Using "junk" DNA To Discredit the Evolution Model

One of the big proponents of the evolution model has been "junk" DNA. The theory goes; If a huge part of our DNA or any animals DNA is actually useless("junk" DNA) to that animal, and it's found in the same locations of genomes in similar animals, then we must conclude this is evolution at work. Supposing further, since it was passed from the parents of that animal, we can now extrapolate that backwards to common ancestors.

Sounds ok, but......
1) You have to make a leap to get back to common ancestors.
1A) Common ancestors have never been seen or found.
1B) Because 1A is a true statement, we must give common ancestors the same treatment evolution modelers give God. We must throw it out with the rest of the Dogma.
2) "junk" DNA is not useless to the animal with which it's in.
2A) Because 2 is a true statement, "junk" DNA can no longer, in and of itself, give credence to the evolution model.

I would look at it like this, your computer stores every bit of information that passes through it ! whether it uses it or not.

reply to post by addygrace


Who are we to say its junk?? It could do something that we don't know about.

reply to post by addygrace


it is premature to refer to such things as "dogma". molecular genetics and phylogeny has only been around for maybe a decade. new stuff is incorporated into the body of evidence all the time. while it is true that evolution has become an easy excuse for the psychological conundrum of modern biology.....it is the best we have at the moment.

while it is very likely (IMO) that the genome is functionally active as a single unfractionable unit, to include the junk dna, i fail to see how affirming said functionality refutes molecular phylogeny? i will warn you that i have extensive education in the field of molecular biology and i will hold you to the fire if you insist on maintaining this line of argument.


.....oh...and, i dont think "proponent" means what you think it does.


...best.

reply to post by SunTzu22

 

Who are we to say its junk?? It could do something that we don't know about.

Scientists have done studies that show some, formerly known as, "junk" DNA has actual function rather than just being left over DNA garbage.

-Noncoding DNA and evolution

Shared sequences of apparently non-functional DNA are a major line of evidence for common descent.[23] Pseudogene sequences appear to accumulate mutations more rapidly than coding sequences due to a loss of selective pressure.[11] This allows for the creation of mutant alleles that incorporate new functions that may be favored by natural selection; thus, pseudogenes can serve as raw material for evolution and can be considered "protogenes".[24] [edit]

-Junk DNA

Junk DNA, a term that was introduced in 1972 by Susumu Ohno,[25] was a provisional label for the portions of a genome sequence for which no discernible function had been identified. According to a 1980 review in Nature by Leslie Orgel and Francis Crick, junk DNA has "little specificity and conveys little or no selective advantage to the organism".[26] The term is currently, however, an outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA.[27] Several lines of evidence indicate that many "junk DNA" sequences are likely to have unidentified functional activity, and other sequences may have had functions in the past.[28] Still, a significant amount of the sequence of the genomes of eukaryotic organisms currently appears to fall under no existing classification other than "junk". For example, one experiment removed 0.1% of the mouse genome with no detectable effect on the phenotype.[29] This result suggests that the removed DNA was largely nonfunctional. In addition, these sequences are enriched for the heterochromatic histone modification H3K9me3.[30]

en.wikipedia.org...

Before looking at genetic codes, I would suggest reading some chemistry books to get the basis. The facts behind evolution are far more complex than you'd probably like.

reply to post by tgidkp

it is premature to refer to such things as "dogma".

I disagree. We have no evidence of common ancestors. It's thrown around like a fact. That's the definition of dogma.

molecular genetics and phylogeny has only been around for maybe a decade. new stuff is incorporated into the body of evidence all the time. while it is true that evolution has become an easy excuse for the psychological conundrum of modern biology.....it is the best we have at the moment.

I'm saying there's nothing in genetics and phylogeny that points to common ancestors.

while it is very likely (IMO) that the genome is functionally active as a single unfractionable unit, to include the junk dna, i fail to see how affirming said functionality refutes molecular phylogeny?

If it's just "junk" DNA that's useless, then we would expect it to be the result of natural random processes. However, we know that this "junk" DNA isn't useless. The fact that it's useful means it no longer points in one direction, towards the evolution model. This also shows the problem with assuming parts of the body have no use. Just because we don't know the use, doesn't mean their is none.

i will warn you that i have extensive education in the field of molecular biology and i will hold you to the fire if you insist on maintaining this line of argument.

I truly welcome this type of response. It helps us both. You get to feel smart, and I may learn something.

.....oh...and, i dont think "proponent" means what you think it does....best.

My sentence I used proponent in, see below.
One of the big proponents of the evolution model has been "junk" DNA.

Definition:pro·po·nent (pr-pnnt)
n.One who argues in support of something; an advocate.

"junk" DNA has been one of the big supporters of the evolution model.

Even though the definition calls for a person or human being, I threw in a monkey wrench. I gave "junk" DNA a human characteristic. This is called Anthropomorphism.


....best.

reply to post by Vio1ion


It doesn't have to be complex if we are willing to learn. We need to get this all out there, so people can make informed decisions. Seriously, in what other part of science can you learn where you come from? There is a lot of disinfo about evolution on this forum. That's why so many people have so many questions.

reply to post by addygrace


You're right, lots of disinformation, like the idea that "junk DNA" doesn't support the evolutionary model. The presence of non-coding segments of our DNA actually supports evolution, but you've already heard that and haven't accepted it.

Hell, there are portions of our DNA that simply regulate the order in which DNA is coded.

More anti-science nonsense all up in this thread.

Originally posted by addygrace
I disagree. We have no evidence of common ancestors. It's thrown around like a fact. That's the definition of dogma.

Really? It sure looks like evidence to me. If you disagree, go ahead and refute every point the article makes.

I'm saying there's nothing in genetics and phylogeny that points to common ancestors.

