Announcement

Collapse

Natural Science 301 Guidelines

This is an open forum area for all members for discussions on all issues of science and origins. This area will and does get volatile at times, but we ask that it be kept to a dull roar, and moderators will intervene to keep the peace if necessary. This means obvious trolling and flaming that becomes a problem will be dealt with, and you might find yourself in the doghouse.

As usual, Tweb rules apply. If you haven't read them now would be a good time.

Forum Rules: Here
See more
See less

A "junk DNA" discussion

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • A "junk DNA" discussion

    There was recently a research article describing the genome of the lone insect native to Antarctica - the university's press release on it is here: https://news.wsu.edu/2014/08/12/rese.../#.U_N7ZEtXrNY

    The most unusual thing about the genome: very little repetitive DNA, very few transposable elements, and shorter introns. The net result is that this is the smallest insect genome yet sequenced. The authors think that the rough environmental conditions have selected for a streamlined genome, and as a result, a lot of the "junk DNA" has been deleted.

    I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA, since a lot of people have lots of misconceptions regarding it. I'll provide a short discussion of what we know, and then i'd be happy to answer any questions people have. (I did about 20 years of research in biology before changing jobs.)

    What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.

    Junk DNA is a subset of the following: disabled genes, disabled viruses, transposable elements, and repetitive DNA. A small subset of this DNA does have a function - for example, there was a recent estimate that a bit under 10% of the disabled genes in the human genome now make RNAs that perform regulatory functions without encoding a protein. But the majority of it performs no known function. And, accordingly, it's not conserved between species - while humans and chickens share many identical coding and regulatory DNA sequences, they share very little repetitive DNA.

    How does junk DNA come about? Several known processes create DNA that performs no useful biological function. For example, many viruses insert into the genome as part of their normal lifestyle - behavior that's good for the virus, but not the owner of the genome. The normal process of copying DNA often makes mistakes when it comes to repetitive sequences (think 37 copies of "AT" in a row), adding to the number of copies. And duplications and deletions of DNA occur all the time (google "Copy Number Variations") and many people have them present in their own genome. All of these processes produce DNA that is not useful to their organism.

    As a result, some amount of junk DNA is inevitable - processes we can observe create it all the time. So the big question is not whether it exists, but how much of it is there. Only two processes can get rid of it: modification into usefulness or deletion. The first has been known to happen; a number of genes in the human genome came about through the modification of pieces of virus DNA. But it appears to be rare; most viruses aren't anywhere near a gene. So the majority of the junk pruning takes place through deletion.

    As a result, the amount of junk DNA in a genome is the balance between the creative processes and deletion of DNA.

    In most cases, organisms seem to tolerate a lot of junk DNA. Pines, for example, all have 12 chromosomes, each of which is nearly as large as the entire human genome - the majority of the DNA is for transposable elements. In contrast, there are a few species, like this Antarctic insects, where conditions are harsh enough that any little bit helps with survival. As a result, these organisms have very little of the repetitive DNA.


    Hopefully, this clarifies the situation somewhat. If there are things people want more details about, I'd love to have a discussion of it.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  • #2
    I started a thread a while back called "the function wars", which was entirely about what constitutes junk DNA. That post had quite a few links to different aspects of the debate. But nobody answered.

    Comment


    • #3
      Originally posted by TheLurch View Post
      There was recently a research article describing the genome of the lone insect native to Antarctica - the university's press release on it is here: https://news.wsu.edu/2014/08/12/rese.../#.U_N7ZEtXrNY

      The most unusual thing about the genome: very little repetitive DNA, very few transposable elements, and shorter introns. The net result is that this is the smallest insect genome yet sequenced. The authors think that the rough environmental conditions have selected for a streamlined genome, and as a result, a lot of the "junk DNA" has been deleted.

      I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA, since a lot of people have lots of misconceptions regarding it. I'll provide a short discussion of what we know, and then i'd be happy to answer any questions people have. (I did about 20 years of research in biology before changing jobs.)

      What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.

      Junk DNA is a subset of the following: disabled genes, disabled viruses, transposable elements, and repetitive DNA. A small subset of this DNA does have a function - for example, there was a recent estimate that a bit under 10% of the disabled genes in the human genome now make RNAs that perform regulatory functions without encoding a protein. But the majority of it performs no known function. And, accordingly, it's not conserved between species - while humans and chickens share many identical coding and regulatory DNA sequences, they share very little repetitive DNA.

