Any experts on evolution here?

I'm not sure exactly what the point is with Muller's ratchet. If the point is that a specific coding once lost is difficult to regain, I buy that. The thing is that there are many solutions to the same task so it isn't really necessary to remain the same at the DNA level as long as there is maintenance of the overall organization/function.

Did you mean something more than that? If you did I'm afraid I missed it.

Regarding entropy, I think it is very useful to contemplate life as the transmission and maintenance on information on how to successfully build a good organism. When the information gets modified often the redundancy buffers the problems therein, but in any case from the possible "ideas" encoded about how to succeed as an organism possible solutions are picked. Which is similar to taking a last best solution permuting/modifying it and testing it for success. Very similar to science in many ways ...

It is interesting to note that new information can be generated this way, you can permute and modify the plans for a toaster and get a toaster oven ... just as long as it passes the test of utility it will be maintained. I think of junk DNA a bit like scratch paper myself. You don't want to start scribbling new ideas on the old plans you need.
Re: reply to Eflex

Originally posted by paulsamuel

you say, "scientists now generally believe that "junk" DNA must contain some kind of coded information."
I don't believe this. Could you supply a reference? No scientist could mistake coding DNA for junk.

Its on the same page that I supplied to you earlier.
(3rd paragraph down)

This page also states

"The idea that a major part of our DNA is "garbage" ignored the fact that a key feature of biological organisms is optimal energy expenditure"

Thus the efficiency debate ensues.
Generally held belief that some of the following parts are unnecessary:


OR are they?
Originally posted by kmguru
Generally held belief that some of the following parts are unnecessary:


OR are they?

The tonsils are mostly composed of lymphoid tissue, which is found thoughout the gastointestinal tract and on the base of the tongue. Lymphoid tissue is composed of lymphocytes...which are mostly involved in antibody production. Since we generally consider antibody production to be a good thing, many studies have been performed to try to clarify the importance of the tonsils. There seems to be no adverse effect on the immune status or health of patients who have had them removed. Any noticable effect has generally been positive. It appears that the tonsils were not "designed" to effectively handle the multitude of viral infections that occur in children in an urban population. Rather, the immune system, including the tonsils and adenoids, developed during a era where the child was rarely exposed to a large number of other people and the germs they carried. It may also be that these organs are relatively more important in dealing with certain types of infections, such as worms or other parasites, that are relatively uncommon in today's society. It is clear that in many cases, the tonsils and/or the adenoids become "dysfunctional" and are more of a liability than an asset.

I think that as we humans continue to drift away from Agrarian lifestyles and towards CITY life, the tonsils will cease to exist.
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Originally posted by kmguru
Generally held belief that some of the following parts are unnecessary:


Among adult humans, the appendix is now thought to be involved primarily in immune functions. Lymphoid tissue begins to accumulate in the appendix shortly after birth and reaches a peak between the second and third decades of life, decreasing rapidly thereafter and practically disappearing after the age of 60. During the early years of development, however, the appendix has been shown to function as a lymphoid organ, assisting with the maturation of B lymphocytes (one variety of white blood cell) and in the production of the class of antibodies known as immunoglobulin A (IgA) antibodies. Researchers have also shown that the appendix is involved in the production of molecules that help to direct the movement of lymphocytes to various other locations in the body.
Originally posted by kmguru
Generally held belief that some of the following parts are unnecessary:


The facts of penis development demonstrate to us that an unusual process separates the foreskin from the glans in its own good time, covering the infant glans tightly to protect it from fecal contamination; covering the glans to protect it when, while its owner is a child, it is not required for procreation; and finally, freeing up the cover when it is needed for reproduction.

