Thursday, February 07, 2008

Theme: Genomes & Junk DNA

Junk in Your Genome

Transposable Elements: (44% junk)

      DNA transposons:
         active (functional): <0.1%
         defective (nonfunctional): 3%
      retrotransposons:
         active (functional): <0.1%
         defective transposons
            (full-length, nonfunctional): 8%
            L1 LINES (fragments, nonfunctional): 16%
            other LINES: 4%
            SINES (small pseudogene fragments): 13%
            co-opted transposons/fragments: <0.1% a
aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.
Viruses (9% junk)

      DNA viruses
         active (functional): <0.1%
         defective DNA viruses: ~1%
      RNA viruses
         active (functional): <0.1%
         defective (nonfunctional): 8%
         co-opted RNA viruses: <0.1% b
bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.
Pseudogenes (1.2% junk)
      (from protein-encoding genes): 1.2% junk
      co-opted pseudogenes: <0.1% c
cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.
Ribosomal RNA genes:
      essential 0.22%
      junk 0.19%

Other RNA encoding genes
      tRNA genes: <0.1% (essential)
      known small RNA genes: <0.1% (essential)
      putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
      transcribed region:  
            essential 1.8%  
            intron junk (not included above) 9.6% d
dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.
Regulatory sequences:
      essential 0.6%

Origins of DNA replication
      <0.1% (essential) Scaffold attachment regions (SARS)
      <0.1% (essential) Highly Repetitive DNA (1% junk)
      α-satellite DNA (centromeres)
            essential 2.0%
            non-essential 1.0%%
      telomeres
            essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)
      conserved 2% (essential)
      non-conserved 26.3% (unknown but probably junk)

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%
For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)





November 11, 2006
Sea Urchin Genome Sequenced

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team.

November 19, 2006
Neanderthal genome FAQ
I've hesitated to comment about the sequencing of Neanderthal DNA 'cause I haven't read the papers. Fortunately John Hawks has made the effort and posted the Neandertal genome FAQ. It should answer all your questions, except why John Hawks calls them "Neandertal" when Science and Nature use "Neanderthal." Personally, I prefer the original "Neanderthal."

December 21, 2006
Mammalian Gene Families: Humans and Chimps Differ by 6%
By scanning the available genome sequences, Demuth et al. were able to cluster all genes into 15,389 groups called "gene families." Of these, 3,114 were single genes confined to a single species. These were presumed to be annotation artifacts and were discarded. Not all of the remaining groups were present in all five species. A total of 2,285 additional groups were confined to distinct lineages on the mammalian tree indicating that they had been "created" after divergence from the common ancestor. This leaves 9,990 groups that were probably present in the ancestor of dog, human, chimp, mouse, and rat.

The question is, how many of these gene families show gain or loss of numbers during mammalian evolution? The answer is 5,622 or 56.3% (5622/9,990).

February 12, 2007
Junk DNA: Scientific American Gets It Wrong (again)
In "Ask the Experts" somebody asked What is junk DNA, and what is it worth?. The question was answered by "expert" Wojciech Makalowski of Pennsylvania State University. Here's the answer ...
In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.
This is very misleading.

March 13, 2007
Genome Size in Birds
One of the things that Gregory works on is the correlation between cell size and genome size. It turns out that the size of the nucleus is related to the size of the cell, such that large genomes give rise to large nuclei and large cells. This is particularly evident when you look at red blood cells and Gregory has a remarkable image showing this correlation on his website [Gregory Lab].

It has been known for some time that birds have smaller genomes than reptiles and mammals. This has natually given rise to an adaptionist explanation;namely, that the small genome is due to selection for small cells in birds because they exert a lot of energy in flight. In other words, small genomes are an adaption for flight.

March 19, 2007
Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome
The graphic above was taken from the Genesweep lottery. This is the betting that Asp refers to. It shows the range of gene number estimates by scientists who were involved in genome sequencing projects. Note that there are many estimates in the 40-50,000 range and a fair number below 40,000. The point is obvious—lots of experts anticipated fewer than 50,000 genes in the human genome (see The nature of the number. Nature Genetics 25:127 (2000)).

March 23, 2007
How Many Genes Do We Have?
The number of genes in the human genome flutuates on a monthly basis as the genome annotators add new genes and remove false positives. It's an ongoing process that's not likely to be complete in the near future.

March 21, 2007
Summary of Genes on Human Chromosomes
I've prepared a table of the number and types of gene on each human chromosome based on the data at the Ensembl site managed by the Wellcome Trust Sanger Institute in Cambridge UK.

The total number of genes comes to 26,290.

April 13, 2007
Testing the Macaque Genome
We've already been looking at the macaque genome for several months but now that the genome paper is being published I thought some of you might be interested in how the preliminary data stacks up to what we expect.

April 29, 2007
Noncoding DNA and Junk DNA
The author of the Scientific American article, JR Minkle, has responded on the Scientific American website [The DNA Formerly Known as Junk]. Minkle is a science writer who has covered a lot of stories in many different fields. As far as I know Minkle has not written very much about biology before summarizing the work in the PNAS paper. There was a time when all the science in that journal was written by scientists who were experts in the field [The Demise of Scientific American]. Anyway, that's not the main point here. JR Minkle has listened to the critics and made a decision to avoid the term "junk DNA" from now on.