      How does junk DNA come about? Several known processes create DNA that performs no useful biological function. For example, many viruses insert into the genome as part of their normal lifestyle - behavior that's good for the virus, but not the owner of the genome. The normal process of copying DNA often makes mistakes when it comes to repetitive sequences (think 37 copies of "AT" in a row), adding to the number of copies. And duplications and deletions of DNA occur all the time (google "Copy Number Variations") and many people have them present in their own genome. All of these processes produce DNA that is not useful to their organism.

      As a result, some amount of junk DNA is inevitable - processes we can observe create it all the time. So the big question is not whether it exists, but how much of it is there. Only two processes can get rid of it: modification into usefulness or deletion. The first has been known to happen; a number of genes in the human genome came about through the modification of pieces of virus DNA. But it appears to be rare; most viruses aren't anywhere near a gene. So the majority of the junk pruning takes place through deletion.

      As a result, the amount of junk DNA in a genome is the balance between the creative processes and deletion of DNA.

      In most cases, organisms seem to tolerate a lot of junk DNA. Pines, for example, all have 12 chromosomes, each of which is nearly as large as the entire human genome - the majority of the DNA is for transposable elements. In contrast, there are a few species, like this Antarctic insects, where conditions are harsh enough that any little bit helps with survival. As a result, these organisms have very little of the repetitive DNA.


      Hopefully, this clarifies the situation somewhat. If there are things people want more details about, I'd love to have a discussion of it.
      There is this opinion from Nature:-

      Furore over genome function

      A recent PLoS had an interesting article:-

      The case for junk DNA

      Comment


      • #4
        It would be interesting to hear from an anti-evolutionist who claims that "junk" DNA does not exist.

        Likely the discussion would follow a path similar to vestigial structures.

        K54

        Comment


        • #5
          Originally posted by TheLurch View Post
          There was recently a research article describing the genome of the lone insect native to Antarctica - the university's press release on it is here: https://news.wsu.edu/2014/08/12/rese.../#.U_N7ZEtXrNY

          The most unusual thing about the genome: very little repetitive DNA, very few transposable elements, and shorter introns. The net result is that this is the smallest insect genome yet sequenced. The authors think that the rough environmental conditions have selected for a streamlined genome, and as a result, a lot of the "junk DNA" has been deleted.

          I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA, since a lot of people have lots of misconceptions regarding it. I'll provide a short discussion of what we know, and then i'd be happy to answer any questions people have. (I did about 20 years of research in biology before changing jobs.)

          What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.

          Junk DNA is a subset of the following: disabled genes, disabled viruses, transposable elements, and repetitive DNA. A small subset of this DNA does have a function - for example, there was a recent estimate that a bit under 10% of the disabled genes in the human genome now make RNAs that perform regulatory functions without encoding a protein. But the majority of it performs no known function. And, accordingly, it's not conserved between species - while humans and chickens share many identical coding and regulatory DNA sequences, they share very little repetitive DNA.

          How does junk DNA come about? Several known processes create DNA that performs no useful biological function. For example, many viruses insert into the genome as part of their normal lifestyle - behavior that's good for the virus, but not the owner of the genome. The normal process of copying DNA often makes mistakes when it comes to repetitive sequences (think 37 copies of "AT" in a row), adding to the number of copies. And duplications and deletions of DNA occur all the time (google "Copy Number Variations") and many people have them present in their own genome. All of these processes produce DNA that is not useful to their organism.

          As a result, some amount of junk DNA is inevitable - processes we can observe create it all the time. So the big question is not whether it exists, but how much of it is there. Only two processes can get rid of it: modification into usefulness or deletion. The first has been known to happen; a number of genes in the human genome came about through the modification of pieces of virus DNA. But it appears to be rare; most viruses aren't anywhere near a gene. So the majority of the junk pruning takes place through deletion.

          As a result, the amount of junk DNA in a genome is the balance between the creative processes and deletion of DNA.

