Monday, September 05, 2016

How many lncRNAs are functional: can sequence comparisons tell us the answer?

A large percentage of the human genome is transcribed at some time or another during development. The vast majority of those transcripts are very rare transcripts that look very much like spurious products of accidental transcription initiation at sequences resembling true promoters. They have been rejected by genome annotators. They do not define genes. They are junk RNA. Pervasive transcription does not mean that most of the genome is functional.

Among the transcripts is a class called long non-coding RNAs or lncRNAs. These are usually defined as capped and polyadenylated transcripts longer than 200 nucleotides. Many of them are processed by splicing. They look a lot like mRNA except they don't encode any polypeptides.1

We don't know how many of these RNAs exist because different labs use different criteria to describe them. Some databases exclude low abundance lncRNAs and some include non-polyadenylated RNAs. There is general agreement that they number in the tens of thousands. A common number in the scientific literature is 60,000 lncRNAs.

Theme
Genomes
& Junk DNA
The latest build of the human genome lists 14,727 lncRNA genes [Ensembl Human Genome] but most workers in the field think this is too low. Let's be clear about these numbers. The Ensembl description is just wrong. They are assuming that the existence of a lncRNA means there is a gene that produces that RNA. But since we don't know whether these RNAs have a biological function, this must mean that Ensembl uses a very loose definition of "gene"—one that includes any sequence that's transcribed whether or not it has a function. This seems to be what they are doing since they include pseudogenes in their gene count and they include an additional 198,000 "gene" transcripts. This is begging the question.2

I will use a definition of "gene" that restricts the term to those sequences that produce a functional product [What Is a Gene?].
A gene is a DNA sequence that is transcribed to produce a functional product.
The key question is not how many lncRNAs there are but how many are functional. That's the question I want to address but, before doing so, let me make it clear that even if all 60,000 lncRNAs are functional it doesn't make much difference in the junk DNA debate. I'll illustrate that with a simple calculation. Assume that the average size of a lncRNA gene is 1,000 bp. If all 60,000 are functional, that corresponds to only 2% of the human genome.

We should also recognize that the terminology is confusing and it muddles the issue. Most workers assume the default explanation is that lncRNAs are functional. As a result, the term has come to be associated with presumed functional sequences. My colleagues, Alex Palazzo and Eliza Lee wrote a review on this topic last year and one of their main points is that this assumption is invalid (Palazzo and Lee, 2015). The true default assumption, according to them (and me), is ...
In the absence of sufficient evidence, a given ncRNA should be provisionally labeled as non-functional. Subsequently, if the ncRNA displays features/activities beyond what one would expect for the null hypothesis, then we can reclassify the ncRNA in question as being functional.
I'll be addressing a paper that looks at sequence conservation as an indicator of function so it's important to keep the correct null hypothesis in mind. We will be looking at the subset of ncRNAs that fit the lncRNA definition but it's hard to overcome the bias associated with the term since it has come to imply function. I'll just call them long low abundance transcripts or LOLATs.

Find a function

How many of the 60,000 or so LOLATs have a biological function? There's only one way to answer that question and that's to examine each and every one of them to see what they do inside the cell. Only a small number of these transcripts have been examined in this way. It's hard to get a handle on just how many have a proven function but I doubt it's more than 200 in humans. That's a small percentage of the 60,000 LOCATs.

Abundance/Concentration

In the absence of a proven function, there are several indirect indicators we can use to make a decision. One of them is the overall abundance of a given LOLAT inside the cell. It is generally agreed that almost all of them are present at less than one copy per cell [reviewed in Palazzo and Lee, 2015: see figure]. It's very difficult to see how anything could have a true biological function at such a low concentration, although that hasn't prevented some wild speculation and bizarre scenarios.

Based on what we know about the levels of these RNAs inside the cell, it's safe to conclude they are most likely due to spurious transcription with no function (junk RNA). The concentration data provides no support for the idea that most of those 60,000 transcripts are functional; therefore, the null hypothesis cannot be rejected.

Specificity

Most of the LOLATs are present in only one cell type or tissue or in a small number of tissues. Many of them are only found in testes or brain—tissues that are notorious for producing junk RNA based on data going back over 40 years.

Proponents of function often claim that patterns of restricted expression are an indication of function. This is a bad argument since spurious transcription—the default explanation—should show the same thing. Different promoters/enhancer are exposed in different tissues and if spurious transcripts come from those regions then they will show restricted expression.

I don't understand why this argument for function is so widely believed. Restricted expression (specificity) does not cause us to reject the null hypothesis since the result is consistent with spurious transcription.

Sequence conservation

The "gold standard" for assessing function is sequence conservation. If the sequence of the LOLAT is conserved in other species then we can assume that it's under negative selection. It must have a function.

How many of the 60,000 LOLATs show evidence of conservation? All of the literature published so far indicates that this number is very low (<1,000). The evidence is reviewed in a paper published on the Nature Reviews Genetics website (advanced online publication).

Ulitsky, I. (2016) Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nature Reviews Genetics: advanced online publication, Aug. 30, 2016 [doi: 10.1038/nrg.2016.85]

You have to read the paper carefully in order to understand the main message, which is that very few LOLATs show any evidence of sequence conservation. The null hypothesis cannot be rejected on the basis of sequence conservation. The conclusion, which is consistent with most of them being junk RNA resulting from spurious transcription, is muddled by frequent terminological issues. Here's an example ...
A key assumption made when using DNA sequence alignments to study lncRNA evolution is that lncRNA exons in one species align to lncRNA exons in the other species. However, transcription typically evolves faster than the underlying DNA sequence and thus, in many cases, lncRNA loci are homologous to non-transcribed sequences in the other species. Therefore, it is important to study lncRNAs by directly comparing lncRNA-producing loci, and such studies in multiple species have uncovered rapid turnover of lncRNA loci. For example, my laboratory found that in 17 vertebrates, more than 70% of lncRNAs have appeared in the past 50 million years. Splicing patterns also evolve rapidly, with only approximately 20% of splicing events in human lncRNAs conserved outside of primates. lncRNA loci are thus commonly gained and lost in evolution, and those lncRNAs that are retained drastically change their exon–intron architecture and their sequences across species in which the lncRNA is present.
It's reasonable to focus attention on exon sequences since, as a general rule, intron sequences are not conserved in functional genes. Ulitsky notes that when you align LOLAT sequences to the comparable region in other genomes, you usually find that the similar sequence in the other genome does not correspond to a known transcript. This is consistent with the idea that the relevant sequences in both genomes are junk DNA but the human region just happens to be transcribed by accident.

It's probably best to avoid using the word "homologous" to describe these similar sequences since that's a loaded word. If the sequences are junk then they will eventually drift apart and all sequence similarity will be lost.

Because there's so little evidence of conservation for most LOLATs, Ulitsky suggests restricting the sequence comparisons to regions where both species have a LOLAT at the same site. This is a small fraction of the total number of LOLATs. When he does this, he discovers that 70% of LOLATs show no evidence of long-term sequence conservation (Herzroni et al., 2015). Transcription appears to have arisen fairly recently (within 50 million years). Less than 100 lncRNA genes are shared between fish and tetrapods and only a few hundred additional lncRNA genes are shared between reptiles, birds, and mammals. About one thousand lncRNA genes appear to be common to various mammalian lineages. Thus, sequence conservation suggests that about one thousand LOLATs out of 60,000 might be functional.

Knowing that most LOLATs are recent, there are two different interpretation. Ulitsky prefers to think of new genes arising in the past 50 million years. I prefer to think of spurious transcription arising in some common ancestor. The bottom line is that even if we restrict our analysis to a particular LOLAT that is present in more than one species (a small subset) there's very little evidence of conservation. Not even the splicing pattern is conserved. Looks like junk RNA to me.

BTW, we also have to be very careful about using the word "conservation." If you compare any two junk DNA regions of the human and chimp genomes you'll find that they are at least 98% similar. That's a very high degree of sequence similarity but it does not indicate "conservation." The word "conservation" should be restricted to sequences that can be shown to be under negative selection. In the case of humans and chimps the sequence similarity would have to be almost 100% over a long stretch of DNA before you could assume conservation.

Sloppy use of "conservation" carries the implication that the sequences are under selection.

Most of the review focuses on issues such as "Classes of lncRNA evolutionary trajectories," "Rapid turnover of lncRNAs in other phyla," "Evolutionary origins of new lncRNAs," and "Routes for increased complexity in lncRNA loci." Nowhere in the abstract or the concluding remarks do you see any mention of what I think is the main result; namely, most LOLATs show no evidence of conservation. I get the impression that the author remains unconvinced by the results of "using comparative genomics to understand non-coding RNAs" (see the title of the article).

Here's the abstract ....
Long non-coding RNAs (lncRNAs) have emerged in recent years as major players in a multitude of pathways across species, but it remains challenging to understand which of them are important and how their functions are performed. Comparative sequence analysis has been instrumental for studying proteins and small RNAs, but the rapid evolution of lncRNAs poses new challenges that demand new approaches. Here, I review the lessons learned so far from genome-wide mapping and comparisons of lncRNAs across different species. I also discuss how comparative analyses can help us to understand lncRNA function and provide practical considerations for examining functional conservation of lncRNA genes.
To me, the rapid turnover of LOLATs indicates that most of them are spurious, non-functional transcripts. But when the author says, "the rapid evolution of lncRNAs poses new challenges" it seems to indicate that these are unusual genes that for some reason don't look conserved. That's a very different conclusion.

The author, Igor Ulitsky, should have directly addressed the important question in this review and given us some indication about what fraction of the 60,000 LOLATs represent truly functional genes and on what evidence he bases his conclusion if it's not sequence conservation.

This field is very confusing. Some labs have characterized individual RNAs and demonstrated that they have a biological function. As I mentioned earlier, there are only 200 or so of these proven genes. Many labs have taken a genomics approach and have promoted the idea that there are tens of thousands of functional lncRNA genes. However, when these labs try to find evidence of function the results are discouraging. The best interpretation is that most LOLATs are spurious, non-functional, transcripts.

That doesn't sit well with researchers who have invested their reputations (and many grants and publications) in the idea that the human genome has a huge number of lncRNA genes. What to do? The answer is to make up excuses to explain why sequence conservation is not a good indication of function and avoid the obvious conclusion that the transcripts are junk. Recall that junk RNA is the null hypothesis; function must be demonstrated, not assumed.