That's a bad decision.

May 25, 2007
SCIENCE Questions: Why Do Humans Have So Few Genes?
Elizabeth Pennisi is a news writer for Science magazine. She has been publishing articles there for at least ten years. She had previously written about genes and genomes, including earlier articles about the number of genes in the human genome.

Pennisi begins with the usual mythology about how surprised scientist were to discover that humans had fewer than 30,000 genes [see Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. She continues by using most of the standard excuses for the Deflated Ego Problem [The Deflated Ego Problem].

May 24, 2007
The Deflated Ego Problem
The human chauvinists are disappointed that our genome isn't as complex as our brains and behavior suggest (to them). They expected to see tangible evidence that humans were at the top of the heap. I call this "The Deflated Ego Problem." The question before us is whether this is a real scientific problem or whether it stems from an incorrect understanding of evolution and development.

Having barely survived a major blow to their ego when the human genome turned out to have fewer than 30,000 genes, the deflated ones have fought back with various schemes to explain the "paradox." What they look for is some special mechanism that we humans possess in order to get a bigger bang for our buck. In other words, they're looking for their missing complexity in other places.


June 13, 2007
WIRED on Junk DNA
Junk DNA is the DNA in your genome that has no function. Much of it accumulates mutations in a pattern that's consistent with random genetic drift implying strongly that the sequences in junk DNA are unimportant. In fact, the high frequency of sequence change (mutation plus fixation) is one of the most powerful bits of evidence for lack of function.

June 14, 2007
Catherine Shaffer Responds to My Comments About Her WIRED Article
Catherine Shaffer says,
I interviewed five scientists for this article. Dr. Francis Collins, Dr. Michael Behe, Dr. Steve Meyers, Dr. T. Ryan Gregory, and Dr. Gill Bejerano. Each one is a gentleman and a credentialed expert either in biology or genetics. I am grateful to all of them for their time and kindness.

June 19, 2007
What is a gene, post-ENCODE?
My initial impression is that they have failed to demonstrate that the rare transcripts of junk DNA are anything other than artifacts or accidents. It's still an open question as far as I'm concerned.

It's not an open question as far as the members of the ENCODE Project are concerned and that brings us to the new definition of a gene.

July 8, 2007
Stop the Press!!! ... Genes Have Regulatory Sequences!
Ira Flatow interviews John Greally (see photo) on Science Friday. Greally talks about the ENCODE project and junk DNA. You might be surprised to learn that the expression of genes is controlled by ... wait for it ... REGULATORY SEQUENCES! According to Greally the discovery of these regulatory sequences reveals that junk DNA isn't junk at all.

July 24, 2007
Junk DNA in New Scientist
I just got my copy of the July 14th issue of New Scientist so I can comment on the article Why 'junk DNA' may be useful after all by Aria Pearson. RPM at evolvgen thinks it's pretty good [Junk on Junk] and so does Ryan Gregory at Genomicron New Scientist gets it right]. I agree. It's one of the best articles on the subject that I've seen in a long time.

September 5, 2007
The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes
Ahituv et al. then deleted the four ultraconserved sequences from the mouse genome using standard knockout technology. Mice that were homozygous for the knockouts showed no evidence of any defect compared to wild-type mice. In other words, the ultraconserved elements seemed to be completely dispensable—a result that is not consistent with their extreme conservation.

September 07, 2007
Adaptive Evolution of Conserved Noncoding Elements in Mammals
"Adaptive Evolution of Conserved Noncoding Elements in Mammals" is the title of a paper that's just been published in PLoS Genetics [Kim and Pritchard (2007)].

With a title like that you'd think the paper would be really interesting because conserved noncoding elements are a hot topic. Recall that these are short sequences in the genomes of diverse mammals that are highly similar. They were thought to be examples of regulatory sequences but deleting them from the mouse genome seems to have no effect [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes]. It's a little puzzling to see "adaptive evolution" in the title since the very fact that these short sequences are conserved implies adaptation.

September 14, 2007
Genome Size, Complexity, and the C-Value Paradox
Forty years ago it was thought that the amount of DNA in a genome correlated with the complexity of an organism. Back then, you often saw graphs like the one on the left. The idea was that the more complex the species the more genes it needed. Preliminary data seemed to confirm this idea.

October 7, 2007
Retrotranspsons
RNA viruses are viruses that contain RNA instead of DNA. When the RNA molecule is injected into the cell it serves immediately as a template for translation. All RNA viruses have a genes for making new viral particles and new copies of the RNA genome.

In eukaryotes, there is a large class of RNA viruses known as retroviruses. They have an obligatory stage where the RNA is reverse transcribed into DNA and the DNA is inserted into the genome where it resides as a provirus.


October 7, 2007
Junk in your Genome: LINEs
About 17% of your genome is composed of L1 LINEs and fragments. It is one of the major sources of junk DNA in your genome.

October 11, 2007
Junk RNA
There are a lot of studies suggesting that a substantial percentage of the genome is transcribed even though less than 5% is known to be functional. This leads to the idea that it encodes some unknown function. The argument is that these regions would not be transcribed unless they were doing something useful.

