Decepticon insignias.


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By Stephanie Rebman/ NEMS Daily Journal
A Tupelo man died Saturday near the Palmetto community after what police believe could be a hit and run.
According to the Lee County Sheriff's Department, police responded to the scene at 5:49 p.m. and Richard Allen Darby, 50, of Tupelo was pronounced dead at the scene.
Police said a preliminary investigation shows Darby appears to have crashed his car and ran off into a ditch. When police arrived they found him laying in Graham Road not far from his vehicle.
The incident occurred just south of the intersection with Mitchell Road.


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Results 1 to 4 of 4
Thread: Neon Tetra-Large Bump?
06-08-2013, 08:57 PM #1Junior Member Guppy
- Join Date
- Apr 2012
- Posts
- 1
Neon Tetra-Large Bump?
Hello, I have a Neon Tetra with what looks like a huge blister. It has had gotten a large black dot on its side a while back, its spine is now curved but it seems healthy and happy otherwise (its color has been as brilliant as all the others). Recently (in the past couple of days) the black dot formed into a rather large whitish blister looking thing. Below are some images of the blister, but unfortunate I don't have any of the original affliction of the black dot.
Some specs my tank. 20 gallon with 11 tetras and many live plants. I do weekly water changes of 1/3 to 1/2 of the water. I have not introduced any new fish in months, long before the black dot appeared.
If anybody might know what this is I would be grateful if they could let me know. thanks for your time.
06-08-2013, 09:06 PM #2Banned CoryCat
- Join Date
- May 2013
- Location
- S. Heaven
- Posts
- 149
Looks like some kind of fungus, and some fin rot. I would get some fungal meds and treat the entire tank. API makes some, as well as Jungle. Wal Mart carries Jungle I believe. Follow the directions, and hopefully it will clear up.
You need to get him out of there and away from your other fish before he infects them all with something unknown. Especially with the mention of his spine being curved. His tail is rotting away, as well, and he looks unwell. Just put him down. Never keep ill fish with your well fish.
Agreed with LH. It's a sure bet he's going to kick it soon. That tail looks like it's going to fall off. Same thing happened to my Black Phantom Tetras, so it could be bad breeding which led to incurable mutations and secondary diseases. Or maybe Neon Tetra Disease. =/ Either way, it's probably uncomfortable and you don't want to risk infecting the other inhabitants.Adventures in Aquaria - The KevinVA Story
When in doubt, ask yourself... W.W.L.S (What would Lee Say)?
Have a fish problem? Fill out and post this completed questionnaire in the General Aquarium Forum, when you start a new thread.


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Web Stories
Alumna to discuss women's leadership
Posted March 5, 2009; 10:31 a.m.
Cedar Crest College President Carmen Twillie Ambar, a Princeton graduate alumna, will deliver the keynote address at an American Council of Education Network event on women's leadership scheduled for 8 to 11:30 a.m. Friday, March 13, in the Multipurpose Room B of the Frist Campus Center.
The theme of the organization's fourth annual Women of Color Breakfast is "Modeling and Advancing Women's Leadership in the Age of Globalization."
Ambar earned a master's in public affairs in 1994 from the Woodrow Wilson School of Public and International Affairs, where she later was assistant dean of graduate education. She was named president of Cedar Crest College in Allentown, Pa., in 2008 after serving as dean of Douglass College at Rutgers University, where she oversaw several initiatives aimed at developing women as leaders.
A $25 registration fee is required to attend. To register, e-mail Barbara Gaba.


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Results 1 to 3 of 3
Thread: Please Help..
19th September 2013 12:58 PM #1
- Join Date
- Sep 2013
- Posts
- 7
Please Help..
Hi. I'm on my 7th month of pregnancy and I just experienced bleeding... is it normal to experience such? This is my first pregnancy.
27th September 2013 09:13 AM #2
Hi Soontobemum
Sorry for the delay in reply. Bleeding can occur in pregnancy for lots of reasons. Some serious some not so. It is always important to have bleeding checked out by your practitioner. How did you get on?Hidden Content Mumof2IVFmiracles Hidden Content
2nd October 2013 06:31 AM #3