          In most cases, organisms seem to tolerate a lot of junk DNA. Pines, for example, all have 12 chromosomes, each of which is nearly as large as the entire human genome - the majority of the DNA is for transposable elements. In contrast, there are a few species, like this Antarctic insects, where conditions are harsh enough that any little bit helps with survival. As a result, these organisms have very little of the repetitive DNA.


          Hopefully, this clarifies the situation somewhat. If there are things people want more details about, I'd love to have a discussion of it.
          You begin by saying: "I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA ..."

          Yet much of what you subsequently write is chock-full of metaphysics. The mere fact that you believe that there is "junk DNA" and then proceed to justify this belief through semantic manipulation of what constitutes "junk DNA" is proof enough of this. This 'contradiction' between what you say and what you do doesn't surprise me in the least but I just wanted to let you know that it did not go unnoticed.

          Do carry on with your thread...

          Jorge

          Comment


          • #6
            Originally posted by Jorge View Post
            Yet much of what you subsequently write is chock-full of metaphysics.
            Coming from a person who thinks basic energy calculations are metaphysically loaded, i'm not at all surprised you'd claim this.
            "Any sufficiently advanced stupidity is indistinguishable from trolling."

            Comment


            • #7
              Originally posted by Jorge View Post
              You begin by saying: "I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA ..."

              Yet much of what you subsequently write is chock-full of metaphysics. The mere fact that you believe that there is "junk DNA" and then proceed to justify this belief through semantic manipulation of what constitutes "junk DNA" is proof enough of this. This 'contradiction' between what you say and what you do doesn't surprise me in the least but I just wanted to let you know that it did not go unnoticed.

              Do carry on with your thread...

              Jorge
              See people -- I told ya so.

              Also, note the projection of that metaphysics crack.

              Jorge, you NEVER cease to entertain!

              Thanks,

              K54

              Comment


              • #8
                Originally posted by Jorge View Post
                You begin by saying: "I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA ..."

                Yet much of what you subsequently write is chock-full of metaphysics. The mere fact that you believe that there is "junk DNA" ...
                The existence of junk DNA in the human genome is a conclusion based on observations, not a metaphysical assumption. Genetic fingerprinting depends on the fact that different people's DNA contains different numbers of repeats of some repeated nucleotide chains. Since the additional repeats exist in some people's DNA and not in others', those additional repeats which are present in only a fraction of the population are apparently not necessary. Thus they are considered to be junk DNA.
                If you have a scientific reason to believe they are not just accumulated junk, feel free to present it.

                Roy
                Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

                Mountain Man: First of all, the Bible is a fixed document.
                Mountain Man: this is how liberals argue these days, with labels instead of ideas.

                Comment


                • #9
                  Originally posted by TheLurch View Post
                  What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.
                  .
                  this is almost like a 'Darwin of the Gaps' argument.


