Junk to the second power

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The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal.

What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.

The paper I will discuss in this essay appeared in 2005, and was authored by Wyers et al. This group was interested in studying the putative substrates of a nucleus-specific RNA degrading protein (Rrp6, a subunit of the nuclear exosome; see my previous essay for a bit more on the exosome, and for other facts that pertain to this essay). The impetus for the careful and systematic studies in this paper were the results shown in Figure 1, which is reproduced here. This is a microarray comparison of genome-wide steady-state RNA abundance in yeast; basically, oligonucleotide probes that together represent all 6400 of known yeast genes, along with 600 probes defined by other criteria (occurrence in SAGE libraries, encoded by the mitochondrial genome, to name but two) were printed on small chips, and these chips were subsequently hybridized with fluorescently-labeled copies of RNA prepared from either the wild-type or otherwise isogenic rrp6 mutant strains. Because fluorescence is easily measured and quantified, it is possible to convert these results to relative abundances of mRNAs corresponding to each probe. Because the “identity” (= sequence) of each oligonucleotide probe is known by definition, the results of this study may be translated into a depiction of RNA abundance along the yeast genome.

Fig1A.jpg

Figure 1. This is actually Fig. 1A from Wyers et al., reproduced here to give the reader a glimpse into what microarray data looks like. The x-axis (note the log scale) represents arbitrary expression units as obtained from chips probed with samples prepared from wild-type yeast RNA, and the y-axis the values obtained from chips probed with samples prepared from the rrp6 mutant. Different classes of genomic region are color-coded. Protein coding regions (“ORFs”) are the tiny black dots; these probes generally fall along the diagonal defined by a line with slope of 1 and intercept 0. Note that the stable RNAs (yellow and red dots) almost all fall well above the diagonal – the part of the graph where RNAs that are stabilized by the rrp6 mutation should fall. What the authors saw and followed up on were the green dots that also fell above the diagonal.

These authors were interested in identifying genes whose RNA products increased dramatically in abundance in the rrp6 mutant compared with the wild-type. And indeed, many were found. As should be expected (see my previous essay), stable RNAs (ribosomal RNAs, snRNA, snoRNAs) were prominently stabilized by the rrp6 mutation. However, among the parts of the genome that apparently encoded rrp6-dependent RNAs were a number of positions that look to have no protein product (“Intergenic” in the figure). That these regions were expressed had been suggested by the existence of so-called SAGE (see footnote 1) tags from these regions. This result – SAGE tags from intergenic regions – is roughly analogous to that which has been seen in the ENCODE study (as I discuss near the end of this essay). What the results shown in Figure 1 suggest is that some of these intergenic transcripts are targets of rrp6-mediated RNA turnover. More than 20% of these probes showed at least a 2-fold greater expression in the rrp6 mutant than the wild-type. A similar bias with the “ORFs” probes was not seen. (For those of you who are inclined, Fig. 1B of the paper deals with this issue, and indicates that a pretty high proportion of the “green dots” are expressed at higher levels in the rrp6 mutant, compared with the “ORFs” probes.)

The source of these RNAs was something that needed to be worked out, so as to better understand what is going on here. Accordingly, the authors chose some of these (indicated in Figure 1 of this essay) for further study. Using a comprehensive range of approaches, the authors showed that these RNAs were the products of transcription by RNA polymerase II. The evidence included that they could be immunoprecipitated with antibodies against the distinctive 5’-cap structure of a typical polII transcript, their synthesis was specifically affected by mutations in a polII subunit but not a polIII subunit, and they were associated in vivo with polII (shown by chromatin immunoprecipitation – see footnote 2).

Further analysis indicated that these intergenic RNAs are usually unstable in wild-type cells (readers are referred to Figure 5 for this result), being stabilized by the rrp6 mutation. In the rrp6 mutant, curiously enough, these otherwise cryptic unstable transcripts were found to be polyadenylated. However, the enzyme responsible for adding these poly(A) tails is not the canonical poly(A) polymerase that adds the poly(A) tail to mRNAs destined for the cytoplasm and translation. Rather, a different nucleotidyltransferase, Trf4 (as well as its cousin Trf5) adds these poly(A) tails. My previous essay described how these enzymes have been shown to be involved in the turnover of RNAs in eukaryotes, and how the polyadenylation harkens to the bacterial mode of RNA degradation. What is important for this essay is that the link with Trf4 argues strongly that these RNAs are destined, from the outset, for degradation. Taken as a complete package, these studies reveal a still-underappreciated phenomenon, that much of the RNA made by a cell is thrown away. This includes RNA encoded by intergenic regions.

What does this say for the larger picture? The ENCODE study, for example, used a similar array of techniques (microarrays, chromatin immunoprecipitation) to show that regions of the human genome with no apparent function are transcribed. The ENCODE studies did not include comparisons with cells deficient in rrp6, other exosome subunits, or Trf4/5-like poly(A) polymerases, so we cannot say for certain that the transcripts identified in the ENCODE project as being derived from non-coding parts of the genome (“junk DNA”) are exactly analogous to the Cryptic Unstable Transcripts identified by Wyers et al. But this is likely, given the broad conservation of the components that degrade these Cryptic Unstable Transcripts in yeast. Which means that all of this excitement about RNAs encoded by junk DNA is not warranted – unless one tends to get excited at the prospects of junk, junk squared, and garbage disposals. In a nutshell, what looks like junk may not only be junk, it may give rise to even more junk.

(There are several other interesting aspects to this story – how does a cell distinguish “productive” from “junk” RNA?, are there implications vis-à-vis gene origination and loss hidden somewhere in all of this? - that will have to wait for future discussions.)

Reference:

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-37. doi:10.1016/j.cell.2005.04.30

Footnotes

1. SAGE = Serial Analysis of Gene Expression. This term represents a high-throughput approach to characterizing and quantifying gene expression. Briefly, the RNA population in a cell is converted to collections of concatameric sequence tags of relatively uniform size, these collections are sequenced en mass, and the occurrences of individual sequences, or of tags that correspond to known genes, are counted. Expression levels may be estimated as the fraction (tags per million, for example) of the total pool of tags that corresponds to a particular gene.