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Turning wine staves into flooring is a tricky process because a wine barrel has both longitudinal and latitudinal curvature. Individual staves are also wider and thicker in the center, tapering to smaller dimensions at the ends. In addition, the inside of the wood is infused with wine.
But all those drawbacks make for a better floor, says WineWood's Charlie Cramer. "What I look for is old barrels that have a lot of character to them," he told us. "We pressure wash the wood but let some of the color stay in the deep parts, which gives it a nice patina."
The company has developed a patented process that flattens the boards, which are then sanded smooth by hand. The process is zero-waste; leftover wood chips are sold to cooking stores for use in barbecuing.
The flooring itself is sold in a variety of styles. One version, called Wine Barrel Flooring, shows off the original shape of the staves, complete with nail holes and light-colored bands that reveal portions of the wood which spent its earlier life concealed behind the barrel's straps.
There's also a more traditional-looking engineered variety that mounts three 2-inch wide strips across in a standard cedar backed 6-inch wide tongue & groove configuration that's 7 feet long. "That's a completely different look; the pattern is made up of pieces that are all a bit different," said Cramer. "A lot of people like that look." All the engineered floors are manufactured using zero-VOC adhesives and supplied unfinished.
Cramer believes that the highest demand for WineWood will come from restaurants and other hospitality-oriented businesses, as well for use as flooring or wainscotting in home wine cellars.
Get More Info!


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Term: aura
Aura: A shell or layer of astral substance that surrounds and permeates the physical body. A halo or sheath of spiritual light/energy that surrounds a person and can be seen by clairvoyants.
source: The Essential Golden Dawn, by Chic Cicero & Sandra Tabatha
An emanation or set of emanations that extends around objects and animals, including the human body. There are multiple beliefs as to the number of different types of auras that extend around the body. Some say there are seven, others say five or three.The aura extends from just above the surface of the skin out to infinity. It becomes more and more ethereal as it extends further from the body, and beyond about three feet even people who can see auras are not able to detect it. The smoothness of each aura level, as well as the pureness of its color, are said to indicate the conditions of the person they surround. In the three-fold system of interpretation, the area closest to the skin is said to relate to your physical well-being. Outside of this physical aura is the mental aura that relates to your state of mind. It could be called the psychological aura. The third part of the aura is the spiritual element. It relates to your spiritual advancement and is further away from the body than is the mental aura. Actually, all three are said to interrelate and overlap according to those who see auras. The chakras, several spinning wheels of vivid color in the aura in front of the body, are also said to be visible.Donald Michael Kraig
Aura: Human energy field that surrounds and interpenetrates the body. The aura contains the chakras and nadis or meridians.
source: Sacred Path of Reiki, by Katalin Koda
An egg-shaped sphere of energy extending as much two to three feet beyond the physical body and viewed by clairvoyants in colorful layers that may be "read" and interpreted.
It includes layers outward from the physical: the Etheric, Astral, Mental, and Spiritual bodies. The aura is also known as the "magical mirror of the universe" in which our inner activities of thought and feeling are perceived in colors. It is also the matrix of planetary forces that shapes and sustains the physical body and the lower personality.
Clairvoyants may analyze the aura in relation to health, ethics and spiritual development, and the aura can be shaped and its surface made to reflect psychic attacks back to their origin.
Suggested Reading:
The human aura is the body's external energy field which is a manifestation of the internal energy system's central core.Carl Llewellyn Weschcke
Introduction. Seeing the Aura is one step, but without the ability to read and Interpret is an "empty" skill. To analyze and interpret observations is a key step to success in nearly any endeavor. Always we start by organizing the ...
Relevance: 100%
Clairvoyant "reading" of the aura to determine the health, character and spiritual development of the person (or animal) by the colors seen. The main factors to consider are: The various fields about the body reflecting the etheric, astral, ...
Relevance: 100%
Mark Smith says that anyone can learn to see auras in only 60 seconds. In his book, Auras: See Them in Only 60 Seconds!, he breaks this instruction down into a few easy steps: Stand the subject eighteen inches to two feet in front of a bare white ...
Relevance: 100%
Introduction: As our goal is to develop the ability, there is an advantage to selecting a teen age or young adult female as your subject. The reason simply is that her aura energy is higher than that of most other subjects. Stand the ...
Relevance: 90%
An interesting law of science is that wherever there is an electrical current there is a concomitant magnetic field. The human body is filled with electricity, especially in the nerves and muscles. It follows, therefore, that there is a field or ...
Relevance: 73%
We can create powerful mind/body interaction to promote better health and fitness. Aura self massage procedures can be adapted to many specific goals. The following is for self-healing. Physical Relaxation. Assume a comfortable seated or ...
Relevance: 43%
Introduction. Our goal here is not so much formulaic as it a reminder of what romance and sexual interaction can be, as it was when "we were young and filled with anticipation for the great adventure that is Love's Promise." Even ...
Relevance: 40%
Introduction. Seeing your own aura has huge benefits for personal health management and advancing your Psychic Development and Self Empowerment. Stand in front of a mirror at least eighteen inches away, further if possible. Place yourself with a ...
Relevance: 33%
The Hermetic Order of the Golden Dawn described the aura "as an etheric structure filled with astral energies" and serving as the "magical mirror of the universe" in which all objects of perception and all inner activities of thought and ...
Relevance: 32%
Introduction. This is, in some ways, one of the more complex procedures because of the various items listed in the following tables that need to be memorized and visualized before the actual exercise is undertaken. The psychic Centres are truly ...
Relevance: 18%