The three most common excuses are ....
  1. Conservation is difficult to detect because the functional part of the exon sequences relies on the formation of secondary structure and not exact sequence conservation.
  2. Most lncRNA genes are species-specific. They have evolved recently and they help define one species from another.
  3. The actual sequence of lncRNA genes isn't important. The function of these genes is simply to produce a transcript of some sort and not one with a particular sequence. (These are "eRNAs" or "enhancer RNAs.")
Remember, these are all attempts to explain why lack of conservation—the expected result for spurious transcription—does not mean that the presumed genes are really junk DNA.3

Here are a couple of abstracts that illustrate this phenomenon. I have underlined some interesting phrases.
Johnsson, P., Lipovich, L., Grandér, D., and Morris, K. V. (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochimica et Biophysica Acta (BBA)-General Subjects, 1840:1063-1071. [doi: 10.1016/j.bbagen.2013.10.035]

Background

Recent advances in genomewide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs.

Scope of review

Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved.

Major conclusions

Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant.
Kapusta, A., and Feschotte, C. (2014) Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. TRENDS in Genetics, 30:439-452. [doi: 10.1016/j.tig.2014.08.004]

Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.


1. There are a few exceptions. Some lncRNAs appear to be translated.

2. The question being begged is how many of those sequences have a true biological function.

3. Don't forget that almost all of these LOLATs are present at extremely low concentrations so they already have one strike against them. (Explaining that problem requires a different set of excuses.)

Palazzo, A.F., and Lee, E.S. (2015) Non-coding RNA: what is functional and what is junk? Frontiers in Genetics, 6. [doi: 10.3389/fgene.2015.00002]

Hezroni, H., Koppstein, D., Schwartz, M. G., Avrutin, A., Bartel, D. P., and Ulitsky, I. (2015) Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell reports, 11:1110-1122. [doi: 10.1016/j.celrep.2015.04.023]

130 comments :

  1. Larry,

    Your view and many others would change drastically if you decided to do your research from a different point of view; form the opposite point of view. That's how I do my research. I always review or want to hear the critics or the opposers of my idea or belief first. Then, I try to research their views first just to see if they hold any merit. If they do, I research further just to see if the view opposite to mine has real evidence. If it does, then I usually abandon my idea (s) and do not look for scraps and pieces of fluffy "research" to prove my point.

    If you did the same, in good faith, you would never post a blog like this. I'm pretty sure of that...

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    1. Thanks. I got a big kick out of reading your advice.

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    2. Larry,

      We both know where you are at and why, so don't try to be sarcastic!

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    3. That sounds like a threat. Goodbye Cruglers.

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    4. In physics, a strong indication that a hot new "discovery" is heading to collapse is that everybody "sees" the effect but nobody gets the same results. lncRNA sounds rather similar to me.

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    5. I suppose Cruglers didn't notice that in this case Dr. Moran did read and write about articles that are based on the opposite view of lncRNA's to his own.

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  2. [This is Sal....]

    "can sequence comparisons tell us the answer? "

    Probably not, it will take some biochemical sleuthing like that used by John Rinn and others to deduce the HOTAIR lnc/linc RNA was transcribed from chromosome 12, sailed on the winds of Brownian motion to precise nucleosomes on Chromosome 2 and docked with the PRC2 polycomb repression complex to modify a single amino acid residue, lysine, on the 27 position of Histone 3. Since then, experiments like ChIRP-seq (chromatin isolation by RNA purification) experiments found out the lnc/linc HOTAIR RNA parked at about 832 biding sites through out the genome. HOTAIR enabled differentiation of skin cells between the soles of the feet and the eyelids. The journal Science was stunned to see trans acting RNAs on one chromosome regulating DNAs on another!

    Rinn and Chang suspect 41,000 such other transcripts that operate in manner like the HOTAIR lnc/linc RNA. Given that it took Rinn a year and a half with a team of 5-10 assistants, if 41,000 such functional lncRNAs are in the human genome, this would be about half-a-million man years of research unless we create some serious high throughput techniques.

    Btw, lncRNA is a bit of a misnomer category, like "miscellaneous". It's hard to draw generalizations about "miscellaneous".

    But if elucidation of such lncRNAs requires a lot of research, a utilitarian strategy is to hustle for grant money to research these RNA molecules rather than decry lncRNAs as necessarily junk. No one really really knows if it's junk, and if history is a lesson, even John Rinn suspected the HOTAIR lnc/lincRNA was junk at first, that's why he called it "HOTAIR".

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    1. Is HOTAIR conserved in sequence comparisons?

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    2. Yes HOTAIR is conserved, but that wasn't what told us it was functional. It was ChIRP-seq combined with the previous understanding of H3K27me histone modifications and PRC2 complexes. No one knows how much background information is needed to make sense of the other lncRNAs. If we didn't know about H3K27me and PRC2, HOTAIR might have been totally non-sensical in what it did. Who knows what else we need to learn before we begin to make sense of the other lncRNAs. The other 41,000 lncRNAs Rinn and Chang propose also have conservation, but they have hardly begun to do the lab experiments necessary, and it won't get very far if there are other protein complexes and histone modifications and a host of other regulatory schemas that are cell type specific that we haven't even discovered yet. HOTAIR, for example was not expressed in certain cell and tissue types. Robert TJian even argues for thousands of cell types, not just the canonical 213 cell types. The low concetrations Larry mentions might be only to isolated cell types and tissues. There are 100 trillion cells in various cell phases. We haven't even begun to catalogue the possibilities...

      So I say, sequence comparisons might point to something interesting, it isn't a biochemical proof of function however.

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    3. liarsfordarwin says,

      ... a utilitarian strategy is to hustle for grant money to research these RNA molecules rather than decry lncRNAs as necessarily junk. No one really really knows if it's junk, and if history is a lesson, even John Rinn suspected the HOTAIR lnc/lincRNA was junk at first, that's why he called it "HOTAIR".

      I am not claiming that all lncRNAs are junk, although I think the available data strongly suggests that MOST of them are junk.

      My major complaint is the opposite problem. Most researchers in this field write and talk as if the default assumption were "functional unless shown otherwise."

      I would be happy to see them write grants where they ask for money to investigate individual lncRNAs while pointing out that they will probably turn out to have no biological function whatsoever.

      We all know that's not going to happen so researchers will continue to find excuses whenever their tests for function come up negative.

      In fact, that's exactly what you're doing, liarsfordarwin. You are exploiting the fact that one particular RNA (HOTAIR) turned out to have a complicated function and using that fact to imply that a large number of lncRNAS might also have a difficult-to-prove function.

      Then you address the concentration issue by making another excuse.

      The bottom line is don't make the extraordinary claim that tens of thousand of these RNAs have a function unless you have the data to back it up. The null hypothesis is "no function." (But that's probably not going to get your grant funded.)

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    4. So I say, sequence comparisons might point to something interesting, it isn't a biochemical proof of function however.

      What alternative explanation do you have for sequence conservation?

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    5. So they're conserved Sal, so we'd already guess they're functional. So sequence conservation can tell us if it's functional. It can't tell us what that function is, but nobody ever thought otherwise.

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    6. John and Rasmussen,

      I used the word "comparison" just as Larry asked in his OP, not "conservation". There is a subtle difference.

      One mouse gene compares and is similar to a human pseudo gene. The human pseudogene transcript has a different function (regulatory) than the similar mouse gene. Hard to say under some of the definitions used by papers in the OP if this would be "conserved".

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    7. One mouse gene compares and is similar to a human pseudo gene. The human pseudogene transcript has a different function (regulatory) than the similar mouse gene. Hard to say under some of the definitions used by papers in the OP if this would be "conserved".

      If we conclude that the human sequence is a pseudogene then that's probably based on sequence comparisons showing that something important hasn't been conserved. It could be the coding sequence, splice sites, or any number of things. I don't think there's a lot of confusion about that.

      If a new function is discovered for that human sequence then it's no longer a pseudogene; it's a different gene that may have arisen from a pseudogene. One expects to see evidence of sequence conservation for the properties of that new function in closely related species.

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    8. Dr. Moran wrote:

      "I would be happy to see them write grants where they ask for money to investigate individual lncRNAs while pointing out that they will probably turn out to have no biological function whatsoever. "

      What would have happened if researches said, "we propose research into lncRNAs (like PRNCR1 and PCGEM1) since they seem associated with prostate cancer. They will probably turn out to have no biological function whatsoever, but we want to look at them any way."

      I don't think that would impress the administrators doling out the grant money.

      In one case, which ever way the following researchers got the research grants (many researchers, not just the authors of the paper), here was the net result:



      http://www.cell.com/trends/molecular-medicine/pdf/S1471-4914(14)00061-6.pdf

      "Long noncoding RNAs (lncRNAs) are rapidly becoming essential pieces in the cancer puzzle. Our understanding of their functional capabilities is in its infancy. One certain fact, however, is that their molecular interactions extend beyond chromatin complexes into diverse biological processes. In prostate cancer, aberrant expression of lncRNAs is associated with disease progression....Recently, Yang et al. described two lncRNAs, prostate cancer noncoding RNA1 (PRNCR1) and prostate cancer gene expression marker 1 (PCGEM1), that are capable of governing AR-mediated gene transcription [21]. PCGEM1 was one of the first oncogenic lncRNAs identified [22]....The importance of PCGEM1 and PRNCR1 in CRPC is beautifully illustrated by the observation that constitutively active truncated AR isoforms (even in the absence of ligand binding) require both lncRNAs to activate transcription [21]. "


      I don't see much benefit of adding a disclaimer "we probably won't find any function whatsoever." I also see little benefit in throwing cold water on the evidently intense motivation to research the connection between lncRNAs and cancer. These guys seem sincere and knowledgeable.

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    9. Dodging the question, Sal. Why isn't sequence conservation "biological proof of function"? You responded with a scenario in which, you imagine, there is sequence conservation and function. You apparently intended it, however, to be an example of function without sequence conservation. But that, if it's anything, is a response to a different claim, that lack of sequence conservation is "biological proof" of non-function. Nobody says that, though it's certainly the way to bet, and sometimes one would be wrong.

      But what about the actual question: Why isn't sequence conservation "biological proof" of function?

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    10. I don't think that would impress the administrators doling out the grant money.