The foreskin covers the elongated shaft of the penis during erection; at other times it protects the sensitive glans penis. The foreskin contains many minute muscle fibers which give it tone. It covers the glans snugly, and helps to prevent the glans from developing a thick, many layered epidermis, which happens in the absence of the foreskin. This thickened epidermis reduces sexual sensitivity
Originally posted by kmguru
Generally held belief that some of the following parts are unnecessary:


What is the function of hair? In modern mammals, hair serves to insulate, to conceal, to signal, to protect, and to sense the immediate surroundings. Insulation serves to conserve heat, but also, as in the case of diurnal desert animals such as the camel, to protect against excessive heat. The color of most species is probably cryptic, matching the animal's background. In some cases, such as the dramatic stripes of zebras or tigers, cryptic coloration can only be properly evaluated when the animal is seen against its natural background. Many mammals are dark dorsally and relatively pale ventrally, a pattern called countercoloration. This makes sense in the case of aquatic or arboreal species (predators above look down on a dark dorsum, matching the depths or forest floor below, while predators below see the pale venter, against light streaming down from above). Its role is less clear in the case of the many countercolored terrestrial and nocturnal rodents. Hair also provides by its color a means of signaling other members of one's own species (e.g., the white tail of the white-tailed deer, flashed by a fleeing animal to signal danger) or members of other species (e.g., the contrasting pattern of striped skunks, a warning to predators). The pelage also serves to protect the skin from abrasion and from excessive UV radiation. And, through specialized vibrissae, it provides a tactile sense, used, for example, to locate prey or to navigate in total darkness.
Junk DNA

Genes may transfer between bacteria strains through plasmid ingestion. Genes may transfer between plants species. (Potential problem with GM crops.) Read of genes injected into blood being incorporated into cells. (Genes were carried in a fatty coating which aided transfer through the cell membrane. Guessing some tranfer would occur even without the coating.) Mosquitoes could presumably act as a vector for gene transmission across animal lines.

This hamster has speculated that a particularly advantageous gene might over time be incorporated into most animal species. Thus only one species need evolve the gene for all species to benefit. Genetic convergence.

The “junk” DNA regions might provide the scratch pad for such beneficial transfers. Some of the “junk” DNA contains old viral DNA.
On organisms good gene is another organisms junk. There are drug resistance genes that are only required in organisms with certain other enzymes for instance. Some metabolic genes might be generally useful, but many genes that are useful to one organism might not fit into the scheme of another.

The techniques used to incorporate DNA into cells/organisms include 1) agrobacterium mediated (only in plants - there's this bacteria that causes tumors in plants by injecting it's DNA and using the plant as a factory for the chemicals it needs), 2) electroporation - give the tissue a shock to cause holes in the membrane and naked DNA is taken up, 3) viral vectors - use viruses with the lytic and replicative machinery replaced with the DNA of interest, 4) Naked DNA uptake - usually PEG or polyethylene glycol is used to help get it through the memebrane though the mechanism is unclear (PEG can trap a lot of water which is a hint).

Generally, DNA is highly charged, which makes it not pass through the hydrophobic environment of the cell membrane very well. Many unicellular organisms do take up DNA but the amount increases greatly when they're stressed. This suggests it may require either disruption of membrane integrity or active uptake done as a last ditch attempt to survive. I'm not totally up to date, but I think people have also suggested that the DNA is taken up due to concentration effects - ie stressed cells tend to be surrounded by dead or dying cells which release a lot of DNA into the surounding environment.
Given those as constraints and limitations of the transmission of DNA it certainly occurs, but my understanding is that it occurs most efficiently between unicellular organisms, much less so from unicellular organisms to multicellular, and almost not at all between multicellular organisms.
reply to scilosopher

The muller's ratchet point I was trying to make was that, once DNA becomes non-functional (junk), it's unlikely to re-gain function.

I'm afraid I have no opinion in regards to the analogy of entropy and biology.

I don't think that DNA, once it becomes junk, that it regains function. I guess it's possible, but it seems to me that redundancy is the key to the derivation of new function.
reply to Eflex

Thanks for the link to the junk DNA site. It's very useful. But, as I stated earlier, my contention is not that all non-coding (doesn't make protein) is junk, it is only that junk DNA exists. I suspect, there will be many examples of non-coding DNA, once thought of as junk, will be found to have function.

Given your responses to examples of purported vestigial anatomical structures, I must ask if it's your contention that all DNA, all morphology is functional?
Scilosopher, thanks for providing some science background for this hamster’s speculation.

Clearly many genes are specialized for a particular species and would provide no benefit to other critters. However there seems to be remarkable conservation of function across animals (even between yeast and man). (Human genes often work fine when use to replace comparable animal genes. The resulting “human” proteins differ from the animal form but seem viable.)

The simple model of speciation seems to be divergence. For asexual reproduction advantageous mutations aren’t shared. For sexual reproduction, advantageous mutations are only shared within a species. This seems highly inefficient given the great similarity across species.