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"How the Sochi Games grew so expensive is a tale of Putin-era Russia in microcosm: a story of ambition, hubris, and greed leading to fabulous extravagance on the shores of the Black Sea. And extravagances, in Russia especially, come at a price."
The new road and railway to Krasnaya Polyana, the mountain resort that will host the ski and snowboard events of the Sochi 2014 Winter Olympics, start in Adler, a beachfront town that has become a boisterous tangle of highway interchanges and construction sites. A newly opened, glass-fronted train station—the largest in Russia—sits like a sparkling prism between the green and brown peaks of the Caucasus Mountains and the lapping waves of the Black Sea.
The state agency that oversaw the infrastructure project is Russian Railways, or RZhD. The agency's head is Vladimir Yakunin, a close associate of Vladimir Putin. It oversees 52,000 miles of rail track, the third-largest network in the world, and employs nearly a million people. The 31-mile Adler-to-Krasnaya Polyana project is among its most ambitious, reminiscent in its man-against-nature quality of the Baikal-Amur Mainline railway built by the Soviet Union in the 1970s and '80s across the remote taiga forests of the Russian Far East. Now, as then, grandeur and showmanship are as important as the finished project. Putin sees the Sochi Games as a capstone to the economic and geopolitical revival of Russia, which he has effectively ruled for 14 years. The route connects the arenas and Olympic Village along the Black Sea with the mountains above. Andrey Dudnik, the deputy head of Sochi construction for RZhD, is proud of his company's accomplishment, given the region's difficult terrain and the rushed time frame for finishing construction. "Few people believed," he says. "But we did it."


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Fischer Audio Aleph
Small IEM from the Signature series.
Fischer Audio Consonance
Frequency range: 20-20000 Hz. Sensitivity: 105 dB. Impedance: 18 Ohm. Input power: 65 mW. Color: black, red, white. Box: gift box. Set: ear tips, plastic case.
Fischer Audio Consonance V2
"The Consonance V2 is a pair of earphones manufactured by Russia-based Fischer Audio which forms part of their Fundamentals lineup. With its in-line microphone and remote control unit and low impedance, it appears to be aimed squarely at smartphone users. As you can tell from the name, the V2 is their latest revision of the well received Conosnance. However, as I have no experience with its..." --fonzler
Fischer Audio Consonance White Earphones, Headphones for New Music Re-Vitalized
"Introduction: Sometimes in life, things kinda catch you by surprise when you least expect it and this is exactly what I found with the Fischer Audio Consonance Earphone. When I purchased my KEF M200s, I thought this would be for life; these were most accurate sounding IEMs I had heard to date. However, there was a downside like with most things in life and that was the..." --mcook1970
Fischer Audio Daleth
Universal fit in ear monitor.
Fischer Audio DBA-02
" Introduction A warning before we even get to the review. This is kinda lengthy. I'm not sure how it got so long since it is just one product but yeah it is a bit long. Fischer Audio has slowly gained popularity over the last year or so and there was quite a buzz on them but nothing interested me enough to go out and purchase them. That changed when LFF posted a review on the DBA 02 and..." --rawrster
Fischer Audio DBA-02 Mk II
" The DBA-02 Mk IIs are getting a lot of the same fame and respect their initial version siblings got. While initial comparisons suggest the Mk IIs are not as distinctive as the originals in shining with as fearless a midrange and treble, the major sonic character seems to have carried. (I never heard the originals but have gathered this from others' opinions.) And..." --ScuderiaHeadFi
Fischer Audio Enigma
Frequency range: 8-22000 Hz. Sensitivity: 102 dB. Impedance: 18 Ohm. Input power: 60 mW. Length of a cable: 1.25 m (4.13 ft). Color: black Box: gift box Set: ear tips, pouch.
Fischer Audio Eterna
" So I owned a pair of CX300II's for over 4 years and finally decided to get a new pair. Of course, I was looking to upgrade from the sennheiser in terms of Bass and overall quality. After reading Jokers 131 IEM thread, I decided to get these. I am extremely pleased with my purchase. I as looking for a IEM that I would use for 1-2 hours at a time on my way to school, and these are..." --2enty3
Fischer Audio Evolution
" I hope this ongoing review will help you guys out a little. I will keep adding to this as time progresses and will maybe end up reviewing more Fischer IEM's in this thread. I am not a professional reviewer like some of you guys here and English isn't my native language so bear with me. Now, onwards! My main mission objective is to find the best sub-$100 IEMs in the world. After reading..." --Negakinu