2. Chromatin immunoprecipitation is a technique whereby one may study the parts of a genome that are associated with a specific protein. In this technique, living cells are treated with formaldehyde, a chemical that promotes chemical crosslinking between nucleic acids and proteins (as well as between proteins and proteins – this is the reason formaldehyde is used as a sort of preservative), then they are broken and the specific protein of interest removed from the cell-free extract by immunoprecipitation. (Immunoprecipitation entails adding antibodies to an extract, and then recovering these with immobilized affinity reagents such as Protein A Sepharose.) After the immunoprecipitates are washed free of non-specifically bound proteins, the formaldehyde crosslinks are reversed by treatment at high temperatures, the DNA that was associated with the immune complex recovered, and PCR analysis performed to estimate the extent to which specific genome regions (which are defined by the PCR primers) are enriched in the immune complexes.

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59 Comments

Arther Hunt you state In a nutshell, what looks like junk may not only be junk, it may give rise to even more junk.

Or a more technical analysis of your paper.

ENCODE SMMMMEMCODE,,,THE GENOME IS JUNK I TELL YOU

Yet you are overlooking at the overall information that must be encrypted in the Genome!!!

To illustrate the complexity and wonder in the DNA of man, let’s look at some of the work of Samuel Braunstein who is a quantum physicist at the Weizman Institute in Israel. Samuel Braustein was asked to present a talk to the science-fiction club in Rehover. What better topic, he thought, than quantum teleportation? Because of the limitations, imposed by the laws of physics, of ever teleporting any material object, Braunstein suggested the secret to teleportation would lie not in transporting people, or material objects, but would lie in teleporting the molecular information about whatever was to be teleported. Somehow, this Star Trek type teleporter must generate and transmit a parts list and blueprint of the object being teleported. This information could be used in reconstructing the object at its final destination. Presumably, the raw materials would be available to reconstruct the object at its final destination. Naturally this process raises a lot of questions that the script writers for Star Trek never answered. For example, just how much information would it take to describe how every molecule of a human body is put together? In a human body, millimeter accuracy isn’t nearly good enough. A molecule a mere millimeter out of place can mean big trouble in your brain and most other parts of your body. A good teleportation machine must be able to put every atomic molecule back in precisely its proper place. That much information, Braunstein calculated, would require a billion trillion desktop computer hard drives, or a bundle of CD-ROM disks that would take up more space than the moon. It would also take about 100 million centuries to transmit the data for one human body from one spot to another. “It would be easier,” Braunstein noted, “to walk.” Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together in just 3 billion base pairs of DNA code. As well, the DNA code somehow contains the “self assembly instructions” that somehow tells all these countless trillions of proteins molecules how to put themselves together into the wonder of a human body. Yet far from the billion-trillion computer hard drives calculated by Braustein, these 3 billion letters of information in the DNA of man could easily fit onto the single hard drive of the computer I’m writing this article on with plenty of room left to spare! That ratio of a billion trillion hard drives reduced to one hard drive is truly an astonishing amount of data compression that far exceeds the capacity of man to do as such. It is abundantly clear that all that required information for exactly how all the protein molecules of man are put together is somehow ingenuously encrypted in some kind of “super code” in the DNA of man. Amazingly, many evolutionary scientists “used” to say the majority of DNA that didn’t directly encode for proteins (genes) was leftover “junk” DNA from man’s falsely presumed evolutionary past.

Someone on this blog once said, “so what a barrel of water has that much information also”…Well the barrel of water will not die if molecules are misplaced!

As well, I find no solid proof of evolution in man, I only find evidence for information being lost in the Genome of man not ever gained!

To further clarify, an example of the principle of Genetic Entropy being obeyed, we can now look at the genome and morphology of man himself.

Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.

“We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.”

Thus the younger races of humans have demonstratively lost genetic information for diversity in the genome and have also visibly lost information for color (I argue lost information for shape as well)!! This clearly seems to be loss of information from parent species! Doesn’t seem to be what we would see if evolution was driving us to new super-species!

Don’t tell them but Europeans (especially the master-race) are actually degrading, as far as information in the genome is concerned, when compared to Africans!

As Well, The highly touted Lactase persistence mutation is actually the loss of an instruction to turn the lactase enzyme off! Thus even it obeys the principle of Genetic Entropy.

Plus you are fighting the fact that the vast majority of mutations are in fact SLIGHTY detrimental when compared to any “hypothetical” beneficial ones (Sanford Genetic Entropy 2005). Thus slightly detrimental mutations are below the power of natural selection to remove from a population before they spread their harmful effects throughout the population! Once again solid proof of evolution destroying things; not building up novel structures!

Lay off the martinis there Bond.

You are of course aware that the facts of genetic diversity in African vs. non-African populations are perfectly consistent with the evolutionary view.

And, not that you answer questions, but about that onion…?

Are people still fisking b…77? I’m looking forward to seeing one, though there’s an awful lot of work there to be done. To spew so much, so quickly implies, a lot of internal pressure.

He gives us junk about junk creating junk.

BJ Bond,

To illustrate the complexity and wonder in the human genome let’s look at endogenous retroviruses. There are millions of copies of SINES and LINES in the human genome. They cause insertional mutagenesis which can cause increased susceptability to disease and even death. Most of the copies are nonfunctional and are probably not even transcribed. The copies that are transcribed often don’t code for any functional protein. The copies that are transcribed and do code for functional protein code for things like reverse transcriptase which serves no useful function in the host, except to cause continued insertional mutagenesis. This process has probably resulted in the extinction of many species and possibly even entire lineages in evolutionary time.

Now I ask you, does that sound like intelligent design? Does that sound like foresight and planning? Does that sound like wonderous complexity? Or does that sound more like the best that one could hope for from an unguided process with no forethought or planning whatsoever?

By the way, if you find no solid proof of evolution in man, perhaps you should look at the evolution of lactose metabolism in different cultures or the evolutionary pressures and adaptions of human skin color in different regions of the world. You might also want to compare the endogenous retroviruses of humans and chimps. The conclusion to be drawn from these data sets is quite clear. Humans evoled from other primates and they continue to evolve whether you have looked at the evidence or not.