One objection to these studies is that the workers are looking at artifacts. The so-called transcripts are just noise from accidental transcription. This ties in with the idea that the EST database is full of examples of "transcripts" that don't make any biological sense.

October 12, 2007
The Genome of Chlamydomonas reinhardtii
The nuclear genome is 121 Mb (121,000,000 base pairs) in size and it's divided into 17 linkage groups (chromosomes). This is a draft genome sequence representing about 95% of the complete sequence with 13x coverage of the sequenced regions. The remaining 5% consists mostly of repeat regions and it's unlikely that they will ever be sequenced.

The preliminary analysis predicts 15,143 protein-encoding genes; three ribosomal RNA clusters; and 259 transfer RNA genes (tRNA).

November 19, 2007
Crystal Tells Us about the Human Genome
This is a video about the human genome. Crystal tells us lots of interesting things about the size of our genome, number of genes, junk DNA, whether the DNA of different races is the same etc. etc.

It makes my blood boil.

November 21, 2007
Bacteria Genomes Are Degrading
At one point in his talk last night Kirk Durston mentioned the bacterial flagella. He acknowledged that the "Darwinists" have proposed an evolutionary pathway from a Type III secretory structure to flagella.

This pathway is improbable, according to Durston, because flagella are more complicated than secretory pores so flagella have to evolve first.

What? Yes, that's right. Scientists have now shown that the most primitive bacteria were very complex and evolution has been all downhill from then on.

November 21, 2007
Bacterial Genomes and Evolution
Ryan Gregory is one of the world's leading experts on genomes and their evolution. He's also a Professor at the University of Guelph. Ryan has published an excellent description of what the Mira et al. (2000) paper shows and what it does not show. You should all read it [Bacterial genomes and evolution].

For Kirk Durston's sake, I hope Ryan Gregory isn't on his Ph.D. oral committee.

November 29, 2007
More Misconceptions About Junk DNA
Lots of scientists use the term "junk DNA." Properly, understood, it's a very useful term and has been for several decades [Noncoding DNA and Junk DNA].

Yes, it's true that journalists often don't understand junk DNA and they are easily tricked into thinking that junk DNA is a discredited concept. The journalists are wrong, not the scientists who use the term.

December 4, 2007
TR Gregory on Junk DNA
Ryan Gregory has posted another interesting discussion about junk DNA [Genome size, code bloat, and proof-by-analogy.]. You should read the entire article but I want to comment briefly on two important points.

December 8, 2007
Junk DNA in the Toronto Star
Cameron Smith writes,

To find answers, molecular biologists had to revise their notions of the genetic code. They knew that a huge number of genes in the human genome, making up more than 98 per cent of the genome, don't code protein. These they had previously dismissed as evolutionary leftovers, or junk DNA.

In an enormous turnaround, they began looking at these non-coding genes more closely and discovered they were not junk after all.

December 11, 2007
Stop the Press - Genes Have Regulatory Sequences!
You heard it here first—well, not exactly. The breaking news was first reported over at Biology News Net. Junk DNA isn't junk at all because it's full of regulatory regions controlling gene expression. This is excuse #5 of The Deflated Ego Problem.

December 27, 2007
The Grapevine Genome
The genome has 19 chromosomes amounting to 487 Mb of DNA (487 × 106 base pairs). This is comparable in size to the three other plant genomes that have been sequenced; rice, poplar, and Arabidopsis.

The published sequence is referred to as a "high-quality draft" by the authors. They report 30,434 protein-encoding genes and 600 tRNA genes.

December 28, 2007
The Second Grapevine Genome Is Published
The genome size is 505 Mb (505 × 106 bp). This is larger than the earlier published sequence (487 Mb). The extra DNA is almost entirely due to inclusion of ribosomal RNA clusters. Velasco et al. (2007) identified 29,585 genes—only slightly fewer than the 30,434 genes reported by Jaillon et al. (2007). Both teams used fairly strict criteria for identifying and annotating genes.

January 13, 2008
How Much Junk in the Human Genome?
Ryan Gregory has another contribution to this question that's well worth a read [Is most of the human genome functional?].

Among other things, Ryan picks on the views of John Mattick who has got to be one of the worst scientists in the field. Whenever I read a paper by Mattick I revise my opinion of the value of peer-reviewed literature. It's bad enough that Mattick has silly ideas but it's even sadder that his "peer" reviewers don't recognize it.

January 15, 2008
Humans Have Only 20,500 Protein-Encoding Genes
This analysis was extended to the other gene catalogs (Vega, and RefSeq) as well as an updated version of the Ensembl catalog (v38). This resulted identification of an additional 1271 valid genes. Adding in the genes in the mitochondrial genome (13) and the Y chromosome (78) gives a total of 20,470 genes.

January 15, 2008
Greg Laden Gets Suckered by John Mattick
Here's what Greg says [Genes are only part of the story: ncRNA does stuff].
The "Junk DNA" story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don't know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of "non-coding DNA." It does really seem that scientists assumed for too long that there was no function in the DNA.

January 17, 2008
A Junk DNA Quiz
Take the junk DNA quiz in the left sidebar to let me know what you think of your genome. How much of it could be removed without affecting our species in any significant1 way in terms of viability and reproduction? Or even in terms of significant ability to evolve in the future? In other words, how much is junk?

