I like Shapiro but accepting the Encode results and then leaping to conclusions as to their signficance is likely to be embarrasing. I stay out of the junk versus design fray. However, the only way to really test the significance of Encode data is to do deletions. In that regard, we have some data – see here =>. http://www.nature.com/news/2004/041018/full/news041018-7.html
Additional reading here http://www.1000genomes.org/home
Single nucleotide polymorphisms (single base pair differences in the population) cover about 1% of the genome (every ~ 100 bases over the 3 billion base pair human genome). Most of these are in non coding regions and cause no cellular defects. Of course those in coding regions might have serious effects. Recent data also shows there are about 14,000 large DNA deletion variations in the human population and many more indels (small insertions/deletions). Again these are mostly in the “low complexity” sequences (repetitive DNA AKA “junk”) and do not show an effect.
Most of what I am hearing is that ID people are wrong to say that anyone ever said there was such a thing as junk DNA. We had it all wrong; that term was never meant to mean that they thought this DNA had no function and that this useless stuff was evidence of undirected evolution.
I think Ohno coined the term “junk DNA” and certainly it is not true that no one used it (see article link above). At first, I think Ohno had in mind pseudogenes, which certainly appear to be either once functional genes that have become damaged and nonfunctional such as the GULO gene in the vitamin C pathway or “genes” that were reverse transcribed from mRNA back into the genome (processed pseudogenes). The best way to understand the junkiness of junk DNA is to understand what the various components are and do. Much of the “junk” consists of repetitive DNA, LTR type transposon and Non LTR types. LTRs are signature retroviral sequences at each end of the retrovirus. Humans contain endogenous retroviral sequences (HERVs) in their DNA. Lines and Sines are Non-LTR retrotransposon where Lines are autonomously replicating fragments that can copy themselves and Sines are not autonomous. Then we have transposons that hop from one place to another. These moveable genetic elements can do damage. There are a number of examples of human genetic diseases where transposons have inserted themselves into functional genes and disrupted the gene. Endogenous retroviruses have been implicated in cancer – for example breast cancer – although that is controversial. Mostly however people have thought that the ability of these sequences to proliferate has expanded the DNA content of the genome as examples of “selfish DNA”. Recently however, cases have been identified were these repetitive sequences have become inserted in introns or near genes and serve to regulate gene expression. So far these examples are rather sparse and are consistent with an evolutionary scenario.
I should add, that some repetitive DNA is obviously structural and serves important functions such as centromeric and telomeric DNA. However, I do not think this was ever considered junk.
I like Shapiro but accepting the Encode results and then leaping to conclusions as to their signficance is likely to be embarrasing. I stay out of the junk versus design fray. However, the only way to really test the significance of Encode data is to do deletions. In that regard, we have some data – see here =>.
http://www.nature.com/news/2004/041018/full/news041018-7.html
Additional reading here
http://www.1000genomes.org/home
Single nucleotide polymorphisms (single base pair differences in the population) cover about 1% of the genome (every ~ 100 bases over the 3 billion base pair human genome). Most of these are in non coding regions and cause no cellular defects. Of course those in coding regions might have serious effects. Recent data also shows there are about 14,000 large DNA deletion variations in the human population and many more indels (small insertions/deletions). Again these are mostly in the “low complexity” sequences (repetitive DNA AKA “junk”) and do not show an effect.
Most of what I am hearing is that ID people are wrong to say that anyone ever said there was such a thing as junk DNA. We had it all wrong; that term was never meant to mean that they thought this DNA had no function and that this useless stuff was evidence of undirected evolution.
I think Ohno coined the term “junk DNA” and certainly it is not true that no one used it (see article link above). At first, I think Ohno had in mind pseudogenes, which certainly appear to be either once functional genes that have become damaged and nonfunctional such as the GULO gene in the vitamin C pathway or “genes” that were reverse transcribed from mRNA back into the genome (processed pseudogenes). The best way to understand the junkiness of junk DNA is to understand what the various components are and do. Much of the “junk” consists of repetitive DNA, LTR type transposon and Non LTR types. LTRs are signature retroviral sequences at each end of the retrovirus. Humans contain endogenous retroviral sequences (HERVs) in their DNA. Lines and Sines are Non-LTR retrotransposon where Lines are autonomously replicating fragments that can copy themselves and Sines are not autonomous. Then we have transposons that hop from one place to another. These moveable genetic elements can do damage. There are a number of examples of human genetic diseases where transposons have inserted themselves into functional genes and disrupted the gene. Endogenous retroviruses have been implicated in cancer – for example breast cancer – although that is controversial. Mostly however people have thought that the ability of these sequences to proliferate has expanded the DNA content of the genome as examples of “selfish DNA”. Recently however, cases have been identified were these repetitive sequences have become inserted in introns or near genes and serve to regulate gene expression. So far these examples are rather sparse and are consistent with an evolutionary scenario.
I should add, that some repetitive DNA is obviously structural and serves important functions such as centromeric and telomeric DNA. However, I do not think this was ever considered junk.