      So you agree that it's all hype in search of grant money? Interesting.

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    11. Sal is so funny. A perfect illustration of the principle that one can possess knowledge, but lack understanding.

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  3. Isn't sequence conservation a clue that there might be something interesting?

    What percentage of known functional sequences are not conserved?

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  4. Larry,

    If you're going to London in November for the Royal Society meeting on the Extended Synthesis, you should stay a couple more days and attend this meeting as well:

    http://www.genetics.org.uk/Conferences/tabid/84/Filter/0%20GS/MeetingNo/GTS_452/view/Conference/Default.aspx

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  5. http://www.genetics.org.uk/Conferences/tabid/84/View/Programme/Filter/0%20GS/MeetingNo/GTS_452/Default.aspx

    Link???

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  6. John Harshman said: "So you agree that it's all hype in search of grant money? Interesting."

    No, and you're typing words into my mouth (so to speak).

    It's actually negative hype to say lncRNAs "are likely to have no function whatsoever." The fair thing to say is that there is a possibility of function, and we won't likely know unless we look. Further, it's becoming practically negligent, bordering on malfeasance if we don't look.

    http://www.nature.com/nm/journal/v21/n11/full/nm.3981.html

    "It is increasingly evident that many of the genomic mutations in cancer reside inside regions that do not encode proteins. However, these regions are often transcribed into long noncoding RNAs (lncRNAs). The recent application of next-generation sequencing to a growing number of cancer transcriptomes has indeed revealed thousands of lncRNAs whose aberrant expression is associated with different cancer types. Among the few that have been functionally characterized, several have been linked to malignant transformation. Notably, these lncRNAs have key roles in gene regulation and thus affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review aims to summarize current knowledge of lncRNAs from the cancer perspective."

    You still insist this is hype?


    So far in this thread, I listed functional lncRNAs:

    HOTAIR
    PCGEM1
    PRNCR1

    I could list some more like

    XIST (X-chromosome regulation/repression)
    PTENnpg1 (pseudogene that transcribes to a lncRNA)
    ....

    So why all the naysaying against the genome? Is this to salvage Ohno's failing hypothesis?

    Thousand of dysregulated or damaged lncRNAs could be involved in cancers. Whether these lncRNAs are merely diagnostic or actually causal, the responsible thing to do is look, not say stuff like, "we want to study this lncRNA molecule even though we might not find any function whatsoever".

    From the paper:
    " For example, the overexpression of the lncRNA HOTAIR promotes the metastasis of breast cancer cells by epigenetically silencing the developmentally important genes in the HOXD cluster, among others6; overexpression of ANRIL (officially known as CDKN2B antisense RNA 1 (CDKN2B-AS1)), which silences the tumor suppressor locus that comprises INK4b, ARF and INK4a (officially known as CDKN2B, CDKN2AIP and CDKN2A), is linked to poor prognosis in prostate and gastric cancer7, 8, 9, 10, 11. LncRNAs are thus functional transcripts that contribute to the hallmarks of cancer (Fig. 1), and they are therefore becoming attractive potential therapeutic targets."

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    1. So when do you get to the part where you actually answer John Harshman's question, Sal? That question,to refresh your memory, was: Why isn't sequence conservation "biological proof" of function?

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    2. John Harshman said: "So you agree that it's all hype in search of grant money? Interesting."

      No, and you're typing words into my mouth (so to speak).


      Hey, you're the one who presented, as the reason for not hyping lncRNAs, that you wouldn't get grants if you didn't. I suppose you don't think about what you type very much. I am also underwhelmed that you are able to list as many as 5 functional lncRNAs.

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    3. liarsfordarwin asks,

      You still insist this is hype?

      Yep. Sure looks like hype to me. It's certainly an evidence-free paragraph.

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    4. "we want to study this lncRNA molecule even though we might not find any function whatsoever"

      Wouldn't that just be an honest statement of fact? Statistically speaking, it is likely that most lncRNA's don't have any function, yet it is still worth it to find out which ones do have a function and what that function is.

      Nobody is saying we should not find out which ones are functional and what that function is. No body.

      "It's actually negative hype to say lncRNAs "are likely to have no function whatsoever."

      No, that's just a concrete reality. Picking a lncRNA at random, it is in fact likely to have no function whatsoever. That still doesn't mean one should not bother to look and find out which ones ARE functional and what that function is.

      Is it sinking in yet? Nobody, no one, no person here is advocating a stop to basic reasearch into human molecular biology. Every time you want to start a new post on this subject, you should remember to put that in as a disclaimer, if for no other reason than to remind yourself when you are about to type out a new lie about what people are actually advocating.

      "The fair thing to say is that there is a possibility of function, and we won't likely know unless we look."

      The "Fair" thing to say is not in contradiction with the evidentially informed thing to say. Both are statements of fact.

      You really are working very hard to try and paint this revisionist picture of history.

      "Whether these lncRNAs are merely diagnostic or actually causal, the responsible thing to do is look, not say stuff like, "we want to study this lncRNA molecule even though we might not find any function whatsoever". "

      No, the responsible thing to do is to correctly relay the facts as best as they are understood by current science. If this isn't producing huge grants because it doens't sound hyped and awesome enough, then the problem is with those who write the grants, not with those that correctly articulate propsals to try and get them.

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    5. No, that's just a concrete reality. Picking a lncRNA at random, it is in fact likely to have no function whatsoever. That still doesn't mean one should not bother to look and find out which ones ARE functional and what that function is.

      But, so that things are clear for Sal, it would be a very wasteful and inefficient way to do this if researchers were to go thru every single lncRNA one by one and try to figure out if it performs a function, which seems to be what Sal is suggesting. (And let's not pretend that he is concerned about finding a cure for cancer. He believes that junk DNA disproves the existence of his god, so he wants to disprove junk DNA instead.)

      This is an example of how ID creationism actually impedes scientific progress. ID scientists (if any such thing actually existed) would be required to devote time and resources trying to find function for stretches of DNA that are obviously junk, because their ideology demands that such function must exist.

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    6. One would have the highest chance of success at finding funtional lncRNAs by testing the most conserved ones first, and conversely the least conserved ones last (if at all).

      So you test the most conserved ones, find the functional ones among them, and then you could move on to gradually lesser conserved ones. At some point you're going to move into territory where you're burning a lot of money testing lncRNA for function, tens, hundreds, maybe thousands of them without finding anything. Should you keep going then? This kind of molecular and cell biology work is regrettably insanely expensive.

      Suppose you've tested 5.000 of the less conserved lncRNAs without finding a single function, you've spend probably tens of millions of dollars and it would have become practically negligent, bordering on malfeasance if you kept looking rather than allocating money to more promising projects.

      So there's a question of degree involved here, it is not totally black and white.

      There is not a camp on one side saying "it's all junk don't bother testing anything ever", yet on the other hand it seems we do have people like Sal insinuating we SHOULD test every single one of them, regardless of sequence conservation, no matter the cost.

      Delete
    7. There is not a camp on one side saying "it's all junk don't bother testing anything ever", yet on the other hand it seems we do have people like Sal insinuating we SHOULD test every single one of them, regardless of sequence conservation, no matter the cost.

      Well, or course. After all, they think they can prove the existence of God by doing that.

      Delete
    8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175327/

      "While thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem cells (ESC) and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ESC regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ESCs and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ESC state.

      ....
      For 137 of the 147 lincRNAs (93%), knockdown caused a significant impact on gene expression (Supplemental Table 3), with an average of 175 protein-coding transcripts affected (range: 20–936) (Figure 1c, Supplemental Figure 2, Supplemental Table 4)."

      A more inclusive overview of the NAT class of lncRNAs is here.

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768148/pdf/nihms374514.pdf

      Delete
  7. lutesuite

    "He believes that junk DNA disproves the existence of his god".

    I don't believe that is true. But even IF that were true, certainly most proponents of ID/creationism do not believe so. I do not believe so. There is no problem, since junk DNA simply means DNA is subject to entropy. Dunning Kruger's almost always underestimate their oponents.

    And please stop writing "ID creationism". These are two different things. Because their professor keeps probably consciently making this mistake, does not mean his pupills have to do the same.

    ReplyDelete
    Replies
    1. But even IF that were true, certainly most proponents of ID/creationism do not believe so.

      If that's the case, why do the ID creationists on Uncommon Dissent and Evolution News and Views spend so much effort trying to disprove the existence of junk DNA? Do they just suffer an irresistible urge to be wrong about absolutely everything? Actually, that would explain a lot.

      (I am, however, glad that you at least acknowledge that ID creationists tend to believe things that are incorrect.)

      And please stop writing "ID creationism". These are two different things.

      It's not really my problem that you don't understand the definitions of "ID" nor of "creationism." But I could stick to just calling you all IDiots, if it would make you feel better.

      Delete
    2. "There is no problem, since junk DNA simply means DNA is subject to entropy."

      No, that isn't what it means.

      Delete
    3. ElShamah777,

      "And please stop writing "ID creationism". These are two different things."

      Why do you insist on denying the obvious? ID clearly is creationism. For example, I told you that the intelligent "agents" you're using as a "basis" for your bullshit, are among the very things you want to explain with "ID," which made ID logically incoherent. You denied that intelligence was related to the complexity, etc, of the very life forms that show intelligence, and you claimed that intelligence is magic and souls. For intelligence to be magic and souls, you would have to hold to a creationist position. There's no way around.

      Historically and by design, ID has always been creationism. This is evident when you notice that no matter how you twist it, ID will lead inevitably to creationism. Why not just admit it right out? Why not just being honest about it? What's wrong with you? Why do you agree to the dishonesty also build into ID historically and by design?

      Delete
    4. Two words: "cdesign proponentsists."

      ID is creationism. End of discussion.

      Delete
    5. ElShamah777 says,

      And please stop writing "ID creationism". These are two different things. Because their professor keeps probably consciently making this mistake, ...

      Allow me to clear up one little problem. I am deliberately. referring to these people as Intelligent Design Creationists because they are creationists. You can drop the "probably."

      You should also drop the pretense. We all know where your objections to evolution are coming from. I suspect you were against evolution long before you ever heard of the Intelligent Design version of creationism.

      Delete
    6. That's an interesting point. I wonder if there has ever been a single person who accepted evolution when its opponents only called themselves "creationists", but who then changed his mind when exposed to the arguments of the creationists who call their movement "intelligent design." I bet this is the case with almost no one.