January 18, 2008
Soybean Genome
A preliminary draft of the soybean (Glycine max) genome has been released on the Phytozome website [Glycine max Genome].

The reported size of the genome is 950 Mb (950 × 106 base pairs). This is considerably larger that the genomes of grape (505 Mb), Arabidopsis (157 Mb), rice (389 Mb), and polar (485 Mb).

January 23, 2008
Ribosomal RNA Genes in Eukaryotes
The "genes" for ribosomal RNAs in eukaryotic genomes are found in separate clusters. One cluster consists of hundreds of copies of the 5S gene. These genes are transcribed by RNA polymerase III [Eukaryotic RNA Polymerases].

The other ribosomal RNA genes are found in an "operon"-like structure that's similar to the bacerial operons [Ribosomal RNA Genes in Bacteria]. Unlike bacterial transcription units, these ones are found in large tandem arrays on eukaryotic chromosomes. There can be hundreds of individual transcription units in a cluster and there can be several clusters. In humans, for example there are five clusters on five different chromosomes and each one has between 50 and 100 transcription units. The large eukaryotic ribosomal RNA genes are transcribed by RNA polymerase I.

January 28, 2008
Junk DNA Poll
Just a reminder to vote in the junk DNA poll seen in the left sidebar. Check out A Junk DNA Quiz and comments for more information.

January 31, 2008
Results of Junk DNA Poll
The results are surprising to me. I would have thought that a far higher percentage would have voted for 50% or more. As it turns out, half of you think that 50% of our genome is essential. That's not right.

February 1, 2008
Human Ribosomal RNA Genes
Total ribosomal RNA genes in the genome:

5S: 100 copies of 2.2 kb repeats = 220 kb. (estimate 100 kb essential, 120 kb junk)

45S: 98 copies of 43 kb repeats = 4214 kb. (estimate 1500 kb essential, 2714 junk)

February 7, 2008
Junk in Your Genome: SINES
Today I want to discuss Short Interspersed Elements or SINEs. These pieces of DNA tend to be only 100-400 bp in length but they contain all the features of transposons at their ends. The most important of these features is a short repeat of genomic DNA.

February 7, 2008
Junk in Your Genome: Pseudogenes
Pseudogenes are non-functional DNA sequences that resemble genes. Much of the DNA related to transposable elements falls into this category. There are ribosomal RNA and tRNA pseudogenes but the term usually refers to sequences that resemble protein-encoding genes.

February 8, 2008
Junk in Your Genome: Protein-Encoding Genes
The typical human gene has eight exons and seven introns (the actual average number of introns is 7.2). These values are based on analysis of 5236 well-characterized human genes with full-length cDNA's (Hong et al. 2006). There are lots of conflicting results in the literature. Most claim there are more introns but the data is based largely on a computational assessment of introns and exons. It includes a number of introns of extraordinary length lying between exons of dubious existence (often non-coding). I'll assume for the time being that there are 7.2 introns per gene, on average, and the average length is 3750 bp (Hong et al. 2006)

February 9, 2008
Junk in Your Genome: Intron Size and Distribution
There have been quite a few studies of average intron size in various species. I selected a number for the average size of introns from Hong et al. (2006). The average intron size, according to them, is 3,479 bp in coding regions. This value is a little deceptive since there are a small number of huge introns that make the average quite large. The median value is 1334 bp or less than half the average value.

February 20, 2008
An IDiot Software Developer Opines About Junk DNA
Randy "I want to believe" Stimpson is a software developer who thinks he understands biology. He has written a post where he claims Most DNA is not Junk. Doppelganger has already pointed out the most obvious faults with Randy's point of view [Software developer PROVES that there is no junkDNA*... and other stuff].I just want to comment on one small paragraph in order to clear up any confusion.

May 23, 2008
Fugu, Pharyngula, and Junk
PZ Myers writes about Random Acts of Evolution in the latest issue of Seed magazine. The subtitle says it all.

May 26, 2008
Centromere DNA
Human centromeres range from 0.3Mb to 5Mb in size (Cleveland et al. 2003). If the average centromeric region is 3Mb (3,000 kb) in size then 23 centromeres represents 2% of the entire genome sequence. Not all of this DNA is essential because, among other reasons, there is considerable variation between individuals in the length of a given centromere. Nevertheless, lets assume for the sake of our junk DNA calculation that all of it is essential.

May 29, 2008
Telomeres
Telomeres are sequences at the ends of linear chromosomes that protect the essential part of the chromosome from damage following repeated rounds of DNA replication.

June 3, 2008
Minimum Centromere Size in Plants
Thus, in a certain sense, some of the "excess" centromeric DNA is required as a buffer against the possibility of future deletions. The extra DNA does not contribute to the viability of the individual carrying it but it does contribute to the survival of that individual's offspring. At some point, the potential advantage in terms of offspring survival will become too small to have any influence on the lineage of an individual. This will define the maximum amount of "excess" DNA at the centromere.

