What about those jumping genes?

Hold on, molbiogirl. You said in Message 76: Then you said in Message 86: Then, when I ask you to explain how transposons are not DNA, you said in Message 89No!I don't understand how a molecular biologist could be so confused about this. If 45% of the human genome comprises transposons, as you claim, then those transoposons and the genomic DNA are one in the same. If you're saying that transposons jump but DNA doesn't then we need to clear up this chronic misunderstanding.”HM

And then WK writes: Yes, I'd have to agree: "not all DNA is equivalent to a transposon." That's silly, isn't it? But transposons are made of DNA, just like other genes. You know that.If transposons jump then DNA jumps. Simple as that. And don't forget the OP in Message 1, which speaks of an entire genome jumping from a prokaryote to a eukaryote: Bacterial genome found within a fly's
DNA transfer from bacteria to animals is more common than thought.”HM

Let's get some quotes from that paper. Since the University of MO doesn't have "premium access" to Nature, I will have to rely on blogs.Wolbachia Genome Discovered Inside Drosophila Genome | Science 2.0 ACCIDENTAL. DISTANT PAST.An entire bacterial genome discovered inside that of a fruit fly | Not Exactly Rocket Science SINGLE ANCESTOR.One species' entire genome discovered inside | EurekAlert! NOT INTENTIONAL. A HUNDRED MILLION YEARS.Application Unavailable | Springer Nature PHAGE.At some point in the very distant past, a bacterial phage TRANSPOSED into the Wolbachia genome. This chunk of phage seems to have given the Wolbachia genome the ability to transfer laterally into a host, ACCIDENTALLY.Then, as a neutral mutation, this chunk-of-phage-in-the-genome spread throughout Wolbachia ... and, since 70% of invertebrates are infected with Wolbachia, throughout invertebrates. There are lots of things that contain NUCLEOTIDES.DNA, several types of RNA (rRNA, mRNA, tRNA, snoRNA, RNP), transposons, viruses, etc.But a transposon is more than its nucleotides.
Just as a virus is more than its nucleotides.
Just as an RNA is more than just its nucleotides.
Just as DNA is more than just its nucleotides.Different = acts different.RNA does a different job than DNA.
RNA has a different structure than DNA.
There are many types of RNA, but just one kind of DNA.Similarly, transposons have a different job than DNA.
Transposons have a different structure than DNA. A transposon = transposase + nucleotides + sometimes one other gene (usually antibiotic resistance).
There are thousands of kinds of transposons, but just one kind of DNA. A transposon is not a gene.
The vast majority of transposons are inactive = do not encode proteins.
A gene encodes proteins.The ability of Wolbachia to transfer its genome happened in the distant past.The ability of Wolbachia to transfer its genome was an accident.The ability of Wolbachia to transfer its genome has nothing to do with transposons.Wolbachia have nothing to do with mariner.Wolbachia have nothing to do with tsetse flies.

molbiogirl writes: As opposed to "ON PURPOSE"? Gee, but I thought all evolution was accidental and happened in the distant past. What's the alternative? "Recent ID"? This is tautological mumbling. I think you're having a temper tantrum because you got caught saying that transposons are not DNA and that DNA can't jump.Well, I say an "accidental" jump is still a jump, whether it's a gene or genome.btw: Who decides what is "accidental" in nature and what is not?”HM

A transposon moves "on purpose".Much as a virus moves "on purpose".Both viruses and transposons have the genetic equipment to move. They evolved to move.A long time ago a bacterial phage dropped a piece of genetic machinery into to Wolbachia genome.It happened on accident. So what?That doesn't mean other genomes have jumped.Have you any proof that other genomes have jumped?

molbiogirl writes: Well, I'll have to agree with you, partly, and Richard Dawkins, too, on one point: genes are 100% deterministic. But does this give them a "purpose"? We'd have run that one up the teleological flagpole agian for yet another round of abuse. And I suppose this gives them a pupose to jump? I don't think so, mbg, you're walking on thin ice here. You mean they didn't mean to? None at all. Have you any proof that transposons have a "purpose"?”HM

Transposons do nothing but jump. Until, of course, they land in a eukaryotic genome. Then they are (usually) disabled.One defintion of purpose is:The proper activity of a person or thing; function/job/role are synonyms.The "proper" activity of a transposon, aka the function/job/role of a transposon, is jumping.

mbg, I think you should reconsider your teleological use of the terms "purpopse" and "function." Firstly, let's go to Webster's Dictionary for a definition of teleology:

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Teleology noun

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1: the study of evidences of design in nature b : a doctrine (as in vitalism) that ends are immanent in nature c : a doctrine explaining phenomena by final causes
2: the fact or character attributed to nature or natural processes of being directed toward an end or shaped by a purpose
3: the use of design or purpose as an explanation of natural phenomena
- tel·e·ol·o·gist