      Delete
    7. Larry wrote:

      " We all know where your objections to evolution are coming from. I suspect you were against evolution long before you ever heard of the Intelligent Design version of creationism."

      Yes Larry, you certainly should know where my objections do come from, since for some time you read my posts.

      And, no, my inferences do not come principally from articles at Evolutionnews, or UD, creation.com, nor Answer in Genesis.

      They come straight from mainstream scientific papers, which show that biocomplexity and diversity is a result of far more than genetic chance.

      At the article : Where Do Complex Organisms Come From? at my virtual library i mention a few mechanisms.

      Cell and body shape, and organism development depends on following :

      Membrane targets and patterns
      Cytoskeletal arrays
      Centrosomes
      Ion channels, and
      Sugar molecules on the exterior of cells (the sugar code)
      Gene regulatory networks

      Various codes and the encoded epigenetic information is required:

      The Genetic Code
      The Splicing Codes
      The Metabolic Code
      The Signal Transduction Codes
      The Signal Integration Codes
      The Histone Code
      The Tubulin Code
      The Sugar Code
      The Glycomic Code

      " Junk DNA "

      MicroRNAs--"Once Dismissed as Junk"--Confirmed To Have Important Gene Regulatory Function

      In 2008 Scientific American noted that microRNAs were "once dismissed as junk" and said the following:
      Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called "junk DNA," sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.

      Delete
    8. Larry wrote:

      "I am deliberately. referring to these people as Intelligent Design Creationists because they are creationists."

      You do it because it gives a pejorative connotation. But that cannot hide that your inferences of the scientific evidence are bunk, and do not withstand scrutiny by any means, Larry.

      Well, who defines what ID is better than the discovery institute ?

      Intelligent Design and Creationism Just Aren't the Same

      http://www.discovery.org/a/1329

      1. "Intelligent Design Creationism" is a pejorative term coined by some Darwinists to attack intelligent design; it is not a neutral label of the intelligent design movement.
      2. Unlike creationism, intelligent design is based on science, not sacred texts.
      3. Creationists know that intelligent design theory is not creationism.
      4. Like Darwinism, design theory may have implications for religion, but these implications are distinct from its scientific program.
      5. Fair-minded critics recognize the difference between intelligent design and creationism.

      Delete
    9. This comment has been removed by a blog administrator.

      Delete
    10. ElShamah777 asks,

      Well, who defines what ID is better than the discovery institute ?

      Me, for one.

      Delete
    11. I'm glad to hear that the IDiots are so opposed to being associated with creationism, if Otangelo is to be believed. So I presume we can expect many forthcoming posts on Uncommon Descent and Evolution News and Views criticizing and disavowing creationist beliefs such as the 6000 year old universe and the denial of universal common descent. That would certainly help convince others of the distinction between ID and creationism. When can we expect this, Otangelo?

      Delete
    12. Lutesuite

      There are ID proponents of all sorts, some are creationists, others are not. As for example Dennis Jones is a atheist, and Berlinski is an agnostic jew. Denton is agnostic and helds no religious beliefs.

      Luskin writes :
      The claim that intelligent design theory proposes a supernatural designer, or that it specifically appeals to God, is a mischaracterization of intelligent design theory, and the critics are not correct.

      Dembski:
      Intelligent design does not claim that living things came together suddenly in their present form through the efforts of a supernatural creator. Intelligent design is not and never will be a doctrine of creation."

      Behe writes:
      "The conclusion that something was designed can be made quite independently of knowledge of the designer. As a matter of procedure, the design must first be apprehended before there can be any further question about the designer. The inference to design can be held with all the firmness that is possible in this world, without knowing anything about the designer."

      So again: Keep misrepresenting what ID theory is, and equal it to creationism, is just a dumb attempt to disqualify it as science, and does not distract from the fact that its explanatory power is far beyond naturalistic explanations.

      A intelligent designer, through power, information input, wisdom, will, is a far better explanation for the physical world than natural, non-guided, non-intelligent mechanisms, that is : random chance or physical necessity, long periods of time, mutation and natural selection, or self organisation of matter.

      That should be clear to any rational, clear thinking person.

      Delete
    13. ElShamah777 says,

      So again: Keep misrepresenting what ID theory is

      Intelligent Design Creationism is not a theory. It is a social movement whose main goal is to promote belief in the supernatural by attacking and discrediting evolution and the scientists who support it.

      A key part of that social movement involves the creation of something called "ID Theory" that attempts to separate their attacks on evolution from a direct connection to supernatural beings. (Maybe it was aliens?)

      The next step is to try and convince people that "ID Theory" is all there is to the social movement known as Intelligent Design Creationism.

      All you have to do is read the books and the blogs to see how ridiculous this is. Intelligent Design Creationism is so intimately connected with religion that none of it's proponents can disguise their beliefs. Just go to Uncommon Descent or Evolution News & Views to see how many posts deal with religion and attacks on evolution vs. how many deal with "ID Theory."

      Delete
    14. There are ID proponents of all sorts, some are creationists, others are not.

      So you and the rest of the IDiots claim. But you did not address the main point of my post. If creationists claim themselves to be part of "ID theory", I presume that includes the Young Earth Creationists. But if "ID theory" is a genuinely scientific endeavour that purports to explain how life arose thru the actions of a "designer", then the issue of the age of the universe is crucial, since a young universe would obviously rule out some of the possible mechanisms by which this "designer" acted. But, as I hope you'll agree, the idea of a young universe is ludicrous and flies in the face of every single scrap of scientific evidence. So why don't the leaders of the ID movement use their fora such as Uncommon Descent to correct their acolytes who insist on holding to Young Earth Creationism? You know, the way Larry uses his blog to correct fellow evolutionists who deny the existence of junk DNA. Wouldn't the ID movement be stronger as a scientific endeavour if fewer of its adherents propounded blatantly anti-scientific ideas like YEC?

      Delete
    15. Larry

      you seem that desperate that you try to keep this strawman of " ID creationism" alive no matter what.

      No, ID does NOT mention ANY supernatural entity. Keep saying that makes you look foolish and ignorant on the subject.

      Does intelligent design postulate a “supernatural creator?”

      http://www.discovery.org/f/565

      Yet actual statements from intelligent design theorists have made it clear that the scientific theory of intelligent design does not address metaphysical and religious
      questions such as the nature or identity of the designer.

      "...... by attacking and discrediting evolution and the scientists who support it."

      Yes, Larry, we know that the holy cow of evolution cannot be sacrificed by proponentists like you, no matter what. Even when ALL scientific evidence falsifies Darwins theory, the ideology driven mid nineteenth century idea must be kept alive, no matter what ( otherwise, a God could enter the door, what scary idea !! )

      What frightening world would that be, if ID theorists would gain overhand over evolution religionists ??

      I do not think that day will come. But that will not be because the lack of evidence, and where it leads to, but because there is a lot of people which do not know the creator and his love for his creation and creatures, specially human kind.

      " (Maybe it was aliens?) "

      Could be. ID Theory does not try to answer these questions. That is left to researchers and inquirers that deal with theology and philosophy. Is there something wrong about separating it ?

      Intelligence is a valid alternative to natural mechanisms of origins of the physical world, that has its own right to be scrutinized and theories upon that possibility elaborated. This is being done with hudge success by the ID community, and important ground has been gained in the last two decades. Nothing will stop this trend. No matter, if the design hypothesis is being excluded a priori by mainstream science, or not.

      Who loses, is science in general, which is only aloud to stick to natural mechanisms, and we see nicely to what that leads. A bunch of bad scientific papers, which cannot other, than start with evolution , end with evolution, no matter where the evidence leads to. A sad situation which proponents and fanatics like you Larry, try to keep alive. It doesn't matter, if you deny it, as you have done in the past..... The landscape of scientific papers testifies this. Show me ONE mainstream scientific paper, which gives a fair consideration to design.....

      We have seen what happens recently, with the paper " Proof of God in the Palm of Your Hand! ". The Tabu was broken, a general outcry, and the authors had to retract, and plos.org had to retract from the paper.......

      Delete
    16. Otangelo,

      Let me try make this simple enough for your feeble mind to follow, (though that is an admittedly formidable challenge.)

      What Larry and I are claiming is that the ID movement is a form of creationism that attempts to gain credibility for itself by denying that it is a form of creationism.

      Now, do you see how it is pointless and self-defeating to attempt to refute this argument by quoting ID creationist denying that ID is a form of creationism?

      Delete
    17. Oh, and Otangelo, could you please explain how whether life was created by aliens is a question that could only answered by theologians or metaphysicians? If we discovered a wristwatch on one of the moons of Jupiter, would it require a theologian to determine whether it had been created by an alien life form?

      Delete
    18. ElShamah777 babbles,

      Yet actual statements from intelligent design theorists have made it clear that the scientific theory of intelligent design does not address metaphysical and religious questions such as the nature or identity of the designer.

      "Unlike the theistic evolution of Francis Collins, however, the theory of intelligent design does not seek to confine the activity of such an agency to the beginning of the universe, conveying the impression of a decidedly remote and impersonal deistic entity. Nor does the theory of intelligent design merely assert the existence of a creative intelligence behind life. It identifies and detects activity of the designer of life, and does so at different points in the history of life, including the explosive show of creativity on display in the Cambrian event. The ability to detect design makes belief in an intelligent designer (or a creator, or God) not only a tenet of faith, but something to which the evidence of nature now bears witness. In short, it brings science and faith into real harmony."

      Stephen C. Meyer
      Darwin's Doubt p. 412

      Delete
    19. Did you not notice the word "God" in that passage, OtangeloElShamah? Do you not understand how saying that "science and faith" can be brought into "real harmony" addresses metaphysical and religious questions, which is something you just denied ID creationism does? Are you now going to deny the words of your most revered IDiots, Stephen Meyer?

      Delete
    20. fully agreed. And your point is ??

      Is it really possible for a human being to be this clueless, or are we just seeing the equivalent of ElShamah sticking his fingers in his ears and hollering "Neener neener neener..."?

      El, in the utterly mystifying event you don't actually realize what the point is, you first blathered at Larry that ID isn't involved with any supernatural entity, then fully agreed with his quote of Stephen Meyer saying ID asserts the existence of a God/Creator.

      You've just completely contradicted yourself, that's what the point is.