                  note that when the ncRNA/ncDNA is deleted or repressed, often its other ncRNA that does the clean up
                  This review includes a summary of seminal findings regarding the impact of ncRNAs on biological and pathological processes, which may be further modified by RNA editing. NcRNAs are non-translated RNAs classified by size and function. Known ncRNAs like miRNAs, smallRNAs (smRNAs), PIWI-interacting RNAs (piRNAs), and lncRNAs play important roles in splicing, DNA methylation, imprinting, and RNA interference
                  http://www.ncbi.nlm.nih.gov/pubmed/23346095
                  Scientists thought DNA that didn't code for proteins (noncoding) must just be junk, SO they didn't bother with it, instead concentrating on the 2% of the genome that did. With newer detection technologies, they discovered that there was actually quite of bit of transcription going on in the parts of the genome that didn't code for proteins, but they dismissed it as "white noise" or "transcriptional noise":
                  Often it takes scientists time to understand the true function of some biological structure that may at first appear purposeless, perhaps even pointless. White matter in the brain, for instance, was long thought to be merely passive tissue, especially when compared to the seemingly more vital gray matter, but now it is known that white matter actively coordinates communication within the brain. Similarly, small non-coding RNAs, which are chaotically distributed throughout a cell, were simply thought to be "transcriptional noise," in the words of Dr. Steven Jones, a professor at Simon Fraser University and the University of British Columbia. After all, scientists could never assign them an actual function or see their connection to any disease. Now, though, Jones and his colleagues have discovered that small non-coding RNAs can be used to predict whether an individual has breast cancer and even more, these molecules may even predict survival outcomes for patients
                  http://www.medicaldaily.com/breast-c...e-cells-269423
                  The ncDNA may not code for protein, but it still performs the important FUNCTION of transcription, and its product is more so-called "junk" , but important ncRNA:
                  Transcription of ncDNA occurs throughout eukaryotic genomes, generating a wide array of ncRNAs. One large class of ncRNAs includes those transcribed over the promoter regions of nearby protein coding genes. Recent studies, primarily focusing on individual genes have uncovered multiple mechanisms by which promoter-associated transcriptional activity locally alters gene expression
                  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149688/
                  one pair of useful ncRNAs is Xist and Tsix
                  THE EPIGENETICS REVOLUTION Nessa Carey ISBN 9780231161169
                  p 163-164
                  ...But before RNA molecules can code for protein, they have to move out of the nucleus and into the cytoplasm of the cell. This is because the ribosomes--the intracellular factories that join amino acids into long protein chains -- are only found in the cytoplasm. But the Xist RNA never moved out of the nucleus, which meant it could never generate a protein....
                  ....but since Xist never actually leaves the nucleus, its lack of potential protein coding is irrelevant. Xist doesn't act as a messenger RNA (mRNA) that transmits the code for a protein. It is a class of molecule called a non-coding RNA (ncRNA). Xist may not code for a protein, but this doesn't mean it has no activity. Instead, the Xist ncRNA itself acts as a functional molecule, and it is critical for X inactivation.
                  p 167-168
                  There is another non-coding RNA, about 40kb in length, in the same stretch of DNA as Xist. It overlaps with Xist but is on th opposite strand of the DNA molecule. It is transcribed into RNA in the opposite direction to Xist and is referred to as an antisense transcript. Its name is Tsix. The eagle-eyed reader will notice that Tsix is Xist backwards, which has an unexpectedly elegant logic to it.
                  This overlap in location between Tsix and Xist is really significant in terms of how they interact, but it makes it exceedingly tricky to perform conclusive experiments. That's because it's very difficult to mutate one of the genes without mutating its partner on the opposite strand, a sort of collateral damage. Despite this, considerable strides have been made in understanding how Tsix influences Xist.
                  If an X chromosome expresses Tsix, this prevents Xist expression from the same chromosome. Oddly enough, it may be the simple action of transcribing Tsix that prevents the Xist expression, rather than the Tsix ncRNA itself. This is analogous to a mortice lock. If I lock a mortice from the inside of my house and leave the key in the lock, my partner can't unlock the door from outside of the house. I don't need to keep locking the door, just having the key in there is enough to stop the action of someone on the other side. So, when Tsix is switched on, Xist is switched off and the X chromosome is active.
                  and other useful ncRNAs from another Epigenetics book:
                  EPIGENETICS The Ultimate History of Inheritance Richard C. Francis ISBN 9780393070057
                  p 130
                  We have already met one type of RNA involved in epigenetic regulation called Xist, which plays a central role in X-chromosome inactivation. Most of the RNAs with epigenetic functions are much smaller than Xist, however. Many, in fact, are extremely small. One important group of these tiny noncoding RNAs is called microRNAs.
                  Epigenetic gene regulation by microRNAs works quite differently than either methylation or histone binding. Most significantly, microRNAs act later in the protein synthesis process. Recall from Chapter 2 that protein synthesis occurs in two stages. During the first stage, called transcription, messenger RNA (mRNA) is constructed from the DNA template. During the second stage, called translation, a protoprotein is constructed from the RNA template. Most epigenetic gene regulation occurs at the first stage, usually by inhibiting transcription MicroRNAs, in contrast, exert their influence during the second stage, translation.
                  Though transcription is highly regulated, it is often the case that there are too many mRNA transcripts from a particular gene for a cell's purpose. If a cell "decides" that this is the case, it deploys microRNAs to remedy the situation. The microRNAs identify the particular mRNAs that are overabundant and mark them for destruction. The microRNAs must physically bind to the messenger RNAs at a site where they are complementary. The microRNA doesn't have to be completely complementary, just complementary enough to stick to the much larger mRNA. That means there can be many fewer types of microRNAs than there are types of mRNA transcripts. Sometimes the binding of a microRNA to an mRNA is sufficient to block the translation of the mRNA into protein. Sometimes the microRNA, in addition, attracts proteins, including enzymes, which actively degrade the mRNA. In either case, the net result is that thre is less mRNA available to serve as a template for protein construction. This microRNA-based form of gene regulation, known as RNA interference, functions as a way to fine-tune the amount of protein that is made from a particular gene. Some have likened it to a light dimmer.
                  MicroRNAs play a major role in normal cellular differentiation. It appears that one of the primary functions of microRNAs at the cellular level is to stabilize the differentiation state of the cell. One study suggests that microRNAs don't drive the differentiation but rather prevent dedifferentiation
                  the discoveries of Functional "junk" is generating books and more books, here, one more:
                  STRESS-INDUCED MUTAGENESIS David Mittelman ISBN 9781461462798
                  p 159
                  MicroRNAs (miRNAs), which offer the advantages of rapid, reversible, and localized protein expression regulation, have recently been recognized as important contributors to the hypoxic stress response (Pocock 2011). Studies have found in excess of 90 miRNAs regulated by hypoxia, though only a few of these have been studied in detail (Pocock 2011). HIF (hypoxis-inducible factors) directly up-regulates at least six miRNAs (miRNA-23, 24, 26, 107, 210, 373)
                  and if you don't like trips to the library or amazon (link above, support TWEB!) plenty of info online medical sites etc, especially since Cancer research involves study of ncRNA
                  Cancer regulator microRNA: potential relevance in diagnosis, prognosis and treatment of cancer.