August 26, 2008
The Trichoplax Genome
Trichoplax adherens is a very simple animal that moves about on surfaces like a gigantic amoeba and ingests any food that it flows over. There are thought to be several species of Trichoplax in addition to Trichoplax adherens. The sequence of its genome tells us something about the origins of animals.

August 28, 2008
Useful RNAs?
Some people think that much of the junk DNA in a genome can be explained away as genes for regulatory RNA. This is nonsense.

August 30, 2008
Genomics and Darwinism!?
The scientific research journal Genome Research is proposing to publish a special issue on "Genomics and Darwinism" to coincide with Darwin's 200th birthday.

September 18, 2008
Everything Is There for a Reason?
Nils Reinton of The Sciphu Weblog has just posted an article entitled Junk, DNA, RNA, Brain, Biology and Possible Solutions.

Nils makes the point that biology is very complex and we may only have scratched the surface.

September 16, 2008
How RNA Polymerase Binds to DNA


As is the case in bacteria, a substantial number of holoenzyme complexes will be bound non-specifically to DNA at any one time. The proportion is much, much higher in mammalian cells because of the presence of so much junk DNA in the genome. This has the effect of soaking up a lot of holoenzyme complexes.

Since the holenzyme complexes, like those in bacteria, are capable of initiating basal levels of transcription, we should not be surprised to find spurious transciption in all parts of the genome. These transcript will be rare but they will come from any site where RNA polymerase holoenzme can bind.

September 19, 2008
An Example of Faulty Logic from Cold Spring Harbor
A press release from Cold Spring Harbor Laboratory promotes the work of Michael Zhang and Adrian Krainer who work with splicing factors. In a typical attempt to hype the significance of the work, the press release claims that each human gene has many different variants produced by alternative splicing [CSHL team traces extensive networks regulating alternative RNA splicing].

That may or may not be correct—I happen to think it's mostly an artifact of EST cloning—but that's not the point I want to make here.

September 23, 2008
Discussing Junk DNA with an Adaptationist
Adaptationists are scientists who like to find adaptive explanations for all features of organism. For them the concept of junk DNA is difficult to swallow in spite of abundant scientific evidence and in spite of the fact that counter-explanations do not account for the data. Nils Reinton is a molecular biologist working in the field of medical diagnostics and he has been challenging the concept of junk DNA in the comment section of a recent posting. The title of that posting, Everything Is There for a Reason?, was direct response to an earlier posting from Nils where he claimed that we shouldn't label DNA as "junk" because it's a science stopper.

September 15, 2008
How Many Genes Do Nematodes Have? - Pristionchus pacificus Genome
A new nematode genome sequence was published this week. The species is Pristionchus pacificus, a parasite of the oriental beetle Examala orientalis (Dieteridh et al. 2008). The authors note that there is a different species of parasitic nematode associated with almost every species of beetle, which means that there are at least as many nematodes as insects.

The Pristionchus pacificus genome is 169 Mb in size, which is considerably larger than the size of the Caenorhabditis elegans genome (100 Mb). P. pacificus has 23,500 genes.

September 28, 2008
Discussing Junk DNA with an Adaptationist, Again
During the discussion in the comment to my posting, I challenged Nils to answer a number of questions. He has responded on his blog SciPhu with Hey junk people, I accept your challenge (part I). I resonded to his answers in Discussing Junk DNA with an Adaptationist.

Now Nils has weighed in with Hey junk people, I accept your challenge (part II).

October 28, 2008
Junk DNA Opponents Are at It Again
You are more than welcome to visit Sciphu and make comments. I can't be bothered.

The articles are just the same-old, same-old, litany of occasional discoveries of functional bits of DNA coupled with a fanatical belief in the biological significance of every single transcript that has ever been reported in the literature.

November 7, 2008
Is Andras Pellionisz a Kook?
Some of you may have heard of Andras Pellionisz. He has three Ph.D.s (Computer Engineering, Biology, Physics) and he maintains that much of what we know in biology is wrong. This is especially true of genomes. Whenever you mention junk DNA on a blog, Pellionisz will show up. Same when you mention the Central Dogma of Molecular Biology. He has a blog site that used to be called Junk DNA but it has morphed into HoloGenomics

January 27, 2009
Science Journalists and Junk DNA
The latest issue of SEED magazine concentrates on the idea that "Science Is Culture"—whatever that means.

One of the things it seems to mean is that good, accurate science reporting is not a high priority.

Junk DNA is one of those subjects that seem to bamboozle science journalists. They just can't seem to accept the possibility that much of our genome serves no purpose. One of the most extreme examples of this bias can be found in an article by Veronique Greenwood titled What We Lose.

February 9, 2009
Evolution of Pine Genomes
It's possible that different species of pine could have larger or smaller gene families. This would mean that the species with larger genomes have many more copies of some genes than species with smaller genomes. However, this is unlikely to account for much of the difference since simultaneous duplication events in all parts of the genome.

The most logical explanation is an increase in the amount of junk DNA, specifically the number of retrotransposons. Flowering plants have retrotrapsposons with long terminal repeats (LTRs) just like those found in animal genomes [Junk in your Genome: LINEs].

February 17, 2009
Junk DNA Is "Dead as a doornail"?
There are some interesting scientific debates about the role of noncoding DNA in large genomes. Much of it is junk but there's lot of other functions that we've known about for decades. Many respectable scientists dispute the notion that most of our genome is junk.