      Delete
    21. judmarc

      please quote where Stephen Meyer said ID asserts the existence of a God/Creator.

      If you are unable to see the subtility of what he said, you might get off your blinkers. That will help you see, or reason with more clarity.

      Delete
    22. To make it clear :

      " The ability to detect design makes belief in an intelligent designer (or a creator, or God) not only a tenet of faith, but something to which the evidence of nature now bears witness. In short, it brings science and faith into real harmony."

      That is OBVIOUS. Once its granted that a intelligent designer is the best explanation for the origin of the physical world, the inquirer can logically go ahead and concile his scientific views based on ID theory with his religious views, whatever they might be.

      That does however not permit the leap to acuse that ID equals creationism.

      Dr. Michael Behe
      "Intelligent design is modest in what it attributes to the designing intelligence responsible for the specified complexity in nature. For instance, design theorists recognize that the nature, moral character and purposes of this intelligence lie beyond the competence of science and
      must be left to religion and philosophy."

      Dr. William Dembski:
      "The conclusion that something was designed can be made quite independently of knowledge of the designer. As a matter of procedure, the design must first be apprehended before there can be any further question about the designer. The inference to design can be held with all the firmness that is possible in this world, without knowing anything about the designer."

      Delete
    23. Originally from some poster over on Panda's thumb:

      Mike Behe:

      “Our intelligence depends critically on physical structures in the brain which are irreducibly complex. Extrapolating from this sample of one, it may be that all possible natural designers require irreducibly complex structures which themselves were designed. If so, then at some point a supernatural designer must get into the picture. I myself find this line of reasoning persuasive. In my estimation, although possible in a broadly permissive sense, it is not plausible that the original intelligent agent is a natural entity. … Thus, in my judgment it is implausible that the designer is a natural entity.” “Reply to My Critics” Biology and Philosophy 16: 685-709, 2001.

      William Dembski:

      “My thesis is that all disciplines find their completion in Christ and cannot be properly understood apart from Christ.” William Dembski, ‘Intelligent Design’, p 206

      “…but let’s admit that our aim, as proponents of intelligent design, is to beat naturalistic evolution, and the scientific materialism that undergirds it, back to the Stone Age. “DEALING WITH THE BACKLASH AGAINST INTELLIGENT DESIGN version 1.1, April 14, 2004”

      Phillip Johnson:

      “This [the intelligent design movement] isn’t really, and never has been, a debate about science, it’s about religion and philosophy.” World Magazine, 30 November 1996

      “The Intelligent Design movement starts with the recognition that ‘In the beginning was the Word,’ and ‘In the beginning God created.’ Establishing that point isn’t enough, but it is absolutely essential to the rest of the gospel message.” Foreword to Creation, Evolution, & Modern Science (2000)

      “Our strategy has been to change the subject a bit so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools.” American Family Radio (10 January 2003)

      Delete
    24. Fucking Phillip Johnson, starting the ID movement and then exposing the whole thing. And then there's "The Wedge" strategy document.

      If you really believe what you write Otangelo, you believe a lie.

      Delete
    25. ElShamah777 says,

      That is OBVIOUS. Once its granted that a intelligent designer is the best explanation for the origin of the physical world, the inquirer can logically go ahead and concile his scientific views based on ID theory with his religious views, whatever they might be.

      That does however not permit the leap to acuse that ID equals creationism.


      Really? What kind of logic do you use to eliminate other possible designers such as aliens, the devil, humans from the future, or Zeus? According to your (false) claim, ID just tells you there's an intelligent designer. It doesn't have anything to do with creationism. Therefore, based only on the "evidence" of ID you have no logical reason to conclude that your god(s) were the designer. In fact, the evidence from ID might actually refute your religious beliefs.

      The very fact that people like you make this illogical leap without seeing the inconsistency shows us that Intelligent Design Creationism is a movement whose goal is to promote belief in god(s) and oppose materialism.

      Delete
    26. Larry wrote

      " What kind of logic do you use to eliminate other possible designers such as aliens, the devil, humans from the future, or Zeus? "

      The steps in the progression go as follows.
      1. Logical fallacy of Strong Atheism
      2. Logical starting point of agnosticism
      3. Proper understanding of science and searching for truth and not
      eliminating theistic implication.
      4. Falsifiable evidence which clearly points to Intelligence
      5. Intelligent Causation leads to agnostic theism.
      6. Specifics about various evidence leads to the conclusion of Infinite
      Creator.
      7. Comparative religions and historical evidence points to God of the Hebrews/Abraham.
      8. Internal evidence constrains the choice of Judaism. Islam, Christianity, and
      born-again Christianity.
      9. Born again christianity is the most consistent view.

      " According to your (false) claim, ID just tells you there's an intelligent designer. "

      Thats not simply according to me. Thats, as i have shown and quoted in various posts above already, the DEFINITION given by the founders of the ID movement, namely Stephen C. Meyer, Dembski, Behe amongst others.

      " Therefore, based only on the "evidence" of ID you have no logical reason to conclude that your god(s) were the designer. "

      Nope. Do you have some comprehension problems, Larry ? Or are you wilfullingly obtuse ? ( based on your trackrecord, i go for the second )

      To cite again http://www.discovery.org/f/565

      While I argue for design, the question of the identity of the designer is left open.

      What about this do you not understand, Larry ?!!

      " Therefore, based only on the "evidence" of ID you have no logical reason to conclude that your god(s) were the designer. In fact, the evidence from ID might actually refute your religious beliefs. "

      absolutely.

      " The very fact that people like you make this illogical leap "

      We don't.

      Get over it. Your insistence in " Intelligent Design Creationism " is a strawman, which you would do better avoiding in the future, for your own good.

      Delete
    27. Does the designer create anything, or just watch? Is it like architect and builder? If so, does the builder creat?

      Delete
    28. It's a very strange idea that Otangelo promotes. He claims that the presence of "design" can be demonstrated, but any speculation on the identity of the "designer" lies beyond the remit of science.

      So that means, while we can determine that the Great Pyramids of Giza were "designed", we have no idea who may be responsible for this "design". It could have been the ancient Egyptians of the 4th Dynasty, or it could have been aliens. There is no way to tell.

      Or, if we identify a Corvette as having been "designed", that is the end of what we can know about it. It could have been built by Chevrolet, or Hyundai. Or aliens.

      I sometimes can't tell if Otangelo is as stupid as he seems, or if his posts simply indicate how stupid he thinks we are.

      Delete
    29. And once again, Otangelo: How does quoting IDiots lying about whether ID is creationism disprove the claim that the IDiots lie about whether ID is creationism? Do you have even the most basic understanding of how logic works?

      Delete
    30. One other point: If Otangelo and his fellow IDiots are telling the truth, then there are no scientists as singularly lacking in curiosity as ID creationists. Could you imagine a real scientist identifying that some intelligent agent was responsible for the existence of life on Earth, but then making no further efforts to learn anything more about this "designer"? Who or what was this designer? Whence did He come? How did He actually design and create all living things? These questions may not be answerable, but that would not be known unless an effort is made to answer them. Yet the IDiots do not make even a token attempt to do so. They just shrug their shoulders and give up.

      If ID creationism really was science, this would be unfathmoable. However, if ID creationism is really nothing more than religious apologetics poorly disguised as science, then this makes perfect sense.

      Delete
    31. Creationism is the view that life and the universe were created by one or more supernatural beings. There are various versions of creationism, most of which are incompatible.

      The ID movement was founded on the idea that creationists could find "scientific" evidence to prove that materialistic explanations cannot account for life on Earth. By discrediting evolution, the creationists hope to convince their followers that the only logical alternative is god(s). It is a creationist agenda based on refuting materialism.

      Intelligent Design is the hypothesis that in order to explain life it is necessary to suppose the action of an unevolved intelligence. One simply cannot explain organisms, those living and those long gone, by reference to normal natural causes or material mechanisms, be these straightforwardly evolutionary or a consequence of evolution, such as an evolved extraterrestrial intelligence. Although most supporters of Intelligent Design are theists of some sort (many of them are Christian), it is not necessarily the case that a commitment to Intelligent Design implies a commitment to a personal God or indeed to any God that would be acceptable to the world's major religions. The claim is simply that there must be something more than ordinary natural causes or material mechanisms, and moreover, that something must be intelligent and capable or bringing about organisms.

      William A. Dembski and Michael Ruse
      in Debating Design (2004) p. 3

      The simple version of that statement is, "ID is the hypothesis that there must be a unevolved, non-material creator."

      Delete
    32. Mikkel

      as Dennis Jones explains:

      ID Theory is much different than it was in the early years. By the time of the Dover trial in 2005, ID had already advanced beyond obsolete creation terminology. The Of Pandas and People textbook version being used in Dover had been corrected, with all creationism content removed from the book. This is all decades ago now.

      The authors of the early writings believed it was only fair to ACKNOWLEDGE creationism, since it is impossible to discuss the controversy without actually reference the terms “creation” and “evolution.”

      I see Larrys pejorative insistence just as a desperate attempt to discredit ID as valid scientific research endaveour on its own right. It has actually exactly the same right of theories and predictions being developed, scrutinized and tested like natural mechanisms aka chance, self organisation of matter, physical necessity, and specially darwins ( falsified and obsolete) theory of evolution through mutations and natural selection.

      The mechanism of intelligence is as much logically possible as natural forces. This justifies it to elaborate ID predictions same as made by the Theory of evolution.

      This has been done, ID predictions have been made, and most, if not all, have NOT been falsified by evolution religionists in the last at least 20 years.

      It has been proven without any doubt, making several ID predictions as FACT, that :
      no natural mechanism is able, capable, powerful and specified enough to produce :

      a) a genetic code, luckily more efficient than any other amongst one million natural codes
      http://www.ncbi.nlm.nih.gov/pubmed/9732450

      b)the minimal instructed complex information content stored in a minimal sized genome to produce the first life:
      http://mmbr.asm.org/content/68/3/518.full.pdf
      ( No proponent of naturalism has EVEN been able to provide a example of CSI emerging by natural means )

      c) the genetic translation system and cipher:
      Eörs Szathmáry writes: “The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.”

      d) The first metabolic network :
      The Implausibility of Metabolic Cycles on the Prebiotic Earth, Leslie E Orgel†
      http://mmbr.asm.org/content/68/3/518.full.pdf

      e) Irreducible complexity, even admitted in some mainstream scientific literature as follows:
      http://link.springer.com/article/10.1007%2Fs00018-013-1394-1
      Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function.