It seems to to me that the term “Junk DNA”, for DNA whose function is unknown, is an example of “Derision is the refuge of threatened ignorance.” Whoever coined the term ought to be ashamed.

As an old-style 20th Century evolutionary biologist, I think if non-coding DNA were truly non-functional, it would not exist. Making the stuff requires a good bit of resources. One would think organisms who did not waste the resources would be fitter than organisms which did. Therefore it must be quite important, and never should have been called junk just because we did not understand how it is important.

I wonder how many of the people pushing back the frontiers of ignorance in molecular genetics have little or no understanding of evolution. People with backgrounds in biochemistry, physics, or whatever, with no or little formal education in evolutionary biology. Would they be able to discuss Hardy-Weinberg, or Simple Darwinian Fitness, for example?

I wonder if at least part of the reason nonfunctional DNA gets transscribed might be because preventing such transcription would require additional regulatory stuff, and the cost of that might exceed the benefit?

(Or was that covered in the paragraphs that went over my head?)

Henry

…let’s look at some of the work of Samuel Braunstein who is a quantum physicist at the Weizman Institute in Israel. Samuel Braustein was asked to present a talk to the science-fiction club in Rehover…

So, Bond, did any peer-reviewed work on any of the biological issues come out of this physicist’s talk at a science-fiction club?

Don’t tell them but Europeans (especially the master-race) are actually degrading, as far as information in the genome is concerned, when compared to Africans!

I’d consider that transparent bigotry, if it, and its author, weren’t so transparently clueless.

David Stanton,

For one, when the fossil record is looked at objectively, instead of through the eyes of the biased imagination, the so called “transition” to man is anything but smooth…or to put it more clearly in Richard Leakey’s words..

“If pressed about man’s ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving”. Richard Leakey, world’s foremost paleo-anthropologist, in a PBS documentary, 1990.

For another thing, similarities in the genome, though suggestive, are not conclusive proof of common decent! You must go deeper my friend to establish the foundation for evolution…This is Hard science, not wishful speculation, we are talking about, is it not?

Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias. For example, naturalists say that evolution is proven true when we look at the 98.8% similarity between certain segments of the DNA in a Chimpanzee and compare them with the same segments of DNA of a Human. Yet that similarity is not nearly good enough to be considered “conclusive” scientific proof. For starters, preliminary comparisons of the complete genome of chimps and the complete genome of man yield a similarity of only 96%. Dr. Hugh Ross states the similarity may actually be closer to 85% to 90%. Secondarily, at the protein level only 29% of genes code for the exact same amino acid sequences in chimps and humans (Nature, 2005). As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from! Clearly, we must find if the DNA is flexible enough to accommodate any type of mutations happening to it in the first place. This one point of evidence, (The actual flexibility of DNA to any random mutations), must be firmly established, first and foremost, before we can draw any meaningful inferences from the genetic data we gather from organisms!! Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is clearly overwhelming, for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

“It is entirely in line with the al nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes ally introduced into any artificial mechanism are predominantly harmful to its useful operation” H.J. Muller (Received a Nobel Prize for his work on mutations to DNA) “But there is no evidence that DNA mutations can provide the sorts of variation needed for evolution… There is no evidence for beneficial mutations at the level of macroevolution, but there is also no evidence at the level of what is commonly regarded as microevolution.” Jonathan Wells (PhD. Molecular Biology)

Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter. Since, it is an established fact that at least 999,999 in 1,000,000 of any mutations to DNA will be harmful and/or , then it is also an established fact that there is at least a 999,999^30,000,000 to one chance that the monkey will fail to reach man by evolutionary processes. The monkey will hit a end of harmful/fatal mutations that will kill him or severely mutilate him before him. The poor monkey barely even gets out of the evolutionary starting gate before he is crushed by blind chance. This would still be true even if the entire universe were populated with nothing but monkeys to begin with! This number (999,999^30,000,000), is fantastically impossible for any hypothetical beneficial mutation to ever overcome! Worse yet for the naturalists, mathematician William Dembski PhD. has worked out the foundational math that shows the mutation/natural selection scenario to be impossible EVEN IF the harmful/fatal rate for mutation to the DNA were only 50%. The naturalist stamps his feet again and says that symbiotic gene transfer, cross-breeding (yes they, desperately, suggested cross-breeding as a solution), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. They say these things with utmost confidence without even batting an eye. Incredibly, this is done in spite of solid evidences testifying to the contrary. Indeed, even if a hypothetical beneficial mutation to the DNA ever did occur, it would be of absolutely no use for it would be swallowed in a vast ocean of slightly detrimental mutations that would be far below the culling power of natural selection to remove from a genome!

“The theory of gene duplication in its present form is unable to account for the origin of new genetic information” Ray Bohlin, (PhD. in molecular and cell biology)

“Evolution through random duplications”… While it sounds quite sophisticated and respectable, it does not withstand honest and critical assessment” John C. Sanford (PhD Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents!)

The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses in complexity any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)! No line of computer code ever written by man approaches that level of data compression (poly-functional complexity). Further evidence for the inherent complexity of the DNA is found in a another study. In June 2007, a international team of scientists, named ENCODE, published a study that indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. This “complex interwoven network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005; page 141). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. Since evolution was forced, by the established proof of Mendelian genetics, to no longer view the whole organism as to what natural selection works upon, but to view the whole organism as a multiple independent collection of genes that can be selected or discarded as natural selection sees fit, this “complex interwoven network” finding is extremely bad news, if not absolutely crushing, for the population genetics scenario of evolution developed by Haldane, Fisher and Wright (page 52 and 53: Genetic Entropy: Sanford 2005)!

http://www.boston.com/news/globe/he[…]eled/?page=1

To put it mildly David Stanton…You got a whole heap of trouble with your beloved theory of RM/NS!

Bond, James Bond, is this your eBay My World page? Interesting stuff. Especially the collection of erasers (41 collectable erasers / rubbers from the 70s and 80s) you’ve sold and the Vintage Italian art CANTAGALLI Firenze holy water font you bought.

“The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses in complexity any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)!”