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Which Tour is Right For Me?
At Escape Adventures we really love what we do. For us, the adventure begins with a favorite trail system, mountain, or national park, and a dream committed to many hours of research and development. Then, because true joy in adventure is sharing it, we reach beyond the masses to the very specific, very unique market who we know will be up to the adventure. But with so many choices, how do you decide which tour is right for you?
Choosing the Right Mountain Bike Tour
Mountain Biking is something we love to share. It provides an opportunity to see the back country in a unique and exciting way and lets you experience a connection with nature. Our tours are designed to accommodate many different riders at various skill levels.
Three easy steps to picking a mountain bike trip:
- Determine when you can travel. Our trips are scheduled when the weather is the most favorable in that area, so your availability can help to narrow down the choices.
- Pick a few trips that interest you within this timeframe. Read each trip description to get a feel for what each trip has to offer.
- Finally, call us for availability and specific questions. Our staff and guides are available to help. You can request an itinerary or speak with a tour guide for more details on your trips of interest. If you are traveling with friends, we can suggest a trip that suits everyone.
On our tour schedule page you may notice that the mountain bike tours are also rated 1 through 10. Please see the fitness and technical scales on our trip ratings page and look for the graphics on our itineraries and trip pages.
Choosing the Right Road Cycling Trip
Are you interested in mountains and coastlines, culture or solitude? The first step in picking a road cycling tour is choosing your ideal destination. You can be assured that we have chosen the best riding on the most scenic roads in the country.
Our road tours are rated by the mileage and overall fitness level needed to complete the rides. The rating is based on an average of each day's climbs, elevation bases, and ride lengths. For example, one trip with longer rides followed by a rest day may be rated the same as a trip with shorter daily rides and no rest days. We understand that mileage is a concern, so if you enjoy an easier pace and prefer scenery to speed, a trip with less than 250 miles is a great choice. If you enjoy a good century every now and then, look forward to the climbs, and love a good workout, then a trip with more than 250 miles is your best choice.
You may notice that some tours list a range of miles (ie. 200-250). On these trips we offer optional rides that can increase the overall distance of the trip. Regardless of mileage and hills, each tour is supported by our professional and attentive guides riding with the group and driving the support vehicle.
We are happy to answer your questions and help you select a trip based on your experience and interests.
Choosing the Right Hiking Tour
We have been outfitting the West for nearly two decades, and we're excited to show you what we've found. There's no better way to appreciate the beauty and solitude of nature than by foot. Most of our tours are designed to accommodate all levels, but we do offer a select few that are more difficult based on the distances and elevation changes. Hiking tours are rated on three levels:
- Easy: Gentle terrain at a leisurely pace.
- Moderate: Longer hikes with mild scrambling.
- Strenuous: Extensive mileage at an athletic pace.
Call us to request a daily itinerary with more details or to speak to a guide.
Choosing the Right Multi-Sport Tour
Our multi-sport tours offer a variety of exciting activities such as rafting, biking, kayaking, hiking and rock climbing. Multi-sport touring is great for people who like to sample a bit of everything an area has to offer. Just about anyone who has a taste for the outdoors and is inclined to try different activities will enjoy our trips. Specially trained and experienced tour leaders will ensure a great time for guests of all ability levels. Each Escape multi-sport trip is slightly different than the next, perfectly tuned into what each destination has to offer. Whether you choose a hike and bike tour with a bit of rock climbing, or a trip with canyoneering and rafting, we're sure you'll love it.
Just ask yourself where you would like to go and what type of activities interest you.


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Sen. Vitter holding up Obama appointments until drilling permits are issued for the gulf.
Sen Mary Landreau tried the same tactic last Fall but was duped into believing they would issue new permits after the moritorium was lifted. Well, it was lifted, she approved an appointment but no permits have been issued!


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Main Content
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Get a winning look that will last in these Triumph walkshorts by O'Neill!
- Contrast interior waistband
- O'Neill logo buttons
- Single button & zip fly
- 22" Outseam
- Silicone washed for softness
- Imported
- O'Neill yarn dye plaid chino walkshort
- 70% Polyester/30% Viscose
- O'Neill logo embroidery
- Two front pockets
- Two back pockets with button closure
- Made in the USA
- Brand: O'Neill
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