      All cited examples above are NOT a argument from ignorance. I explain at my virtual library, at following article, why:
      Is Intelligent Design based on gaps of knowledge and ignorance?

      Delete
    33. Larry wrote:

      " The ID movement was founded on the idea that creationists could find "scientific" evidence to prove that materialistic explanations cannot account for life on Earth."

      All you try to do, is to discredit ID as a valid scientific endeavor, by arguing that ID makes allusion to the supernatural, or that it tries to identify the intelligent force, and is therefore a hidden form of creationism. If you were successful by doing so ( you are not ) you could argue that ID is religion, not science.

      My second post which does not appear ( either you deleted it, or it went to your spam box ) , answered this point.

      There is no logical constraint or fallacy to mention intelligence as one of the possible forces and mechanisms to explain the origin of the physical world.

      ID has exactly the same right of theories and predictions being developed, scrutinized and tested like natural mechanisms aka chance, self organisation of matter, physical necessity, and specially darwins ( falsified and obsolete) theory of evolution through mutations and natural selection.

      The mechanism of intelligence is as much logically possible as natural forces. This justifies it to elaborate ID predictions same as made by the Theory of evolution.

      This has been done, ID predictions have been made, and most, if not all, have NOT been falsified by evolution religionists in the last at least 20 years, being a powerful convincing explanation for the ones, that are not blinded by their prejudice and wilful ignorance for whatever reason that might be......

      Delete
    34. All you try to do, is to discredit ID as a valid scientific endeavor, by arguing that ID makes allusion to the supernatural, or that it tries to identify the intelligent force, and is therefore a hidden form of creationism. If you were successful by doing so ( you are not ) you could argue that ID is religion, not science.

      I have argued on many occasions that much of what passes for ID is science. For example, all attempts to refute evolution are scientific in my view. They are just BAD science.

      I have also argued on many occasions that science is not restricted by methodological naturalism; therefore, is perfectly okay by me to use science to investigate the supernatural. I see no reason why scientists couldn't investigate and identify the intelligent designer, if there was one.

      I see nothing wrong with Intelligent Design Creationism attempting to prove the existence of a supernatural creator using the scientific way of knowing. You would know this if you had paid attention to my posts over the past ten years.

      I have concentrated (successfully in my view) on showing that Intelligent Design Creationists do bad science. They are wrong about most of what they say concerning biology and evolution. I have never argued that we should ignore Behe and Meyer and others just because they are creationists. We should ignore them because they are wrong about the science.

      Just like Otangelo Grasso is wrong about the science.

      Delete
    35. Otangelo, do you believe if you repeat the same lies often enough, they will magically become true?

      If so, I hate to be the own to break the news, but it doesn't.

      Delete
    36. "ID Theory is much different than it was in the early years. By the time of the Dover trial in 2005, ID had already advanced beyond obsolete creation terminology. The Of Pandas and People textbook version being used in Dover had been corrected, with all creationism content removed from the book. This is all decades ago now."

      Wow, just wow. This is so patently false I'm without words. Literally they simply replaced the words "creationism" and "creator" with "intelligent design" and "intelligent designer". The whole goddamn thing is the same, only that single word is replaced. It doesn't stop being religious creationism just because you stop using the specific word "creationism" or "creator".

      Why does this have to be explained to you? Should a grown man not have the intellectual capacity to work this out himself? What IS wrong with you?

      Delete
    37. Larry wrote:

      " I have argued on many occasions that much of what passes for ID is science. For example, all attempts to refute evolution are scientific in my view. They are just BAD science. "

      Please back up why you think so. In regard of the origin of life, i have posted above five relevant points, from, why i think ALL abiogenesis proposals failed until now, and will keep failing, and why life's origin is better explained through the action of a intelligent agency. Could you answer, how each of the five points are better explained through natural mechanisms , and why chance tops the action of a ID in your view ? the points to address is the origin of 1. the best possible genetic code out of a million, 2. the gene content in the first living cell. 3. the genetic cipher, 4. the origin of the irreducible metabolic network, and 5. how the irreducible genome, proteome, and metabolic network could emerge without directing and creative force ?

      " I have also argued on many occasions that science is not restricted by methodological naturalism; therefore, is perfectly okay by me to use science to investigate the supernatural. I see no reason why scientists couldn't investigate and identify the intelligent designer, if there was one."

      So if that is ok for you, have you EVER in the past proposed how the supernatural could be investigated ? And, even easyer for you, let us just restrict to inteligence. Have you ever established what could be recognized as design in nature - Something having the PROPERTIES that we might attribute to that of a intelligently designed system , and then investigated if such properties are encountered in the natural world ?

      " I have concentrated (successfully in my view) on showing that Intelligent Design Creationists do bad science. "

      Pfff haha.... In your view maybe. I have never seen a convincing alternative coming from your camp.....

      " They are wrong about most of what they say concerning biology and evolution.I have never argued that we should ignore Behe and Meyer and others just because they are creationists. We should ignore them because they are wrong about the science. Just like Otangelo Grasso is wrong about the science. "

      I do not know any other scientific camp or endaveour, where obviously false and impossible inferences are made and kept with such insistence and conviction, and over many decades, as in biology. Amazing.

      But since you disagree with me, Larry - feel free to address the five points made above, and refute my views. Thats a good chance you have right now to back up your assertion :=))

      Delete
    38. "1. the best possible genetic code out of a million"

      So what? Why does that make evolution or a natural origin of life impossible?

      "2. the gene content in the first living cell."

      All the worlds scientists will readily admit they do not know what genes the first living cell contained, or even if it had a genome in a way analogous to how cells do now.

      So what?

      "3. the genetic cipher"

      What the hell is that?

      "4. the origin of the irreducible metabolic network"

      Never heard of that one, which one is that?

      "5. how the irreducible genome, proteome"

      Never heard of these either, where are you getting this crap from?

      "... could emerge without directing and creative force ? "

      Yeah, why not?

      "Pfff haha.... In your view maybe. I have never seen a convincing alternative coming from your camp."

      Yes you have, maybe a hundred times at least. You just don't like it because it doesn't include your silly bronze-age superstition.

      Delete
    39. I'm kind of interested in seeing how these other million possible genetic codes were worked out, and how it was determined that the present one is the "best." I wonder if Otangelo will be able to provide an actual valid scientific citation for this, or if it is just another of his myriad lies.

      Anyone want to make a bet?

      Delete
    40. Actually that one isn't total bullshit. There are something like 10^84 possible genetic codes possible using triplet codons and a 4 letter genetic alphabet. Some research has shown the caconical code is among the best ones(such that 1 out of 1 milliion codes are equally good), though strictly speaking it isn't the best one possible among the entire 10^84 codes. IIRC Eugene Koonin and others have shown there are better codes near to the canonical one in the sense that it require relatively few changes to improve it. As one can guess there are evolutionary reasons why the code is why it is now and why it hasn't continued to evolve and improve.

      No, what happened to Otangelo is he read sonething with big numbers and the genetic code he doesn't understand, but it sounded sciency (big numbers, codes, oooh, ahhh) so... you can guess the rest.

      Delete
    41. Notice the last sentence in the abstract of this paper: http://www.ncbi.nlm.nih.gov/pubmed. Oh the irony.

      Delete
    42. Sorry here is the link: http://www.ncbi.nlm.nih.gov/pubmed/9732450

      Delete
    43. Here's the Koonin & Novozhilov paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

      From the discussion:
      "However, there is also a flip side to the adaptive theory as the standard code appears not to be particularly outstanding in terms of error minimization and, apparently, easily reachable from a random code with the same block structure. Statements like “the genetic code is one in a million” (or even in 100 million) are technically accurate but can be easily misconstrued should one overlook the fact that there is a huge number of possible codes that are significantly more robust than the standard code that sits on the slope of an unremarkable local peak in an extremely rugged fitness landscape."

      Delete
    44. please quote where Stephen Meyer said ID asserts the existence of a God/Creator

      Sure: Nor does the theory of intelligent design merely assert the existence of a creative intelligence behind life. It identifies and detects activity of the designer of life

      Delete
    45. Mikkel wrote

      " No, what happened to Otangelo is he read sonething with big numbers and the genetic code he doesn't understand, but it sounded sciency (big numbers, codes, oooh, ahhh) so... you can guess the rest. "

      Your incapability to not resort to personal attacks is remarkable. Your case is death, so it does not wonder you resort to these cruches. What a pitty.

      If you disagree with the science i mentioned, you should question the authors of following paper, not me.

      The genetic code is one in a million.
      http://www.ncbi.nlm.nih.gov/pubmed/9732450
      if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

      Your inability of learning is also remarkable. I posted several times here and League of Reason forum : EVOLUTION CAN ONLY ACT UPON DNA REPLICATION. There was no evolution before life got the amazing ability of replicate itself. Life depends imho of a fully setup genetic code, so the genetic code could not be result of evolution.

      Its remarkable how proponents of naturalism go great lenghts to try keep their DEATH patient ( naturalism ) alive, and behave as if nobody would see and perceive the situation. And on top of that, they think their patient is on best health. Amazing, how Dunning Kruger's effect can affect people that have aparently no problem to use their thinking capabilities.

      If you wan to learn what a cipher is, check at my virtual library following topics :

      The genetic code, insurmountable problem for non-intelligent origin

      The origin of the genetic cipher, the most perplexing problem in biology

      Origin of translation of the 4 nucleic acid bases and the 20 amino acids, and the universal assignment of codons to amino acids

      The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book ( for example hamlet) being written in english translated to chinese in a extremely sophisticared hardware system. The conclusion that a intelligent designer had to setup the system follows not based on missing knowledge ( argument from ignorance ). We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time. The genetic code and its translation system is best explained through the action of a intelligent designer.

      Delete
    46. Wow, just wow. This is so patently false I'm without words.

      Indeed, it was literally proved false in a court of law - "cdesign proponentsists," for anyone like El who's apparently been successful at intentionally blocking the memory.

      Delete
    47. Life depends imho of a fully setup genetic code, so the genetic code could not be result of evolution.

      ElShamah has an opinion, thus a century and a half of careful research by tens of thousands of scientists is out the window.