When you google this text you will find it in these places: It Seems Frontloading is Everywhere

Design: All The Way Down

Ruse versus Nelson: What Would Make Us Change Our Minds? An Unconventional Debate, October 4

The Image of Pots and Kettles ….

Cephalopod development and evolution. Get ready to become a christian

Thus, it is unlikely that anybody reads Bond’s stuff. I guess even his friends at UD scroll down when they see this spam.

No line of computer code ever written by man approaches that level of data compression (poly-functional complexity).

Next thing you’ll come up with is a function of Alu elements es god’s comment tags in the genome.

Why would god need to put comments in the code? ;)

Why would god need to put comments in the code? ;)

So Jesus would know what bits to modify in order to correct God’s mistakes? ;)

For another thing, similarities in the genome, though suggestive, are not conclusive proof of common decent!

Yeah, thanks, I’ll remember that dodge next time some woman I shagged tries to make me take a paternity test.

So what’s your alternative explanation of all those similarities, BJB? And how would we go about testing it? Until you can come up with one, we’ll stick with the only explanation offered so far.

**ahem** *tune*

He’s hijacking the thread, he’s hijacking the thread.

Hi, ho, so clue-less-o, he’s hijacking the thread.

BJB in a nutshell:

It’s a big number !!!!!!!!

Also, I haven’t found what I don’t want to find.

Although I love genetics, most of the technical details have difficulty sticking to my brain. I just want to make sure I understand this correctly: Just because “junk DNA” can be transcribed into RNA, we should not assume that it has a function.

It makes sense. Any DNA sequence, “junk” or not, can, theoretically, be transcribed and, theoretically, code for a protein. If said protein is useful (or even stable, or not harmful) is another matter.

Any DNA sequence, “junk” or not, can, theoretically, be transcribed and, theoretically, code for a protein.

Might have to be a start and stop codon in there before transcription can occur, but other than that, I agree.

Henry

No line of computer code ever written by man approaches that level of data compression (poly-functional complexity).

People don’t write code in compressed form, for a number of obvious reasons. They also don’t generally (brainfuck is one exception) use programming languages that provide for multiple interpretations of the code by choosing different starting points, again for obvious reasons. I’m not clear on how “no human would do it that way” became a positive indicator of intelligent design in BJB’s addled brain.

Hi all,

A few notes. First - if you don’t reply to BA77, he’ll go away. (Aside to BA77 - if your next post doesn’t include the names of the majority of co-inventors who Sanford worked with, it will be severely trimmed.)

Henry J:

I wonder if at least part of the reason nonfunctional DNA gets transscribed might be because preventing such transcription would require additional regulatory stuff, and the cost of that might exceed the benefit?

(Or was that covered in the paragraphs that went over my head?)

I wonder exactly as you do. You’re missing nothing here.

Jim Thomerson:

I think you can view the term “junk” as both a shorthand (for DNA that does not encode protein or is transcribed into rapidly turned over RNA or is not transcribed or can be deleted with no effect or .…) and something to get attention.

As far as the resources that go into the making of “junk DNA”, and moreover into its expression as RNA, I think it’s probably not appropriate to think of eukaryotic cells as so energy and resource poor that they cannot afford these expenditures. In the overall scheme of thing, DNA and RNA takes up a pretty small part of the cell’s budget. Enough so that thinking of “junk” in terms of advantage and selection (with regards to energy costs) may not be suitable.

Finally, I would be remiss if I didn’t thank Dave Wisker for reading my latest two essays and making good suggestions, and Reed Cartwright for helping get the latest one online.

Henry J:

Any DNA sequence, “junk” or not, can, theoretically, be transcribed and, theoretically, code for a protein.

Might have to be a start and stop codon in there before transcription can occur, but other than that, I agree.

Henry

Yea. I realised that about four minutes after I posted it.

**ahem** *tune*

He’s hijacking the thread, he’s hijacking the thread.

Hi, ho, so clue-less-o, he’s hijacking the thread.

now you know why i haven’t spent time here since the contributors have decided to allow two rather large idiots to troll EVERY SINGLE THREAD.

First - if you don’t reply to BA77, he’ll go away.

no, he won’t.

To put it mildly David Stanton…You got a whole heap of trouble with your beloved theory of RM/NS!

This is somewhat like saying that the beloved theory of heliocentrism was in trouble because of the complexity of Earth’s orbit. You would think that someone who calls himself “James Bond” could grasp that dealing with “trouble” is what scientists do – not run home to mommy/God.

First - if you don’t reply to BA77, he’ll go away.

What makes you think so? The evidence doesn’t support it. Will ID also go away if we don’t respond to it? The argument has been made that lurkers might get the wrong impression if folks like BJB aren’t answered, so it may be useful to address their major misconceptions and misrepresentations. In any case, it’s human nature that someone will respond to him. The “if you don’t reply, he’ll go away” line has been issued many thousands of times on the internet, but I’ve never seen a case where it was effective.

Aside to BA77 - if your next post doesn’t include the names of the majority of co-inventors who Sanford worked with, it will be severely trimmed.

Bravo. It’s about time that resident trolls BJB, Mats, and realpc were curtailed.

As far as the resources that go into the making of “junk DNA”, and moreover into its expression as RNA, I think it’s probably not appropriate to think of eukaryotic cells as so energy and resource poor that they cannot afford these expenditures. In the overall scheme of thing, DNA and RNA takes up a pretty small part of the cell’s budget. Enough so that thinking of “junk” in terms of advantage and selection (with regards to energy costs) may not be suitable.

Given the inexorable algorithmic optimization of natural selection, I think it is always suitable to think in those terms, especially in ancient mechanisms. However, one must not think about it naively. As Henry suggests, keeping something from happening may be more costly than letting it happen. And we should be wary of the implicit teleology in the language I just used; NS optimizes locally, not globally, and a path to a more efficient mechanism may simply never have occurred historically.

NS optimizes locally, not globally

Sorry, that was a rather sloppy way to put it, as NS is certainly a global process, and even RM has global effects on the phenotype. More accurate is to say that evolution is stepwise, bottom-up, and not goal-directed.