                  Fiorucci G1, Chiantore MV, Mangino G, Percario ZA, Affabris E, Romeo G.
                  Abstract
                  MicroRNAs (miRNAs) are small (typically 22 nucleotides) non-coding, endogenous, single-stranded RNAs. MiRNA genes are evolutionarily conserved and are located within the introns or exons of protein-coding genes, as well as in intergenic areas. Before the discovery of miRNAs, it had been known that a large part of the genome is not translated into proteins. This so called "junk" DNA was thought to be evolution debris with no function. Recently, the explosive research in this area has established miRNAs as powerful regulators of gene expression. While only about 1,424 human miRNA sequences have been identified so far, genomic computational analysis indicates that as many as 50,000 miRNAs may exist in the human genome, and each may have multiple targets based on similar sequences in the 3'-UTR of mRNA. MiRNAs have been implicated in different areas such as the immune response, neural development, DNA repair, apoptosis, oxidative stress response and others and it is impressive the list of diseases which have recently been found to be associated with abnormal miRNA expression
                  http://www.ncbi.nlm.nih.gov/pubmed/22204349
                  But its hard to keep up with all the new ncRNAs, an interesting one for example "HOTAIR"
                  A particularly interesting example of myogenic hypermethylation was HOTAIR, a HOXC noncoding RNA gene, which can silence HOXD genes in trans via recruitment of polycomb proteins. In myogenic progenitor cells, the preferential expression of HOTAIR was associated with hypermethylatino immediately downstream of the gene. Other HOX gene regions also displayed myogenic DNA hypermethylation despite being moderately expressed in myogenic cells. Analysis of representative myogenic hypermethylated sites for 5-hydroxymethylcytosine revealed little or none of this base, except for an intragenic site in HOXB5 which was specifically enriched in this base in skeletal muscle tissue, wherea myoblasts had predominantly 5-methylcytosine in the same CpG site.
                  CONCLUSIONS
                  Our results suggest that myogenic hypermethylation of HOX gens helps fine-tune HOX sense and antisense gene expression through effects on 5' promoters, intragenic and intergenic enhancers and internal promoters. Myogenic hypermethylation might also affect the relative abundance of different RNA isoforms, facilitate transcription termination, help stop the spread of activation-associated chromatin domains and stabilize repressive chromotin structures.
                  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750649/
                  BUT over expression of HOTAIR might have something to do with Cancer progression
                  Previously unexamined, this study focuses on HOTAIR over expression and compares the relationship in different cancers. Here, it is suggested that HOTAIR might serve as a general biomarker for neoplastic diseases. Moreover, further investigation of HOTAIR’s presence and mechanism of action could result in less invasive therapies and diagnostic tests with direct applications in a clinical setting...
                  Introduction

                  The human genome project discovered that only about 20,000 genes encoded protein, while the remaining 99% of the genome was left non-coding and hence non-functional (Lander et al., 2001). The current opinion in genetics, however, suggests the opposite.