Paulsamuel’s “Muller’s ratchet” does seem to indicate problems with deriving advantageous genes from “junk”. The greater the random walk distance from a useful protein the less likely a useful protein would ever result. (Hamster guess.) Thus there would be a strong algorithmic advantage to starting with “good” genes. (Indeed this is a reason sexual reproduction is so powerful.)

Recombining gene fragments from good genes (both inactive redundant genes and those accidentally incorporated into the human genome by virii) should significantly increase the odds of a favorable protein resulting from a random event. (This hamster has designed successful scheduling algorithms based on this principle.)

This hamster’s intuition is that a “convergent” mechanism (e.g. viral or mosquito transfer of DNA) would confer significant evolutionary advantage over long time periods. Actual transfer of DNA across species might be very rare and yet still provide significant “algorithmic” advantage.

This hamster doesn’t have the breadth or depth of genetics knowledge to evaluate the real world likelihood of this speculation. Greatly appreciate the insight offered by others on this thread.
Re: Junk DNA

Do you have a reference for inter-specific gene transfer in plants or animals? I can't think of any instances in which this occurs, although I admit the possibility of a disease organism as a genetic vector between species, however if it occurs, I think it must be rare. But, let's read the literature and see.

We know about mosquitoes as vectors for disease transmission (malaria, etc.) but, although this has been extensively studied (there are literally tens of thousands of references in regards to malaria and mosquitoes), I know of not one instance where it's been shown (or even proposed) that mosquitoes were vectors for interspecific gene transfer. This is probably because the diseases that insect vectors are responsible for transmitting, are species specific.

I understand your point about one species evolvoing a gene in which all species benefit by interspecific gene transfer. However this is not a very realistic scenario, and it's not genetic convergence.

When you say;
"The “junk” DNA regions might provide the scratch pad for such beneficial transfers. Some of the “junk” DNA contains old viral DNA," I assume that you think that "junk" DNA can somehow become coding DNA (make proteins). I don't believe that this can occur. Can you provide some mechanism for this to happen?
I think one of the main problems with easy transfer of DNA betweern many organisms is the possibility of such mechanisms being exploited by parasites.

I only said that the junk might me useful for structural and regulatory purposes. The functionally important sequences in these regions are ~10bp and very degenerate in many cases so they can pick up functionality much more easily. Clustered very low affinity sites can work as well so there are many ways to generate a control element. Most such control elements can be oriented upstream, downstream, or even in the introns of genes. Cis regulatory sites that can recruit enzymes which modify histones can also be important in affecting local gene regulation.

Regarding genes I believe duplication and divergence is quite important, and agree that most proteins don't just randomly occur in junk DNA.

Without hearing a description of what exactly constitutes junk I think we'll just not communicate efficiently. My reply to IH2 is relevant to this as well.

I would not suggest that non coding DNA in a region of junk is likely to become coding. In fact I said an un-needed copy due to duplication would be available for diverging to a new function.

The main function I proposed it might serve was structural or regulatory. This is more likely due to the mechanisms involved. Still it is more likely the more DNA there is mutating. Therefore since it isn't as big a energetic load for multicellular organisms who maintain most of their cells for longer more is kept around.
reply to scilosopher

Well, I'm glad we agree on some things.

I won't disagree in regards to non-functional DNA becoming functional in a non-coding sense cause I don't know enough about the mechanisms by which this non-coding DNA work.

It would be useful to know the origins of this non-coding, but functional DNA. Any references out there? Seems it could arise by obtaining function by accumulation of random mutations until functionality arises, or evolution by descent (heritibility) or a combination of both. Other questions are, does all junk DNA have an equal chance to become functional? How is it adaptive to maintain junk DNA for some future potential (you cannot evoke group selection)? Are there any phylogenetic analyses of these non-coding but functional regions of DNA (this would show evolution by descent)?
I don't disagree with you on a lot of things. It's just when I agree and don't have anything to add I don't say anything.

There have been some promoter studies that have done comparisons of promotor regions of specific genes, but the large scale comparisons are just going to be possible soon due to the sequenceing of briggsae for elegans, mouse for human, and psuedoobscura for melanogaster.