As an old-style 20th Century evolutionary biologist, I think if non-coding DNA were truly non-functional, it would not exist. Making the stuff requires a good bit of resources. One would think organisms who did not waste the resources would be fitter than organisms which did. Therefore it must be quite important, and never should have been called junk just because we did not understand how it is important.

These facts are not in evidence. It is not at all clear that DNA synthesis or even “junk RNA” synthesis is a major cost in terms of carbon or energy, compared to the heavy transcription/translation that actually produces proteins etc. As the volume of the cell increases the relative cost declines, which is one (of many) ideas about why the amount of DNA per cell correlates not with “complexity” or whatever but with cell volume.

(prokaryotes, typically very small, probably do have strong enough selection against large amounts of useless DNA)

Google “c-value paradox” or “c-value enigma” to get the big picture…also “onion test”.

Nick

Dawkins explains “junk” or selfish DNA this way.

If it costs more in fitness to get rid of it than to leave it, it will stay.

FWIW, in terms of the whole organism, maintaining a certain size of DNA seems to be a minor cost. A cell may replicate once but live for decades, metabolizing with energy and mass to make RNA and proteins which turnover with half lives on the order of days.

Where streamlining the genome seems important is in bacteria which tend to have much smaller amounts of noncoding and viruses which have even less.

It seems to to me that the term “Junk DNA”, for DNA whose function is unknown, is an example of “Derision is the refuge of threatened ignorance.” Whoever coined the term ought to be ashamed.

Nice Emily Litella imitation. The coined term was “junk” DNA – note the scare quotes.

Dear Bornagain Bond

You left some unanswered questions at the Cal Lit Review site where Behe’s latest alimentary output was examined. Perhaps you could wander back over there again and we could proceed to kick your sorry butt some more. Or perhaps you finally figured out that your understanding of biology is on a par with the evidence that you have a clue (i.e. less than zero).

Since B77 doubts common decent of modern apes and humans, I’d like to hear what he thinks about the similarities between human chromosomes 2 and chimpazee chromosomes 2p and 2q? Specifically, how does ID explain the presence in human chromosome 2 of a pre-telomeric sequence, followed by a telomeric sequence, an inverted telomeric sequence, and an inverted pre-telomeric sequence, if not through the fusion of the two aforementioned chimp chromosomes? The chimp chromosomes also have the same banding pattern as the corresponding arm of the human chromosome, human chromosome 2 and chimp 2p share the same centromere location, and there are the remains of a centromere on the q arm of human chromosome 2 corresponding with the centromere of chimp 2q. What’s ID’s explanation?

BJ Bond,

I have no idea what you are talking about. I never even mentioned the fossil record in this thread. But, as long as you mention it, you are completely wrong in your statements regarding the fossil record. You are also completely wrong is all of the other crap you posted. You are not on-topic at all here. Do you just cut and paste all that crap for no reason at all? Nothing you wrote has anything whatsoever to do with junk DNA. Why should anyone bother to read anything you post if that is what you do. Please just go away.

And by the way, you also failed to respond to any of the questions I realy did ask, once again. Please go away and don’t come back until you are able to discuss the topic of the thread in a scientific manner. If you respond by cutting and pasting off-topic nonsense I guess I should just respond in kind. There are a lot of good web sites on Europa that I could post in reponse to your nonsense.

This is interesting, but IMO a pointless refutation of ID. What we ought to point out instead is that ID doesn’t predict that no DNA is junk to begin with. All it “predicts” is that wherever The Designer has intervened we will see whatever the unknown designer of unknown capabilities and unknowable motives wanted, presuming things haven’t changed naturally since the time of the intervention.

IOW, ID doesn’t predict anything at all.

BJB rants, while trying to demonstrate that Human DNA encodes humans down to the molecule…

“Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together”

Um, no, it doesn’t. For proof of this you need to look no further than identical twins, who receive the exact same DNA, yet are often substantially different. Even when they’re quite similar they are never microscopically the same, this can easily be demonstrated in the fact that they will always have different fingerprints.

Bobby:

This is interesting, but IMO a pointless refutation of ID. What we ought to point out instead is that ID doesn’t predict that no DNA is junk to begin with. All it “predicts” is that wherever The Designer has intervened we will see whatever the unknown designer of unknown capabilities and unknowable motives wanted, presuming things haven’t changed naturally since the time of the intervention.

IOW, ID doesn’t predict anything at all.

Exactly, although some IDers have managed to take some creationist talking points about “junk” DNA and pretend that it is an ID relevant prediction.

Bobby makes an important point. Predictions as in guesses by individuals are irrelevant. What matters are predictions from theories – empirical statements that are entailed by a theory. And ID entails nothing. All the creationists can offer is “theism would have predicted this” – after the fact. It’s utter BS, and shows that they have no grasp of what science and prediction are about.

Does anyone hear know if Mr Bond, Plagiarist for Jesus, has ever responded to my question on what Intelligent Design says about why tetraodontid puffers lack so much “Junk DNA” so as to have the smallest vertebrate genomes ever known?

Hey BJ Bond.

All of your ‘logic’ is a red herring. To mix a metaphor: it’s a building without a foundation. If you postulate the existence of a designer, you must also consider the origin of said designer. If the designer is not a deity, it had an origin. If the designer is a deity, it also had an origin.

If the universe needed a designer, so did the designer. And that designer too. And the designer of that designer three. (Iterate infinitely.)

It’s turtles all the way down.

Refute.

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Yes, BJB’s posts make about as much sense.

I vote that bornagains posts get sent to the bathroom wall.

In one thread on uncommon stupidity Bornagain77 gave the www.whale.to website as a scientific reference.

born again antivaccine stupidity

It must take some effort to achieve this level of scientific illiteracy.

It must take some effort to achieve this level of scientific illiteracy.

Even some of the Uncommonly Dense posters corrected his idiocy.

Ah ha, I see Burn(ed) again’s logic here, it makes perfect sense: Junk to the second power describes his/her posts perfectly!

“Junk” DNA has a function? Of course! The Designer doesn’t like to waste things! Everything He does must have a function.

“Junk” DNA has no function? Of course! The Designer is an Artist and sometimes likes beauty for beauty’s sake. Who are you to question His motives?