                  The functions of non-coding RNA have begun to emerge with compelling evidence of a role in gene regulation. The transcriptome is defined as the total RNA transcribed from DNA and includes both coding and non-coding transcripts. Within the non-coding transcript there are two sub divisions: long ncRNA (lncRNA) and short ncRNA (sncRNA), both of which are characterized physically by the sequence length of the transcript. The functional definition of the non-coding transcript is accepted as the genetic information that does not code for protein, the latter being the functional unit of life. Consequently this definition yields little importance to the non-coding portion of the genome. However, it cannot be overlooked that the non-coding transcript comprises 99% of the genomic information. Thus, it is no surprise that these non-coding transcripts do indeed possess functions that are important. The importance of these non-coding transcripts has only recently been elucidated (Dermitzakis et al., 2005)
                  http://www.jyi.org/issue/the-rna-hot...ion-in-cancer/
                  but if HOTAIR gets out of hand, maybe it can be "knocked down"
                  BY ANOTHER PIECE OF "JUNK"!!, the noncoding RNA called 'siRNA' (small inhibitory RNA):
                  "All cells in a single organism carry the exact same genome, so how do we end up with so many varieties of tissues and organs? Scientists know that transcription of many genes in eukaryotic cells is repressed, or "silenced," but in some cases, genes are transcribed into mRNA that never gets translated. Various post-transcriptional mechanisms are in place to add another level of control over the already complex systems that regulate eukaryotic gene expression. These mechanisms are the result of small, noncoding pieces of RNA called siRNA (small inhibitory RNA), or interference RNA, and miRNA (microRNA), or antisense RNA."
                  http://www.nature.com/scitable/topic...xpression-1078
                  a KNOCK DOWN,
                  Inhibition of HOTAIR Reduced Invasiveness of GC Cells
                  To further examine the functional role of HOTAIR in GC cells, AGS cells, which expressed high level of endogenous HOTAIR, were transfected with siRNA duplexes against HOTAIR. The successful knockdown of HOTAIR expression was confirmed by real-time RT-PCR (Figure 3A). Transwell Matrigel invasion assays showed that down-regulation of HOTAIR by siRNAs caused significant decrease in the cell invasiveness.
                  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708039/
                  I been told, "ain't science great"
                  yeah, ain'it
                  To say that crony capitalism is not true/free market capitalism, is like saying a grand slam is not true baseball, or like saying scoring a touchdown is not true American football ...Stefan Mykhaylo D

                  Comment


                  • #10
                    Originally posted by jordanriver View Post
                    tScientists thought DNA that didn't code for proteins (noncoding) must just be junk, SO they didn't bother with it, instead concentrating on the 2% of the genome that did.
                    I don't think this is quite correct. There were some parts of the genome which were known to be functional other than for protein generation - centromeres, for example - before the protein code was worked out. Although scientists did concentrate on the DNA that coded for proteins, there was never any assumption that everything that didn't code for proteins was junk.

                    Roy
                    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                    mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

                    Mountain Man: First of all, the Bible is a fixed document.
                    Mountain Man: this is how liberals argue these days, with labels instead of ideas.

                    Comment


                    • #11
                      Originally posted by Roy View Post
                      The existence of junk DNA in the human genome is a conclusion based on observations, not a metaphysical assumption. Genetic fingerprinting depends on the fact that different people's DNA contains different numbers of repeats of some repeated nucleotide chains. Since the additional repeats exist in some people's DNA and not in others', those additional repeats which are present in only a fraction of the population are apparently not necessary. Thus they are considered to be junk DNA.
                      If you have a scientific reason to believe they are not just accumulated junk, feel free to present it.

                      Roy
                      I wish certain people were brighter and more honest, but that's just a wish.

                      I'll write a few comments towards your nonsense and leave it at that ...............