In terms of sites that recruit enzymes which modify histones and such, much less has been done as the sites aren't very well characterized yet and few have been experimentally characterized so it is hard to know what components are required.

One of the main problems with studying this kind of stuff is the density of sequence needed over evolutionary distances. Since it is much more variable, and indeed needs to be so to suit the different organisms uses of genes, you see very little in highly diverged organisms. Also since the functional aspects are poorly understood of these regions and what the necessary rules are for assembling protein complexes on these regions (and often what the complexes even consist of in detail) it gets quite fuzzy.

The basics exist in bacteria and are a little more clear there due to the reduction in coding sequence. There is a paper "The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons." by Rajewsky N, Socci ND, Zapotocky M, Siggia ED that does a comparison among 5 bacteria. I think that is probably the best for promoters.

There's also a paper that discusses quite briefly the situation for intron control regions in C elegans "Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment." by Kent WJ, Zahler AM.

There might be better papers where single genes are compared, but I am not aware of them.

DNA having a structural role is more a common conjecture that makes some sense given the way chromosomes are anchored to the nucleus, space is needed to separate protein complexes assembled on DNA, etc. I don't think anyone has directly studied it, but it is an appealing idea that is consistent with the available data.

Mosquito transmission of DNA is wild speculation based on a lab using coated DNA injected into a blood stream in successful gene engineering. Doubt anyone has ever looked into this possibility. Could be very difficult to show. Suspect a first step would be lab experiments to discover the conditions under which naked DNA can be taken up and incorporated into a cell’s DNA.

If cross species DNA transfer does occur, it might well use a mechanism completely unknown at this time. This hamster only provided example mechanisms to show the possibility of such transfers.

This hamster guesses it would be easier to show genes crossing species by direct comparison of genomes than by observing the mechanism of transfer. One would only see the evidence if one were directly looking for the possibility.

As information about the genomes has come to light, this hamster has been surprised at the similarity between animal genomes and the conservation of function across many different animals.

This hamster has wondered why various animal genomes don’t differ more than they do. Common origin and the necessity of preserving critical functionality explain some of the similarity. (Perhaps all of it.) This hamster wonders about other possibilities. (This hamster has also read of bacteria “sharing” immunity to antibiotics and conjectured that similar mechanisms might occur for multi-cellular animals.)

(Also it would be cool if development in one species furthered the development of another. The hamster likes symbiosis and cooperation.)

“I assume that you think that "junk" DNA can somehow become coding DNA (make proteins). I don't believe that this can occur. Can you provide some mechanism for this to happen?”

The easy answer is “nope”. Lots of different stuff in that “junk”. Most of it couldn’t become anything. This hamster recalls some of it being remnants from old viral attacks. In this hamster’s naïve view, “good” DNA might be scattered throughout the junk. A mutation affecting “start” or “stop” codes or a chromosomal copying error might lead to this DNA being transcribed and edited differently, resulting in a new functional protein. The transcription process is far from being fully described. (At least based on the articles announcing new discoveries that appear each month.)

(Part of this hamster’s motivation in pursuing this question is in learning more about the transcription process from the experts on this thread.)

(Paul, this hamster will look for articles discussing DNA transfer across species. Recall articles on bacteria and plants. Only reference to animals was the viral DNA and that is far from transfer of a functional gene. Tend to feel that scientists wouldn’t be so successful in transferring genes between species if nature weren’t already doing it somehow.)
Paul, here’s an excerpt from a site that describes gene transfer among bacteria.

“Bacteria can acquire resistance by getting a copy of a gene encoding an altered protein or an enzyme like beta lactamase from other bacteria, even from those of a different species. There are a number of ways to get a resistance gene:
· During transformation - in this process, akin to bacterial sex, microbes can join together and transfer DNA to each other.
· On a small, circular, extrachromosomal piece of DNA, called a plasmid - one plasmid can encode resistance to many different antibiotics.
· Through a transposon - transposons are "jumping genes," small pieces of DNA that can hop from DNA molecule to DNA molecule. Once in a chromosome or plasmid, they can be integrated stably.
· By scavenging DNA remnants from degraded, dead bacteria.
Unfortunately, if a bacterium gets a resistance gene stuck into its chromosomal DNA or picks one up in a free-floating plasmid, all of its progeny will inherit the gene and the resistance it confers.”