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Etymology: New Latin teleologia, from Greek tele-, telos end, purpose + -logia -logy -- more at WHEEL

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Teleology and ID are joined at the hip, you know.So, I'll try to sum things up here about jumping genes:1. Transposons, also called “jumping genes” because they can jump from one DNA molecule to another, are themselves made of DNA and occasionally have RNA intermediates, but in either case they are always made of nucleic acids.2. Transposons can be of Class I”retrotransposons, which are very much like retroviruses and may require RNA intermediates”they jump and stick via cut-and-paste insertion.3. Transposons can be of Class II”DNA transposons, which do not have RNA intermediates”they can jump and stick by cut-and-paste insertion, but some of them are actually able to replicate on the host DNA.Wikipedia, for what it’s worth, adds this clarifier to the definition of transposons:

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Both classes of transposon may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other transposons are still producing the necessary enzyme.

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4. Class II transposons include a "mariner" family, as Frederic Bushman explains in his book Lateral DNA Transfer (2002, p. 277):

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The Tc1/maqriner family of transposons contains some of the simplest mobile elements known. These elements are structurally related to the insertion sequence (IS) elements of prokaryotes and consist of a transposase gene flanked by inverted repeat DNA sequences that contain transposase-binding sites. The Tc1/mariner family elements are relatively small, on the order of 1.6-2.3kb, and thus have limited coding capacity.

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Therefore, the mobility and versatilty of jumping genes has tentative importance in our complete understanding of biological evolution. But are their talents for mobility and versatility enough to enable them to jump from insects to humans? Do we carry around jumping tstetse-fly genes in our genome?To these questions may I present again, as I did in Message 44, Exhibit A as tentative evidence for those possibilities:Exhibit A”In Chapter 19 of Bushman's book he pursues the question: "DNA Transposons of Eukaryotes: Mariners Sailing to Survive?" In that pursuit he observes (p. 282): "Consider the cecropia family of Tc1/mariner elements, named for the giant silk worm moth Hyalophora cecropia, in which the first family member was found (Fig. 9.7) [see below]. Members of this family have been found in insects, flatworms, a hydra, and humans." "Figure 9.7. Sequence relationship among mariner elements of the cecropia subfamily. Note that a human element clusters with several insects, whereas a prosimian sequence clusters in a different part of the tree with other insects." (p. 282)From all of the foregoing information the only conclusion I can make is that shreds of insect DNA are jumping around in our genome and may or may not have participated in our evolution. It's creepy, I know, but it now seems possible, at least to me. Still, it would be only an extension of the know evolution mechanism called "gene flow."”HM

Hoot.I give up.You have no evidence that a piece of the tsetse fly genome has the capability to move from a fly to a human.We've already been over the reasons why.As I've explained and as WK has explained, the evidence you've offered supports the hypothesis that a common parasite that infests humans and tsetse flies gave both humans and flies the transposon.The same way that the homology between the human genome and the chimp genome suggests a common ancestor.It does not suggest that a human mated with a chimp a long time ago.Nor does it suggest that chimps some how managed to transpose their genetic material into humans.It suggests a common ancestor.The homology between the tsetse fly mariner element and the human mariner element similarly suggests "a common ancestor" (a common parasite that both species share).You're on your own from here on out.

molbiogirl writes dramatically: No! No! You're walking out on me? After all of our expensive dates?”HM

Which was shockingly exactly the conclusion you had already arrived at before looking at that information and one still totally unsupported by the facts.Just look at that tree! You might as well say we have flatworm DNA or Cnidarian DNA jumping around in our genomes. If anything the tree casts serious doubts on any sort of direct insect to human transition, and even more if they had included other primates which would virtually all have treed out with H. sapiens.If you had an ounce of integrity you could reach the same conclusion that molbiogirl and I have been suggesting for this whole thread. That rather than all of these similar sequences being transferred from species to species their distribution is more consistent with their being introduced from a common infective source, such as an intracellular parasite or virus.The sequence being similar to that found in insects no more makes it 'Insect DNA' than the fact that hundreds of genes being highly similar to invertebrate forms due to the restrictions of biochemistry on their function makes those conserved genes 'Insect DNA'.TTFN,WK

WK wrote: Yes, you and molbiogirl are right, and I am partly wrong here. The tree shows ancestral asasociations, not jumping-gene pathways. But this thread is about jumping genes and jumping genomes, and unless they originally stick and become heritable in other genomes they are meaningless to any population. Wouldn't any ancestral association have to depend upon that?So the question still remains: Did transposons introduce, trans-species-wise, this alien genetic material? In other words, did they jump? Or did these shreds of DNA in question appear in genomes by some other means? And what would prevent a jumping gene, insect or otherwsie, from jumping into many, many genomes that are encountered by way of insect bites?”HM