                      "The existence of junk DNA in the human genome is a conclusion based on observations, not a metaphysical assumption." WRONG! From the very first time that non-coding DNA was discovered it was immediately labeled "junk" by the Evo-Faithful. Why? Because this was interpreted as "evidence" of an Evolutionary history leaving behind "discarded remnants". That interpretation was via a metaphysical position that assumed Evolution. Since those early beginnings, what have we ACTUALLY observed? We've observed more and more that what was once thought to be "junk" is actually highly functional - hardly "junk". That's an observed, verifiable fact.


                      "Genetic fingerprinting depends on the fact that different people's DNA contains different numbers of repeats of some repeated nucleotide chains. Since the additional repeats exist in some people's DNA and not in others', those additional repeats which are present in only a fraction of the population are apparently not necessary. Thus they are considered to be junk DNA." Not knowing the function of something does not logically imply that it's not needed. Even the most dense amongst you people should have learned that lesson by now. TO WIT: once upon a time the list of vestigial organs was quite lengthy. Today that list is essentially non-existent. Why? Because in time the (critical) functions of those "useless" structures were discovered. Yet you people continue making the same stupid mistake, this time with "junk" DNA. Some people just never learn.


                      "If you have a scientific reason to believe they are not just accumulated junk, feel free to present it."
                      Don't be so freagin' naive or dishonest or both! If I knew what the function was of all of the non-coding DNA, I'd be packing my bags right now for Stockholm to pick up my two or three Nobel Prizes.

                      I can, nonetheless, give you perfectly logical, supported arguments to believe that they are not just accumulated junk. The support comes from the scientific findings to date. Hardly a day goes by without some news about a scientific discovery about the function of a previously-thought section of "junk" DNA.

                      The trend is clear except to those that wish to defend their Sacred Cow (Evolution) to the bitter end. I'll even make a prediction here and now and in black and white:
                      as time goes on, more and more and more evidence will continue to accumulate that the only "junk" is the notion of "junk DNA". While there may be some - a very, very minute quantity - of DNA that has been turned to (actual) junk (i.e., rendered useless/harmful) through a number of possible causes, generally speaking there is no "junk" in the DNA. That's my prediction ... now just wait and see.

                      Jorge

                      Comment


                      • #12
                        [QUOTE=Jorge;90797]"The existence of junk DNA in the human genome is a conclusion based on observations, not a metaphysical assumption." WRONG! From the very first time that non-coding DNA was discovered it was immediately labeled "junk" by the Evo-Faithful.
                        Could I get a citation for this? Because (as i mentioned in the original post) some non-coding DNA was known to be functional back in the 1960s. I'm not sure we had much of a sense that there was non-coding DNA before then.

                        Originally posted by Jorge View Post
                        Not knowing the function of something does not logically imply that it's not needed.
                        Ok, but let's say polymerase slippage adds a couple of copies of AT to a long stretch of ATs. Are the extra copies needed? If so, why weren't they there before?

                        I can make other arguments based on similar events like transposon hops or CNVs.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • #13
                          Originally posted by Jorge View Post
                          "The existence of junk DNA in the human genome is a conclusion based on observations, not a metaphysical assumption." WRONG! From the very first time that non-coding DNA was discovered it was immediately labeled "junk" by the Evo-Faithful...
                          What other people may have stated in the past is completely irrelevant to the concrete example I provided.

                          "Genetic fingerprinting depends on the fact that different people's DNA contains different numbers of repeats of some repeated nucleotide chains. Since the additional repeats exist in some people's DNA and not in others', those additional repeats which are present in only a fraction of the population are apparently not necessary. Thus they are considered to be junk DNA." Not knowing the function of something does not logically imply that it's not needed.
                          Not knowing the function of what? The DNA sequences that frequently are not there? Either you are claiming that something not present may be necessary, or, more likely, you couldn't be bothered to actually read what I wrote and are simply firing off standard responses that are inapplicable to this example.
                          "If you have a scientific reason to believe they are not just accumulated junk, feel free to present it."
                          Don't be so freagin' naive or dishonest or both! If I knew what the function was of all of the non-coding DNA, I'd be packing my bags right now for Stockholm to pick up my two or three Nobel Prizes.
                          So you have no reason to think the specific DNA sequences I referred to are not just accumulated junk.