Unfortunately, very little of that interesting scientific debate can be seen on András Pellionisz's website. Instead, I direct you to the site in order to see a classic example of a modern kook in action. The site has all of the characteristics of kookdom (see crank) and serves as a self-evident answer to the question Is András Pellionisz a Kook?.

Tuesday, May 24, 2011
Junk & Jonathan: Part 6—Chapter 3
The title of Chapter 3 is Most DNA Is Transcribed into RNA. As you might have anticipated, the focus of Wells' discussion is the ENCODE pilot project that detected abundant transcription in the 1% of the genome that they analyzed (ENCODE Project Consortium, 2007). Their results suggest that most of the genome is transcribed. Other studies support this idea and show that transcripts often overlap and many of them come from the opposite strand in a gene giving rise to antisense RNAs.

Wednesday, May 25, 2011
Junk & Jonathan: Part 7—Chapter 4
Nothing new here. We know about binding sites and we know that most of them are 10 bp or less. Their presence makes no significant difference in our calculations of junk DNA. I get the distinct impression that Wells and the other IDiots don't really understand splicing and alternative splicing.

March 16, 2009
Casey Luskin on Junk DNA and Junk RNA
Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA.

The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA].

April 2, 2009
Dynamic Genomes
There may have been a time in the past when scientists imagined a static genome that only changed slowly over millions of years. However, beginning in the 1960's we began to see the genome as a much more dynamic entity. The first evidence of this kind of genome came with the discovery of huge amounts of variation between individuals in a species.

This was followed by the discovery of transposons and junk DNA. We began to see genomes as rather sloppy DNA molecules with lots of pieces hopping in and out on a timescales of generations. We began to realize that many genomes were full of pseudogenes.

April 21, 2009
How to Evaluate Genome Level Transcription Papers
Here's two criteria that I use to evaluate a paper on genome level transcription.

1. I look to see whether the authors are aware of the adaptation vs noise controversy. If they completely ignore the possibility that what they are looking at could be transcriptional noise, then I tend to dismiss the paper. It is not good science to ignore alternative hypotheses. Furthermore, such papers will hardly ever have controls or experiments that attempt to falsify the adaptationist interpretation. That's because they are unaware of the fact that a controversy exists.1

2. Does the paper have details about the abundance of individual transcripts? If the paper is making the case for functional significance then one of the important bits of evidence is reporting on the abundance of the rare transcripts. If the authors omit this bit of information, or skim over it quickly, then you should be suspicious. Many of these rare transcripts are present in less that one or two copies per cell and that's perfectly consistent with transcriptional noise—even if it's only one cell type that's expressing the RNA. There aren't many functional roles for an RNA whose concentration is in the nanomole range. Critical thinkers will have thought about the problem and be prepared to address it head-on.

May 6, 2009
How to Frame a Null Hypothesis
The point is not whether you believe that all transcription is adaptive and functional, or whether you believe that most of it is noise. The real point is that it is very bad science to ignore the null hypothesis and publish naive speculation as if it were the only possible explanation.

Whenever you see a paper that fails to address the null hypothesis you can be sure that you are reading bad science. Everything else in the paper is suspect.

May 29, 2009
The Mouse Genome is "Finished"
The total length of protein-encoding exons in the mouse genome is 33,500 Kb (33.5 Mb). The revised genome size is 2,660,000 Kb (2.66 Gb). Thus, protein-encoding regions represent only 1.3% of the genome. This is similar to the value in the human genome (1.1% or 32.6 Mb out of 3.08 Gb).

There are many important non-coding sequences including centromeres, telomeres, origins of replication, scaffold attachment regions etc. All genes have substantial regulatory regions that aren't counted in the 1.3% of the genome that encodes protein. In addition, there are hundreds of tRNA genes, ribosomal RNA genes, and genes for essential small RNAs.

Nevertheless, a substantial proportion of the mouse genome (>90%) appears to be junk DNA with no known function. Most of it (~50%) consist of active and degenerate transposons similar to the LINES and SINES found in all other mammalian genomes.

July 8, 2009
Junk DNA and the Scientific Literature
The skill in reading the scientific literature is to put things into perspective and maintain a certain degree of skepticism. It's just not true that everything published in scientific journals is correct. An important part of science is challenging the consensus and many scientists try to make their reputation by coming up with interpretations that break new ground. The success of science depends on the few that are correct but let's not forget that most of them turn out to be wrong.

The trick is to recognize the new ideas that may be on to something and ignore those that aren't. This isn't easy but experienced scientists have a pretty good track record. Inexperienced scientists may not be able to distinguish between legitimate challenges to dogma and ones that are frivolous. The problem is even more severe for non-scientists and journalists. They are much more likely to be sucked in by the claims in the latest paper—especially if it's published in a high profile journal.

September 21, 2009
More Junk DNA Fallacies
BiOpinionated is a blog written by a molecular biologist named Nils Reinton. He tries to see every side of an argument but there are times when this attempt goes astray.