      Y'know, Larry, I'm not sure calling ID creationism, though that's certainly accurate, really gets to the core of the matter. For folks like El Shamah, I think the core is really arrogance.

      Delete
    48. He's "born again". Which is really just a term for having left behind the ability to even consider he might be wrong.

      @Otangelo

      Thank you for the references I already posted myself, which clearly show the code to be an evolved rather than designed entity. I suggest you read both of them for comprehension all the way through, rather than skim them for fancy-sounding snippets you can patch together into a fallacious argument for god.

      Delete
    49. I wonder if Otangelo would be inclined to explain why he thinks the fact that there are millions of possible genetic codes makes it less likely that it could have evolved. Otangelo: Suppose a lottery drew millions of winning numbers, instead of just one? Would that increase or decrease your chances of winning?

      Delete
    50. "Life depends imho of a fully setup genetic code, so the genetic code could not be result of evolution."

      Your opinion is of zero value or consequence. Thousands of scientists the world over have brought evidence that shows the genetic code and translation system to be a product of an evolutionary process.

      There is much debate about many aspects of the codes origin and evolution, there is almost none about whether it evolved. Because the evidence gathered so far shows that it clearly did. I have explained some of this evidence to you before. You clearly, provably did not understand it. You don't know what a phylogeny is, for example, how it is made and what it implies when it is possible to construct one from sequence data. Yes, I know, everything I just wrote is utterly beyond you.

      Regardless, I have shown you this evidence and it still exists. It did not stop existing just because you don't understand it, or because you don't like it, or because you forgot about it, or because one of your go-to ID-proponent authors is guilt of the appeal to personal incredulity-fallacy to try and dismiss it.

      This evidence is not rendered invalid by yours or anyone's opinions.

      It's remarkable how proponents of supernaturalism go to such great lenghts to try and keep their corpse (supernaturalism) animated, and behave as if nobody can see through the the bluster and ridiculous technical jargon. On top of that, they have deluded themselves so much they think their corpse is actually alive. Amazing how the Dunning Kruger-effect can influence people such that they apparently have insurmountable problems using their critical thinking abilities.

      Delete
    51. haha.

      please post how the genetic code supposedly evolved.

      Delete
    52. "please post how the genetic code supposedly evolved."

      Oh but this is not an argument from ignorance, right? Haha.

      Delete
    53. Otangelo seems unaware of a key concept in evolutionary theory, by which a biological trait or process can be optimized over successive generations as a result of random variation and differential survival. This concept is known as "natural selection". A gentleman by the name of Charles Darwin first described it. I would expect someone who claims the expertise that Otangelo ascribes to himself to be conversant with this concept, so it's puzzling that he would ask such a question.

      Delete
    54. His response to my post is a concrete instance of what I keep saying: He doesn't understand what we write.
      I told him we know THAT the code evolved, that there is evidence of this. But now he is aking me to describe HOW it evolved.

      That's not what I said. It is a triviality to demonstrate that one can know that the distance from A to B was traversed by foot without knowing what exact route was taken and where every foot was planted. This is how it is with the code and translation system. We have fragments of its history embedded in DNA and protein sequences coding for key pieces of the translation system with phylogenetic information. That would ONLY be the case if it evolved(it would be absurdly improbable that a designerbwould just so happen to design it like that). Given this, this data would be entirely unexpected on a design hypothesis and as such can only be evidence for evolution and against design.

      And now over to Otangelo's 2nd round of proving by example that he still doesn't understand any of this... (he will try to google his "virtual library" for keywords he spotted in my post and link or copy paste some irrelevant apologetics he thinks fits because it contains some of the same words).

      Delete
    55. Hey Otangelo, I have another question for you.

      I know you don't believe the genetic code evolved, but suppose for the sake of argument there was such evidence. Suppose tomorrow some scientists you trust find really good evidence the genetic code evolved. If that happened, would you then believe the genetic code evolved?

      Delete
    56. Mikkel

      i am amused, but i should actually be sad about how delusional you are towards yourself.

      Origin and evolution of the genetic code: the universal enigma
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
      In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made.
      Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.

      " suppose for the sake of argument there was such evidence. Suppose tomorrow some scientists you trust find really good evidence the genetic code evolved. If that happened, would you then believe the genetic code evolved? "

      Of course. I acknowledge without problems what is fact. In regard of evolution, that is:

      Principal Meanings of Evolution in Biology Textbooks
      http://www.jodkowski.pl/ke/Meanings2000.pdf
      What is fact :
      1. Change over time; history of nature; any sequence of events in nature
      2. Changes in the frequencies of alleles in the gene pool of a population
      3. Limited common descent: the idea that particular groups of organisms have descended from
      a common ancestor.
      4. The mechanisms responsible for the change required to produce limited descent with modification; chiefly natural selection acting on random variations or mutations

      Photosynthesis wrote:

      " Oh but this is not an argument from ignorance, right? Haha.".

      No, its not. We know that intelligence is able to invent languages and alphabets.
      We do not know of natural, aka non intelligent mechanisms with the same hability.

      We can safely conclude therefor, intelligence explains best the origin of the genetic codes.

      Thats a inference based on knowledge.

      Delete
    57. We can safely conclude therefor, intelligence explains best the origin of the genetic codes.

      Thats a inference based on knowledge.

      This fails to rise to the level of a drunken late night college dorm bullshit session, let alone decent science.

      Delete
    58. Hey, Otangelo - How did we get different languages? Did it all happen at the Tower of Babel (creationism), or did languages change over time (evolution)?

      Delete
    59. And there we have it, he did exactly what I predicted and simultaneously proved he understood nothing of what I wrote. Oh man, I could enjoy this and laugh if it wasn't so sad what religion has done to a probably perfectly nice and friendly person.

      Delete
    60. "Of course. I acknowledge without problems what is fact."

      Thank you for proving your so-called "design-inference" is at bottom an argument from ignorance.

      Delete
    61. Hey Otangelo, can you try to explain how the quote from Koonin & Novozhilov contradicts anything I wrote?

      Delete
    62. We know that intelligence is able to invent languages and alphabets.
      We do not know of natural, aka non intelligent mechanisms with the same hability.


      Hey, Otangelo, can you give an example of a "language" or "code" whose meaning can be revealed without being interpreted by an intelligent agent? For instance, if you lay a cake recipe down on your kitchen counter, does a cake suddenly appear? Or do buildings magically arise from blueprints without anyone reading them?

      Delete
    63. OG/EL of the many names states that "EVOLUTION CAN ONLY ACT UPON DNA REPLICATION." In another thread, he stated that natural selection can only happen once DNA exists.

      As a debating ploy, this could be useful; define natural selection or evolution as not occurring before DNA, and then natural selection and evolution cannot produce DNA. By definition. If this were true, all we'd have left would be the "tornado in a junkyard" version of the evolution of life, and we can all agree that didn't happen.

      Problem is, OG/EL's statement doesn't have much connection with reality. In the earliest organic chemical sludge on earth, more stable compounds would tend to accumulate, because they are more stable. Molecules that can catalyze the production of similar chemicals would accumulate, because they can, sort of, replicate. RNA, proteins, and similar chemicals would accumulate. Any molecule that happened to catalyze reactions that make it more stable or caused it to make copies would increase. In short, there was a gradual increase in complexity and replication of non-living organic chemistry before DNA was more than a rare accident, whether OG/EL wants to call this natural selection or not.

      Delete
    64. Yeah it's not like it's been proven evolution can happen before genes: Evolution before genes.

      Delete
    65. Interesting. And I'm impressed that there are people for whom "polyhypergeometric distribution" has meaning. Cool word!

      Delete
    66. Above, I asked OtangloElShamah77 the following question:

      But if "ID theory" is a genuinely scientific endeavour that purports to explain how life arose thru the actions of a "designer", then the issue of the age of the universe is crucial, since a young universe would obviously rule out some of the possible mechanisms by which this "designer" acted. But, as I hope you'll agree, the idea of a young universe is ludicrous and flies in the face of every single scrap of scientific evidence. So why don't the leaders of the ID movement use their fora such as Uncommon Descent to correct their acolytes who insist on holding to Young Earth Creationism?

      Unfortunately, it appears that Otangelo is too cowardly, too stupid or both to answer the question. But, luckily for us, one of the high priests of the ID Creationist movement, Stephen Meyer, has addressed that question, in a matter of speaking:

      http://freethoughtblogs.com/pharyngula/2016/09/12/the-age-of-the-earth-has-become-a-strangely-toxic-issue/

      PZ Myers does a good job of summarizing Stephen Meyer's pontifications, so it's not necessary to watch the whole video (unless you're a masochist). It's just worth noting that the reason the IDiots are so hesitant to address this question is that "the age of the earth has become a strangely toxic issue" among Christians. One should also note what Stephen Meyer considers the highest priority in his investigations. In his own words: “The first issue is the reality of god — is god real or imaginary?”

      Tell us again, Otangelo, how religion has nothing to do with ID creationism.

      Delete
  8. This comment has been removed by a blog administrator.

    ReplyDelete
  9. It is interesting, to this statistician and outsider to biology, to see the similarity in strength of science denial exhibited by these ID non-science creationist folks and the rejection of science exhibited by the anti-vaccine folks (they are quite strong in my region in Michigan). Both groups seem to believe that strong foot-stomping is all that is required to prove that their falsehoods are anything but false.

    ReplyDelete
    Replies
    1. It's known as "crank magnetism." Climate change denial is rife amongst the same crowd.

      Delete
    2. @Otangelo Grasso

      There are three common, non-standard, amino acids that are inserted into growing polypeptide chains during protein synthesis. They are: N-formylmethionine, pyrrolysine, and selenocysteine. Do you know the process for inserting these amino acids? Do you understand what it has to do with the evolution of the standard genetic code?

      There are several species of bacteria that cannot attach asparagine or glutamine to specific tRNAs because they lack the proper aminoacyl-tRNA synthetases. Nevertheless, they are able to insert those amino acids at the proper place during protein synthesis. Do you know how they do this? Do you understand what it means for understanding the evolution of the standard genetic code?

      Delete
    3. Laurence asked several questions.

      My answer : A no to all of them.

      Now please explain, how the answers explain the natural origin of the genetic code.