                          I can, nonetheless, give you perfectly logical, supported arguments to believe that they are not just accumulated junk. The support comes from the scientific findings to date. Hardly a day goes by without some news about a scientific discovery about the function of a previously-thought section of "junk" DNA.
                          And hardly a day goes by without news verifying that some DNA considered junk is actually junk and we know why it accumulates. Your argument is as illogical, and as incorrect, as Colombus arguing that since he was sailing westwards through unexplored ocean, all the unexplored terrain between Europe and Japan would be ocean too.

                          The trend is clear except to those that wish to defend their Sacred Cow (Evolution) to the bitter end. I'll even make a prediction here and now and in black and white: as time goes on, more and more and more evidence will continue to accumulate that the only "junk" is the notion of "junk DNA". While there may be some - a very, very minute quantity - of DNA that has been turned to (actual) junk (i.e., rendered useless/harmful) through a number of possible causes, generally speaking there is no "junk" in the DNA. That's my prediction ... now just wait and see.
                          That 'prediction' was disproved decades ago.

                          Roy
                          Last edited by Roy; 08-21-2014, 12:51 PM.
                          Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                          mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

                          Mountain Man: First of all, the Bible is a fixed document.
                          Mountain Man: this is how liberals argue these days, with labels instead of ideas.

                          Comment


                          • #14
                            When you define "function" as "it does something" then even real junk can be said to have function. The junk in your kitchen trash can does something, it releases odor molecules into the air. The junk at a landfill does something, it takes up space. A broken down TV that has fallen apart over millions of years still does something, it collects dust. That is the definition of function that the ENCODE study used. They may as well claimed that 100% of the genome has function since 100% of it is replicated with each cell division.

                            A sane definition of function is that it does something that benefits the organism. In that sense, only 10% or so of the human genome shows signs of having function. As Graur et al. (2013) put it:

                            "A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. "
                            http://gbe.oxfordjournals.org/conten...e.evt028.short


                            If you are going to argue for 100% functional genomes, you need to explain how the sequences can change so much without losing function, and why there is no signal of negative selection in those sequences.

                            Comment


                            • #15
                              [QUOTE]
                              Originally posted by Method View Post
                              When you define "function" as "it does something" then even real junk can be said to have function. The junk in your kitchen trash can does something, it releases odor molecules into the air. The junk at a landfill does something, it takes up space. A broken down TV that has fallen apart over millions of years still does something, it collects dust. That is the definition of function that the ENCODE study used. They may as well claimed that 100% of the genome has function since 100% of it is replicated with each cell division.

                              A sane definition of function is that it does something that benefits the organism. In that sense, only 10% or so of the human genome shows signs of having function. As Graur et al. (2013) put it:

                              "A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. "
                              http://gbe.oxfordjournals.org/conten...e.evt028.short
                              If so much is conserved, maybe its because they still have a necessary function, hundreds of millions of years seems like an awful long time for "junk" to survive if there is no cost benefit.

                              If you are going to argue for 100% functional genomes, you need to explain how the sequences can change so much without losing function, and why there is no signal of negative selection in those sequences.
                              I don't know if 100% is argued for, but there is negative selection/purifying selection/, outside of conserved noncoding sequences.

                              at least that's what I've read.

                              oh, welcome to these forums, Method
                              To say that crony capitalism is not true/free market capitalism, is like saying a grand slam is not true baseball, or like saying scoring a touchdown is not true American football ...Stefan Mykhaylo D

                              Comment

                              Related Threads

                              Collapse

                              Topics Statistics Last Post
                              Started by shunyadragon, 10-17-2020, 05:11 PM
                              7 responses
                              33 views
                              0 likes
                              Last Post rogue06
                              by rogue06
                               
                              Started by shunyadragon, 10-09-2020, 09:25 PM
                              0 responses
                              22 views
                              0 likes
                              Last Post shunyadragon  
                              Started by rogue06, 10-09-2020, 03:29 PM
                              6 responses
                              50 views
                              1 like
                              Last Post shunyadragon  
                              Started by shunyadragon, 10-07-2020, 12:11 PM
                              0 responses
                              10 views
                              0 likes
                              Last Post shunyadragon  
                              Started by Sherman, 10-06-2020, 03:31 PM
                              33 responses
                              212 views
                              0 likes
                              Last Post Leonhard  
                              Working...
                              X