November 17, 2009
Genetic Load, Neutral Theory, and Junk DNA
A species cannot afford to accumulate deleterious mutations in the genomes of its individuals. Eventually the number of "bad" mutations will reach a level where most genes have multiple "bad" alleles and it becomes impossible to produce offspring.

This phenomenon is referred to as genetic load. It means that species can only survive if the genetic load is below some minimum value. A good rule of thumb is that there can't be more than 0.1 deleterious mutations per individual per generation but in actual populations this value can be a bit higher.

December 15, 2009
Does Excess Genomic DNA Protect Against Mutation?
One of the adaptive explanations for this excess DNA is that it protects the functional DNA from mutations. Ryan Gregory thinks this is a serious scientific hypothesis even though he's skeptical. He has a wonderful post that reviews the history of the idea and how the hypothesis should be tested [Does junk DNA protect against mutation?].

The bottom line is that this hypothesis is not taken very seriously by the scientific community for some very good reasons.

May 4, 2010
Shoddy But Not "Junk"?
The purpose of this posting is not to review the points that John Avise makes but to comment on one of the points made by Philip Ball. At the end of his Nature review he says,
However — although heaven forbid that this should seem to let ID off the hook — it is worth pointing out that some of the genomic inefficiencies Avise lists are still imperfectly understood. We should be cautious about writing them off as 'flaws', lest we make the same mistake evident in the labelling as 'junk DNA' genomic material that seems increasingly to play a biological role. There seems little prospect that the genome will ever emerge as a paragon of good engineering, but we shouldn't too quickly derogate that which we do not yet understand.

May 20, 2010
Junk RNA or Imaginary RNA?
RNA is very popular these days. It seems as though new varieties of RNA are being discovered just about every month. There have been breathless reports claiming that almost all of our genome is transcribed and most of the this RNA has to be functional even though we don't yet know what the function is. The fervor with which some people advocate a paradigm shift in thinking about RNA approaches that of a cult follower [see Greg Laden Gets Suckered by John Mattick].

May 23, 2010
Junk DNA on BIOpinionated
Nils Reinton and I are discussing junk DNA on his blog [More crap from the junkies]. It might surprise you to learn that this "junkie" still isn't convinced that junk DNA is dead. Nils isn't convinced that junk DNA exists.

This is what a real scientific controversy looks like.

May 28, 2010
Junk DNA and Genetics Textbooks
One of the things textbook authors have to careful of is discarding solid, well-established, models (like junk DNA) based on the results of a few modern experiments. Yes, it's true that new discoveries often overthrow old concepts, but it also true that when new "facts" disagree with established models it's usually the new facts that turn out to be wrong. The idea that theories are frequently overthrown by "nasty little facts" is a myth.

August 25, 2010
Bated Breath
Jonathan Wells made an annoucement that sets my heart all aflutter. I just can't wait for his new book to appear Zombie Genes?.
Richard Dawkins, Douglas Futuyma, Michael Shermer, Philip Kitcher, Kenneth Miller, Jerry Coyne and John Avise have also written recent books in which they argue that much of the human genome consists of "junk DNA" that provides evidence for Darwinian evolution--and evidence against intelligent design.

But the notion of "junk DNA" owes more to the historical contortions of neo-Darwinian theory than to biological evidence. In fact, there is now a large and growing body of evidence that Collins, Dawkins, Futuyma, Shermer, Kitcher, Miller, Coyne and Avise are dead wrong on this point--as I will show in my forthcoming book, The Myth of Junk DNA.

November 12, 2010
Darwinism and Junk DNA
I don't want to defend Francis Collins. I want to emphasize something else; namely that the concept of junk DNA is about as far removed from "Darwinism" as you can possibly be and still be an evolutionary biologist. If it has any meaning at all, "Darwinism" has to be a synonym for the belief in natural selection as the most potent mechanism of evolution. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory."

February 27, 2011
Debating the Existence of Junk DNA
The sixth question for my students is ...
Do you think that most of the DNA in our genome is junk? Explain your answer.

May 8, 2011
What's in Your Genome?
This posting is a summary of the known components of the humna genome and how much of it is junk.
Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%

Tuesday, March 31, 2011
Junk & Jonathan: Part 1—Getting the History Correct
This is the first in a series of postings about a new book by Jonathan Wells: The Myth of Junk DNA. The book is published by Discovery Institute Press and it should go on sale on May 31 2011. I'm responding to an interview with Jonathan Wells on Uncommon Descent.

Friday, April 1, 2011
Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
It's in the best interests of the IDiots to promote the idea that all "Darwinists" believed in the "myth" of junk DNA and that it wasn't until the predictions of the IDiots were confirmed (not) that the biologists changed their minds.

The truth is somewhat different. Wells says, "Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”" The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk.

Thursday, April 7, 2011
Jonathan, Moonies, and Junk DNA
This video is supposed to support the evolution side versus the Intelligent Design Creationists. There are two major flaws in this presentation.

First, it spends too much time on the background of Jonathan Wells. While it's interesting to know where he's coming from, his motives are less important that the "scientific" case he's making. His religious motivation explains WHY he gets the science wrong but the important point is that the science IS wrong.

May 3, 2011
Junk & Jonathan: Part 3—The Preface
Here's the preface to The Myth of Junk DNA by the IDiot, Jonathan Wells. After each paragraph I've inserted a short version of the truth just so you don't get misled by all the untruths and distortions that are found in creationist books.