We can’t find out whether “junk” DNA has a function or not? Of course! The Designer loves to work in mysterious ways. We can’t always understand everything, and it’s just as well.

See? Everything and its contrary is compatible with ID. Everything can be retrofitted as an ID “prediction”. IDists are spin artists, in that they don’t hesitate to spin like a top in order to always face what finally appears to be the right direction. What’s the use of a discussion with them? It’s like wrestling a dead, giant octopus.

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D’oh! I’ll try again.

Bornagain77 Wrote:

For one, when the fossil record is looked at objectively, instead of through the eyes of the biased imagination, the so called “transition” to man is anything but smooth…or to put it more clearly in Richard Leakey’s words..

”If pressed about man’s ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving”. Richard Leakey, world’s foremost paleo-anthropologist, in a PBS documentary, 1990.

So, Bornagain77, what do you think this means?

I think it means that the picture of hominin evolution is more complicated than was at first envisaged. While we have several good fossils that indicate the transition from Australopithecus to Homo, the actual evolution of Homo species is more complex and subtle than a simple single lineage, and we would need many more fossils from the relevant periods to tease apart the complex picture.

Having said that, just because we cannot dissect the detail of what occurred does not invalidate the broad conclusion, that the first Homo species probably evolved from one of several Australopithecene species, and that Homo species have become less like Australopithecenes and more like modern humans as time passed, although there are probably several lineages of extinct Homo species.

For another thing, similarities in the genome, though suggestive, are not conclusive proof of common decent!

There are several things wrong with this sentence: (1) Similarities in the genome are not just broad and general similarities; they are very specific, and set within the context of a great deal of difference. (2) These specific similarities constitute fairly strong evidence in favour of common descent, especially when considered in the proper context. (3) In science, nothing is ever “proven” conclusively. Instead, scientists must live with the facts that (a) we are working with an incomplete data set, so the possibility always exists that new evidence may come to light that sheds more light on the subject of the investigation; and (b) a better hypothesis may exist, but it is not one that anyone has yet thought of. Of course, we can know that our models of how the world works (of which MET is but one) are, at the very least, close approximations of reality. The preponderance of evidence indicates that MET is correct beyond any reasonable doubt.

You must go deeper my friend to establish the foundation for evolution…This is Hard science, not wishful speculation, we are talking about, is it not?

Sadly, you seem to be far more familiar with the latter than with the former.

I thought it had been established that BJ Bond and BA77 were one and the same. If evidence of this does exiist, then they should both be banned. Of course, I guess it is possible that they could both cut and paste the same off-topic nonsense by coincidence. Now let’s see, what are the odds that this was unintelligently designed?

I thought it had been established that BJ Bond and BA77 were one and the same. If evidence of this does exiist, then they should both be banned.

??

The first post in this thread is from “Bond, James Bond; bornagain77”. Sometimes he leaves off one part or the other of that, but he isn’t sockpuppetting. I think his trolling ass should be banned, but not for that reason.

Or a more technical analysis of your paper. ENCODE SMMMMEMCODE,,,THE GENOME IS JUNK I TELL YOU

Firstly, the ENCODE evidence is based on common descent. Since you reject common descent, you don’t have the ENCODE evidence to use.

However, even with ENCODE, that still leaves some 80+% of our DNA able to freely mutate without consequence.

Yet you are overlooking at the overall information that must be encrypted in the Genome!!! To illustrate the complexity and wonder in the DNA of man, let’s look at some of the work of Samuel Braunstein who is a quantum physicist at the Weizman Institute in Israel. Samuel Braustein was asked to present a talk to the science-fiction club in Rehover. What better topic, he thought, than quantum teleportation? … That much information, Braunstein calculated, would require a billion trillion desktop computer hard drives, or a bundle of CD-ROM disks that would take up more space than the moon. …Yet far from the billion-trillion computer hard drives calculated by Braustein, these 3 billion letters of information in the DNA of man could easily fit onto the single hard drive of the computer I’m writing this article on with plenty of room left to spare! That ratio of a billion trillion hard drives reduced to one hard drive is truly an astonishing amount of data compression that far exceeds the capacity of man to do as such.

You have confused creating information (of the type you mean here) with altering information. It’s not like the DNA, mRNA, etc. create carbon atom ex nihilo. Before they are acted upon, the atoms already had spatial information, bonding information, etc., they were just altered by the biological system. There is nothing at all difficult about writing a, for example, 3000 byte program that can alter the information on a quadrillion-byte drive, which is the same ratio of packing.

Amazingly, many evolutionary scientists “used” to say the majority of DNA that didn’t directly encode for proteins (genes) was leftover “junk” DNA from man’s falsely presumed evolutionary past.

Many people thought the earth was flat, too. Evolutionary theory never ruled out a purpose for non-coding DNA, even if a minority of scientists did.

Someone on this blog once said, “so what a barrel of water has that much information also”…Well the barrel of water will not die if molecules are misplaced!

It will freeze if the temperature drops, causing wide-spread changes in spatial information.

As well, I find no solid proof of evolution in man, I only find evidence for information being lost in the Genome of man not ever gained!

Random mutation does not decrease information (in the Shannon sense), in the long run.

To further clarify, an example of the principle of Genetic Entropy being obeyed, we can now look at the genome and morphology of man himself.

There is no such principle that has been scientifically verified. Making one up is not impressive.

“We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.”

This would be a typical result of a small subset of the population of Africa being the source for the populations of Eurasia, and small subset of Eurasia being the source for the populations of the Americas.

Thus the younger races of humans have demonstratively lost genetic information for diversity in the genome and have also visibly lost information for color (I argue lost information for shape as well)!!

Last I checked, most of the Eurasian and American populations were not albinos, so they obviously have not lost “information for color”.

This clearly seems to be loss of information from parent species! Doesn’t seem to be what we would see if evolution was driving us to new super-species!

Evolution does not drive to super-species, just to better survival. If losing traits results in better survival, a population may well lose traits.