      And you wrote above :

      " I have concentrated (successfully in my view) on showing that Intelligent Design Creationists do bad science. "

      You need a case that stands on its own. Its your turn to show that naturalism provides " good " scientific explanations.

      I gave you oportunity above, to answer five questions.

      Will you ignore them and lose the excellent oportunity i am giving you, Larry ?

      But don't worry. I know about the daunting task you have. To make shit up and sell it as if it were smelling like a Versace classic perfume, is a impossible task. So i don't expect you to succeed well.....

      Delete
    4. Otangelo Grasso,

      Why do you think Larry and people like him can make shit up and get away with it? How in the world, where the vast majority of people believe in God/Supernatural/ID/Creator etc. the minuscule minority can make up shit, have no evidence for their shit and claim it is science and put it in text books? How is it possible? Can you explain?

      Delete
    5. We are all so grateful for being given these excellent opportunities.

      Delete
    6. Laurence asked several questions.

      My answer : A no to all of them.

      Now please explain, how the answers explain the natural origin of the genetic code.


      Reading Otangelo's proud statement of his ignorance, and his continued certainty in spite/because of it, one is reminded of the philosopher and theologian Bishop Nicholas of Cusa, who once wrote, "Ignorance will enlighten us in incomprehensible ways."

      Delete
  10. Velhovsky asked:

    " Why do you think Larry and people like him can make shit up and get away with it? "

    Larry et al do not get away with it within ID theorists. There is maybe no other scientific endaveour, which has misled more people and over a bigger period of time, than biology through Darwins Theory of evolution. The result is many generations of biologists, which have been indoctrinated in a theory, which was based on bad pseudo scientific claims, sold as if they were facts. But the courtine is being lifted, and the real situation is coming up to light. This is not something, that will happen from night to day. It will take at least a generation. We are in the middle of it. It started twenty years ago. The extended evolutionary synthesis (EEL) is very shy with its renewed proposals of predicitions, and is running behind new findings, and is not incorporating the fully extended and manyfold, cell and organism-wide mechanisms that have been discovered, to elaborate new predictions. But back to your question. I see a few reasons. 1. People are lazy to think. 2. Confirmation bias. 3. People like to believe authorities of science, without looking themself into the science 4. Most people do not understand biology and the theory of evolution 5. People do not like the philosophic and religious implications by admitting design and creationism. 6. People love their sinful life and reject God , and search reasons to deny his existence. 7. People are unable to think logically and clearly.

    ReplyDelete
    Replies
    1. All those biologists sure are dummies. Good thing you are on the case. All these biologists are out poking around in the rain forest and in labs all over the world when all one really needs to do is sit in one's favourite chair and think really hard. Bunch of dummies. Doing it all wrong!

      Delete
    2. Now, now. Don't ignore all those breakthroughs and discoveries that have been made by "ID theorists." Such as, well, uhh....

      Delete
    3. "1. People are lazy to think. 2. Confirmation bias. 3. People like to believe authorities of science, without looking themself into the science 4. Most people do not understand biology and the theory of evolution 5. People do not like the philosophic and religious implications by admitting design and creationism. 6. People love their sinful life and reject God , and search reasons to deny his existence. 7. People are unable to think logically and clearly."

      https://en.wikipedia.org/wiki/Psychological_projection.

      Delete
    4. All those biologists sure are dummies. Good thing you are on the case. All these biologists are out poking around in the rain forest and in labs all over the world when all one really needs to do is sit in one's favourite chair and think really hard. Bunch of dummies. Doing it all wrong!

      Delete
    5. The many faces of Otangelo Grasso:

      "Otangelo Grasso September 8, 2016 at 3:47 pm
      ID will never be a position held by the majority, or a real status quo shifter . Simply, because if you accept it, you need to accept logically God. Most proponents of evolution do not keep their belief in it, because its rationally the best explanation, and where science leads to, but they are driven by the wish and will of God not to exist. First, they want God out of their lives, and then they do everything to justify their prejudice rationally."

      Delete
    6. It's quite amusing how Otangelo tries to spin the fact that the IDiots are almost monolithically Christian fundamentalists into a claim that it is those who accept evolution that are motivated by religious prejudice.

      Delete
    7. His views also completely fails to account for christian religious believers who do accept evolution. People like Francis Collins and Kenneth Miller come to mind. And then there's those among the founders of the modern synthesis like Dobzhansky and probably many more I don't even know about. All of the god-believing christians who think Evolutionary theory is the evidentially best supported and tested, scientific explanation for extant biodiversity.

      Delete
    8. It's almost certainly the case that the large majority of people who accept evolution also believe in God, just by statistics alone. In the US, only 7% of people identify themselves as "atheist" or "agnostic", whereas 60% accept evolution. Even if you remove the 24% who believe evolution was guided by a "supreme being", that still leaves a large excess for which Otangelo has to account. I wonder if he can perform simple addition and subtraction?

      http://www.pewforum.org/2013/12/30/publics-views-on-human-evolution/

      https://en.wikipedia.org/wiki/Religion_in_the_United_States#Pew_Research_Center_data

      Delete
    9. Yeah there is a large difference however between the general public, and scientists. The most "atheistic" fields in science are evolutionary biology (at something like 97% of biologists with a degree in something evolution-related IIRC), followed by cosmology and astrophysics.

      It's funny that those are the two scientific fields apologists and theologians claim most testify to god's existence, yet the people who studied, got their degrees and do research and publish in them came to diametrically opposite conclusions.

      Oh wait sorry I forgot, it's because they just hate god and want to sin.

      Delete
    10. Ontagelo Grasso,

      You are right on the money. I put pretty much the same you said in the terms of "truth", which also depends on ones prospective. But what you need to remember that the first is:

      what people want to hear
      what people want to believe
      everything else, then there is there’s the truth!

      Why would the truth be the last? Because the truth means responsibility, which is why almost everyone dreads it!

      Delete
    11. luitesuite,

      It's almost certainly the case that the large majority of people who accept evolution also believe in God, just by statistics alone. In the US, only 7% of people identify themselves as "atheist" or "agnostic", whereas 60% accept evolution. Even if you remove the 24% who believe evolution was guided by a "supreme being", that still leaves a large excess for which Otangelo has to account. I wonder if he can perform simple addition and subtraction?

      http://www.pewforum.org/2013/12/30/publics-views-on-human-evolution/


      Well, since the support seems so strong for your beliefs, do you think that nobody has to do any experiments anymore? As far as I remember there is not one piece of experimental evidence for the origins of life, eukaryotic cells origins, which are the essential components of your beliefs. Why would you think that even 99% support of US overeducated nation would fill this huge gap? Just because the majority of ordinary people and scientists don't understand what "evolution" means? Well, let me assure you that nobody does... and this is the ONLY FACT about your religion called evolution!

      Delete
    12. "I put pretty much the same you said in the terms of "truth", which also depends on ones prospective...

      what people want to hear
      what people want to believe
      everything else, then there is there’s the truth!"


      Oh look, more https://en.wikipedia.org/wiki/Psychological_projection.

      "Because the truth means responsibility, which is why almost everyone dreads it!"

      Same dumb shit again. Seriously, do you really, REALLY believe people just decide to not believe in something just because they might not like it? Last I checked, the world is full of terrible things I despise and would like changed, yet I still believe them. For example, Donald Trump is running for US president. What a preposterous state of affairs. Yet I can't deny it, I just don't work like that. I can't just make myself not believe in things I don't like.

      My grandfather on my father's side died a few years ago. I loved him very much and I would honestly, truly welcome it, if it could be shown to me there's an afterlife where I'd get to hold just one more conversation with him.

      The current president of North Korea is a brutal, despicable dictator that holds an entire country of tens of millions of people hostage in the most brutal and unjust regime in human history. The amount of suffering and injustice taking place in that country is unimaginable. How I would love it if there really was a just and merciful God that could right that wrong. If there's a person one could argue would really deserve a visit to hell, It'd be Kim Jong Un.

      I'm sorry to say this, but this emotional rationalization you guys make up about why atheists and evolutionists don't accept your religious views simply don't hold up to scrutiny. It is an excuse your tell yourselves because the very existence of nonbelief is a threat to the truth of your religion.

      In actual fact, the people who's views are the most colored by wishful thinking and denial, are yours. You want afterlives and an enternally loving father to watch over you. You are children who can't bear the reality you live in.

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    13. "Because the truth means responsibility, which is why almost everyone dreads it!" I agree. There isn't a god, so it's up to us humans to feed the hungry, care for the sick, help the poor, etc. In order to help the greatest number of people, we need to fund programs like SNAP (formerly, food stamps), WIC, welfare, and universal health care. These programs cost money and we, all of us, have a responsibility to pay that money (taxes). More taxes than we now pay. Too many people want to deny God's absence and thus deny or evade the responsibility we have to care for each other.

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    14. @ Velhovsky,

      How about you first understand what I was actually writing about, then ask some questions about that, rather than just spewing irrelevant inanities. TIA.

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    15. do you think that nobody has to do any experiments anymore?

      You haven't visited a college library and read an academic journal in, oh, forever, have you?

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  11. So it's a giant conspiracy by people who hate god and only people who believe in god can see through it. Funny that.

    Oh btw, this is all about science not about religion and gods. Says "born again" Otangelo.

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  12. Off topic, but a while back, Larry blogged about the questions posed to US presidential candidates by the Science Debate. Trump has finally answered. Mostly he's bullshitting, trying to be appear to be answering the question while not answering it. But his constant references to "priorities" seem to imply cutting research funding and doing nothing about global warming.

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    1. His responses are pretty much in line with the current Republican stance: emphasize the evils of government environmental actions, make sure all views of "the people" are heard, ignore climate change ("perhaps" by concentrating on issues - which are are, in fact, exacerbated by climate change) and so on.

      In short: nothing new to see in his responses, more of the same denial of both the importance of basic science and the urgency of dealing with climate change.

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  13. How can any look at this most definitely functional lncRNA structure which helps control plant flowering and not conclude that it is a well-designed complex digital code?

    http://www.lncrnablog.com/study-unveils-hidden-molecular-machinery-in-rna-processes/

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    1. What exactly makes you think that it's a well-designed complex digital code? I see a bunch of "stems" and "loops" of the kinds that naturally form in most random RNA molecules.

      (Careful there! I did not say that the molecule is random, I said that similar bunches of stems and loops form naturally in random molecules. So, I'm not surprised by the structure.)

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