Monday, May 16, 2011
See the IDiots Gloat over Jonathan Wells
This the start of the discussion now that Wells' book has been published. It doesn't start well ...
The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a "pillar" of support for evolution. That's hard to do when their understanding of evolution is so flawed that they don't see the difference between "Darwinism" and evolution by random genetic drift.

Sunday, May 22, 2011
Junk & Jonathan: Part 4—Chapter 1
I received a copy of the book a few days ago and this is my first posting on its contents....

Chapter 1 is "The Controversy over Darwinian Evolution." It has nothing to do with junk DNA.

Monday, May 23, 2011
Junk & Jonathan: Part 5—Chapter 2
Wells fails to distinguish between those biologists who recognize the existence of junk DNA (e.g. pseudogenes) and those who thought that most of our genome is junk. I still believe that only a minority of biologists think that most our genome is junk. I also think that many biologists make a distinction between "junk" and "selfish." I know I do. In my mind "selfish" DNA, such as active transposons or endogenous retroviruses, isn't junk.

Tuesday, May 24, 2011
Junk & Jonathan: Part 6—Chapter 3
The title of Chapter 3 is Most DNA Is Transcribed into RNA. As you might have anticipated, the focus of Wells' discussion is the ENCODE pilot project that detected abundant transcription in the 1% of the genome that they analyzed (ENCODE Project Consortium, 2007). Their results suggest that most of the genome is transcribed. Other studies support this idea and show that transcripts often overlap and many of them come from the opposite strand in a gene giving rise to antisense RNAs.

Wednesday, May 25, 2011
Junk & Jonathan: Part 7—Chapter 4
Nothing new here. We know about binding sites and we know that most of them are 10 bp or less. Their presence makes no significant difference in our calculations of junk DNA. I get the distinct impression that Wells and the other IDiots don't really understand splicing and alternative splicing.

Thursday, May 26, 2011
Junk & Jonathan: Part 8—Chapter 5
Chapter 5 is Pseudogenes—Not so Pseudo After All. This is the chapter where Jonathan Wells takes the standard creationist approach to the problem of pseudogenes—he denies that they exist!
Tuesday, August 11, 2011
Junk & Jonathan: Part 9—Chapter 6

The title of Chapter 6 is "Jumping Genes and Repetitive DNA." Wells describes transposons as jumping genes and includes them in the category of "Repetitive Non-Protein-Coding DNA." This category makes up 50% of the genome, according to Wells. The breakdown is as follows. LINES 21%; SINES 13%; retroviral-like elements 8%; simple sequence repeats 5%; and DNA-only transposons 3%. These percentages are similar to those published in a wide variety of textbooks and scientific papers.
Monday, August 23, 2011
Junk & Jonathan: Part 10—Chapter 7
The title of Chapter 7 is "Functions Independent of Exact Sequence." This is potentially the most important chapter in the book because it should address some of the serious arguments for function in the genome. We already know that sequence is not conserved in the vast majority of the genome that we call junk so in order for it to have a function it must be due to the presence of built DNA.
Thursday, August 25, 2011
Junk & Jonathan: Part 11—Chapter 8
The title of Chapter 8 is "Some Recent Defenders of Junk DNA." It is Wells' attempt to deal with a very small percentage of the criticisms of his claim.
Tuesday, October 11, 2011
Junk & Jonathan: Part 12—Chapter 9
The title of Chapter 9 is "Summary of the Case for Functionality in Junk DNA." It is Wells' attempt to summarize the "evidence" he has presented so far.

Wells tells us that the "evidence" falls into two broad categories: (1) evidence that putative junk is probably functional, and (2) evidence that small specific bits of the genome are functional.
Friday, January 25, 2013
How Many Genomes Have Been Sequenced?
How many "finished" or permanent draft complete genome sequences have been published?

How many of them are eukaryotes?





2 comments:

  1. it's great material...
    your blog will make me to improve my biology
    thanks...
    By:
    http://biology-community.blogspot.com/

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  2. Advancing Genomics Mandates Prior Rethink-Update Of Genetics

    On “Time’s Arrow” and on “Genetic Mutation Rate”

    A. Evolution Points Time’s Arrow
    http://universe-life.com/2013/01/09/randomness-is-impossible-in-the-universe/

    An evolving system EVOLVES continuously, without randomness. The universe evolves, cyclically, between its all mass pole and all energy pole.
    Period.

    B. A Genetic Mutation Rate???
    http://news.sciencemag.org/sciencenow/2013/03/clocking-the-human-exodus-out-of.html?ref=em

    Exasperating ignorance.

    Genetics is THE PROGENY of culture.
    Genes (and genomes) are organisms, molded (i.e. are expressions modified) via natural selection by their reactions to their circumstances (i.e. by their culture).

    Look up Pavlov and Darwin…

    Respectfully,

    Dov Henis
    http://universe-life.com
    My Don Quixotic mission: Un-theosophize religious “Science” of trade-union-church AAAS.

    Genetics is modifications of genome’s expressions in response to cultural variations, which is behavioral modifications in response to circumstantial variations. DH

    ReplyDelete