Plus you are fighting the fact that the vast majority of mutations are in fact SLIGHTY detrimental when compared to any “hypothetical” beneficial ones (Sanford Genetic Entropy 2005). Thus slightly detrimental mutations are below the power of natural selection to remove from a population before they spread their harmful effects throughout the population! Once again solid proof of evolution destroying things; not building up novel structures!

Except when slightly detrimental mutations have a side effect that is highly beneficial in some environments, such as sickle-cell trait.

For one, when the fossil record is looked at objectively, instead of through the eyes of the biased imagination, the so called “transition” to man is anything but smooth…or to put it more clearly in Richard Leakey’s words.. ”If pressed about man’s ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving”. Richard Leakey, world’s foremost paleo-anthropologist, in a PBS documentary, 1990.

Abrupt on an evolutionary scale would be in a couple of hundred thousand years.

For another thing, similarities in the genome, though suggestive, are not conclusive proof of common decent!

You can always choose to find any amount of evidence inconclusive. There are many other types of evidence for common descent besides fossils and genomic similarities. All of them point to not only common descent, but a virtually identical branching structure on the evolutionary bush.

You must go deeper my friend to establish the foundation for evolution…This is Hard science, not wishful speculation, we are talking about, is it not?

www.talkorigins.org/faqs/comdesc

Lots of hard science there.

Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias.

I can’t even find the principle of genetic entropy explained in CreationWiki. No wonder it gets ignored. Sounds like emphasized disbelief. I presume it’s some sort of claim that all genetic changes are deleterious?

For example, naturalists say that evolution is proven true when we look at the 98.8% similarity between certain segments of the DNA in a Chimpanzee and compare them with the same segments of DNA of a Human. Yet that similarity is not nearly good enough to be considered “conclusive” scientific proof.

Not in and of itself. It’s merely one feature of the wide body of proof.

Secondarily, at the protein level only 29% of genes code for the exact same amino acid sequences in chimps and humans (Nature, 2005).

Which means what for common descent?

As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish?

Yes. Just like some of your cousins are Africans, so you are an African.

Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly?

Yes. Just like some of your cousins are Asians, so you are an Asian.

Our DNA is 75% similar to a worm; So are we 75% worm?

Yes. Just like some of your cousins are Europeans, so you are a European.

No, of course not!!

Really?

Clearly, we must find if the DNA is flexible enough to accommodate any type of mutations happening to it in the first place.

We already know it is flexible enough to accommodate several different types of mutation.

This one point of evidence, (The actual flexibility of DNA to any random mutations), must be firmly established, first and foremost, before we can draw any meaningful inferences from the genetic data we gather from organisms!! Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)!

Gerrish and Lenski’s work applied to asexual reproduction, where recombination did not occur. So, that slows down evolution for a few species of lizards, but has no effect on human evolution.

Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy.

It’s hard to violate a non-existent principle. Still, I’d say that nylon-eating bacteria fill that role nicely.

“It is entirely in line with the al nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes ally introduced into any artificial mechanism are predominantly harmful to its useful operation” H.J. Muller (Received a Nobel Prize for his work on mutations to DNA)

You only need a few.

Jonathan Wells (PhD. Molecular Biology)

You mean, the guy who got a Ph. D. just so he could use it to sound authoritative when attacking evolution?

then it is also an established fact that there is at least a 999,999^30,000,000 to one chance that the monkey will fail to reach man by evolutionary processes.

You are committing several errors in that number, such as assuming independence where not established, incorrect multiplication, and using a number for asexual reproduction in a species with sexual reproduction.

William Dembski PhD.

Dembski has had his work has been refuted in just about every way possible.

The naturalist stamps his feet again and says that symbiotic gene transfer, cross-breeding (yes they, desperately, suggested cross-breeding as a solution), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. They say these things with utmost confidence without even batting an eye. Incredibly, this is done in spite of solid evidences testifying to the contrary.

Provide it, if you can.

Indeed, even if a hypothetical beneficial mutation to the DNA ever did occur, it would be of absolutely no use for it would be swallowed in a vast ocean of slightly detrimental mutations that would be far below the culling power of natural selection to remove from a genome!

Hand-waving is not proof.

“The theory of gene duplication in its present form is unable to account for the origin of new genetic information” Ray Bohlin, (PhD. in molecular and cell biology)

Another person who, according to his own biography, made up his mind before getting his education.

“Evolution through random duplications”… While it sounds quite sophisticated and respectable, it does not withstand honest and critical assessment” John C. Sanford (PhD Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents!)

Committed young-earth creatonist.

No line of computer code ever written by man approaches that level of data compression (poly-functional complexity).

Generally, randomly created strings are far less compressible than designed strings. What’s amusing is that you think non-compressibility is evidence against randomness being a part of the process, while it really favros randomness being involved.

… the genome contains very little unused sequences

This is not what ENCODE found.

and, in fact, is a complex, interwoven network. This “complex interwoven network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005; page 141).

Except, it doesn’t. It means changes can have multiple effects.

Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was.

Of course, you have to weigh benefit to harm in the environment.

… finding is extremely bad news, if not absolutely crushing, for the population genetics scenario of evolution developed by Haldane, Fisher and Wright

So, you are arguing against stuff that is 50 years old?

Hey!! I claimed coinage of the term “junk RNA” at sandwalk, back in july: https://www.blogger.com/comment.g?b[…]678735266043 It is kind of obvious…maybe this term, born first on the web, will become of common use…soon!

I’ve found the comments on the energy budget of a cell, and the selective pressure due to cost of transcription, quite interesting. If anyone would like to expand on the topic as a full post, I would be an appreciative reader.

I don’t remember seeing BJB, ba77 post under both names at the same time until I recently pointed out they must be the same guy. Anyway, I always thought it would have been much cooler if Mr “Genetic Entropy, It’s Not Just For Breakfast Anymore!” had chosen Bourneagain77 to go with the secret agent theme AND the 4 Spiritual Laws theme at the same time. Holy poly-coding sock-puppetry, Batman!

I’m going to claim credit for chasing away BJB. No IDist ever responds to my challenge.

I agree that calling it junk DNA was a mistake, since not enough was known at the time or still about non-protein or non-structural RNA coding DNA, but it is still likely that the majority of that sequence is non-functional and is the product of the accumulation of degraded transposons, genes and random duplications of “junk” DNA, or some other mechanisms. While it is costly to replicate a large genome full of supposedly useless DNA, selection may not be able to act if a population is too small or generation times are too long due to a greater genetic drift effect. In fact I think there has been a correlation found between larger animals having larger genomes, and larger animals tend to have smaller populations and longer generation times. However, there have been some lineages that have shrunk their genome size, for example the Fugu puffer fish. So it seems it is possible for an organism to evolve a leaner genome. Also something to consider is it may sometimes be selective to have a larger genome size since there seems to be a conserved and powerful connection between the amount of DNA in a cell and cell size. So large genome size may not always be a net fitness negative.

djlactin Wrote:

I’m going to claim credit for chasing away BJB.

Have you not been around very long? The fact that they leave for a day or two proves nothing. They’ll either ignore your challenge and pop up on another thread, or ignore your challenge and pop back up on the same thread.

No IDist ever responds to my challenge.

Mine, either: “Did God leave scientifically verifiable fingerprints on creation?” (No = ID is silly, Yes = faith is superfluous)

Very interesting. And now I understand and appreciate the earlier post better.

Another thing I hadn’t appreciated was how much of the genome ENCODE found transcribed. (I misunderstood the numbers.) But browsing the report I wonder how reliable their methods are? Their repeats vary quite a bit, and using 3 or more methods lower the intersection of transcripts to something like 30-40 % of the investigated bases (as taken out of a figure).

The current picture is quite exciting in my view. Complementing the blocking and enhancing of coding regions is a more dynamical method of regulating functionality. It is displaying more of dynamical feedback, which is an interesting (and technically well known) method of enhancing quality and regulating functionality at the same time.

I wonder if this is an ancestral method of stabilizing functionality? Support for that could perhaps be:

- Works on RNA.

- Permits reading while AFAIU derived coding regions may not (so much), perhaps suggesting it was in place before DNA.

- Double function in correcting and regulating.

- Possibly evolved function from one to several adenylations.

- Coding regions have AFAIU more and contrived methods for regulation.

- Simple built in function for recycling tagging compared to, say, ubiquitin for proteins.

Wouldn’t it be ironic if this self-proclaimed “triumph for ID” (read: ‘problem for evolution’) is really opening up not only possibilities of understanding (and manipulating) genome functionality but also evolution and its history? I can’t see why it shouldn’t.

I agree that calling it junk DNA was a mistake,

TR Gregory at Genomicron has a lot to say on what he insists labeling non-coding DNA:

As Gould (2002, p.503) stated, “A rose may retain its fragrance under all vicissitudes of human taxonomy, but never doubt the power of a name to shape and direct our thoughts”.

Because it is generally no longer applied in its original meaningful sense, because the type of DNA to which it actually relates now has a more descriptive name (pseudogenes), and because of its connotations of total phenotypic inertness, the term “junk DNA” should probably be abandoned in favour of less subjective terminology. “Non-coding DNA” serves this purpose quite well.

It should come as no surprise (and indeed, it probably does not) that new roles are being discovered for non-coding DNA and that some of yesterday’s buzzwords – including “junk DNA” – are destined for the dustbin.

He suggests specifying the function (or not) of DNA instead, AFAIU. Perhaps “(suspected) non-functional DNA” is appropriate:

Just to clarify, I think the term could be useful – indeed, it was useful when Ohno coined it. The problem is that it is seldom used in an appropriate way.

If the meaning were specified explicitly to be “regions strongly suspected of being non-functional with evidence to back it up” (which, incidentally, is not the original definition according to Ohno (1972) or Comings (1972)), and if people used it only in this way, then I would not have a problem with this. But given the difficulty that people seem to have in accepting that some DNA may truly not have a function at the organism level, I don’t know if we could ever get it to be used with such precision. [Link removed.]

Btw, I note there are some qualitative differences between “junk” DNA and “junk” RNA.

IIRC someone noted that besides Ohno’s picture it is still a reusable resource for variation. It is also “junk in the attic”.

But recyclable RNA isn’t junked in evolutionary useful pieces. It is more akin to garbage recycling. So if “junk DNA” then “garbage RNA”?

Bill Gascoyne:

The fact that they leave for a day or two proves nothing. They’ll either ignore your challenge and pop up on another thread, or ignore your challenge and pop back up on the same thread.

You’re right as far as that goes. I’ve been around long enough to notice such things. My point is that debating IDists’ attempts to discredit evolution (on the basis of the false premise “Evolution wrong = ID right”) is misguided. It’s a distraction from the fundamental point that ID/creationism explains nothing.

The solution to trolls is simply to pose the challenge whenever they appear. Every time. Poof! Gone!

Making the stuff requires a good bit of resources. One would think organisms who did not waste the resources would be fitter than organisms which did. Therefore it must be quite important, and never should have been called junk just because we did not understand how it is important.

I don’t agree. Considering the amount of energy required just to get things into and out of a cell at any given moment, and that DNA replication only occurs leading up to mitosis (or meiosis), it seems that in terms of overall energy expenditure, DNA replication is small potatoes. Further, since so much of this ‘junk DNA’ can be mutated or even expunged with little or no discernible effect on the organism, it appears that some of it may well just be ‘junk.’

I don’t think we should expect biology to be cost-effective and efficient, because it isn’t.

Bornagain, BJB, or whatever sez:

blah, blah, blah.…To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older.…blah, blah blah.

For the THIRD TIME– Wrong! 1470 was later found by Leakey’s own team to be more recent than Lucy. This is a well-known incident in the history of paleontology.

There was no excuse for using Leakey’s quote the first time you did so, BJB, since his premise has long since been proven incorrect and the most modest literature search could have told you that. But to use the same quotation over and over and over no matter how many times you are corrected– that’s just trolling of the worst ilk.

Write sense, BJB, or write some more original nonsense. Or, failing that, don’t write anything at all.

“If it costs more in fitness to get rid of it than to leave it, it will stay.” Good explanation…

About this Entry

This page contains a single entry by Arthur Hunt published on October 11, 2007 1:22 PM.

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