Everything in genetics points to a common ancestor. For starters I could mention rRNA of every organism alive.

If it's just "junk" DNA that's useless, then we would expect it to be the result of natural random processes. However, we know that this "junk" DNA isn't useless. The fact that it's useful means it no longer points in one direction, towards the evolution model. This also shows the problem with assuming parts of the body have no use. Just because we don't know the use, doesn't mean their is none.

The vast majority of so called junk DNA serves just one function, it could be taken into use in the future. None of junk DNA is ever transcribed to RNA (reason why we call it junk). However some of it (like inverted repeats) probably serve as protein binding sites, etc. Likewise some of it might add structural support to our chromosomes. There are some other possibilities too. Still, vast majority of it has no function at all at the time..

Also if we found out that all junk DNA serves some function (not going to happen) this would not point to evolution being wrong. It would simply mean that we failed to recognize its role before. Such discovery would grant you a Nobel!

post by madnessinmysoul

You're right, lots of disinformation, like the idea that "junk DNA" doesn't support the evolutionary model. The presence of non-coding segments of our DNA actually supports evolution, but you've already heard that and haven't accepted it.

Non-coding segments of our DNA influences the behavior of the the coding DNA. So....how does that support evolution? The fact that these segments aren't coding means nothing for evolution, because they do have uses.

Hell, there are portions of our DNA that simply regulate the order in which DNA is coded.

That would be called "junk" DNA, or non-coding DNA. They are the regulators of coded DNA.

More anti-science nonsense all up in this thread.

How is this anti-science? I guess you would rather somebody say, "God did it". That way you wouldn't actually have to back up your claims, and you could dismiss it outright.

reply to post by addygrace
This is somewhat of an inane attempt to disprove evolution. "Junk" DNA is the evidence of common lineage. The groups of organisms we would expect to be closely related conform to the mechanisms of genetic drift acting on DNA that undergoes no selection pressure. And the DNA lines up sufficiently with the fossil evidence to assert the probability of common ancestry.

Your argument is apropos to saying "just because we are standing on the ground doesn't mean gravity exists, as we have no actual evidence of a tangible thing called gravity, therefore gravity is just a big of a leap of faith as god"

To give you an idea about how strong molecular phylogenetics is as a field, there is more evidence for the evolution than there is for gravity.

The only reason it is called junk DNA is because we have yet to figure out it's usage. We are in our infancy when it come to understanding molecular biology (my mother is a cellular, molecular, microbial biologist) and have plenty more to learn.

Just because we cannot figure out what it does now does not mean we never will.

Pred...

reply to post by rhinoceros

...None of junk DNA is ever transcribed to RNA...

in the image below is shown a transcriptome chip analysis of human chromosomes 21 and 22. the "exon density" graph shows the positions where transcriptionally active genes are located. just below that, in the "positive probe density" graph, you can see that there are RNA transcripts of very nearly the ENTIRE chromosome. granted, these mRNA never actually get translated. but more than 95% of the RNA transcripts made by the cell are of non-coding "junk". it is not known how these transcripts are produced nor what function they serve.

[atsimg]http://files.abovetopsecret.com/images/member/f8636a8460d4.jpg[/atsimg]



reply to post by addygrace


i am still unclear about your argument. whether or not the genetic sequences are the result of positive selection via phenotypic inheritence, the fact remains that ALL sequences are inherited from parental generations. thus ALL sequences may be analysed for phylogenetic similarity.

take the below analysis of mitochondrial DNA taken from living humans:

[atsimg]http://files.abovetopsecret.com/images/member/c56bd7b3a6d8.jpg[/atsimg]

ALL of the grey dots which link the ancestry are INFERRED by sequence similarity of the entire mitochondrial chromosome. it is merely an extension of the observable concept that genotype is passed from parental generations. thus parent and offspring have a high degree of similarity. thus phylogenetics is based on non-similarity (divergence).

whether or not any actual "missing link" is found between organisms, their relationship is strongly implied by their diverging genomic sequences.

and one last note about "dogma". dogma is better defined as "fitting the evidence to the theory"....as is often the case with religious dogma. however, in science we "fit the theory to the evidence". this can easily be shown by the following image which shows how phylogenetic statistical analysis is blinded to ensure non-bias. it is distinctly NON-dogmatic.

[atsimg]http://files.abovetopsecret.com/images/member/73e5f43dcd9f.jpg[/atsimg]


simply coming up with an explanation of the data is not dogma.


please clarify your arguments.

reply to post by tgidkp

To me all "junk" DNA is DNA that is never transcribed (however not all non-transcribed DNA is "junk"). I didn't say nor imply that all transcribed DNA is translated. E.g. ribosomal RNA or transfer RNA's are never translated, but it doesn't mean that the genes coding them are junk. Also, to contradict myself I find it likely that also some of transcribed and even translated DNA is junk in a sense that it contributes nothing to the survival of the organism (as witnessed by knock out mice).

reply to post by tgidkp

in the image below is shown a transcriptome chip analysis of human chromosomes 21 and 22. the "exon density" graph shows the positions where transcriptionally active genes are located. just below that, in the "positive probe density" graph, you can see that there are RNA transcripts of very nearly the ENTIRE chromosome

Any source for this claim? Transcriptome is just a small part of whole genome, 5 % according to my source:

Is a transcriptome the same as a genome?

No, a transcriptome is different from a genome, which is the entire DNA sequence of an organism. A transcriptome represents the very small percentage of the genome - less than 5 percent in humans - that is transcribed into RNA molecules. A gene may produce many different types of mRNA molecules, so a transcriptome is much more complex than the genome that encodes it.

www.genome.gov...-2

Junk DNA as originaly defined is an outdated concept. However, there are large portions of genome that indeed seem to serve no function at all.

Still, a significant amount of the sequence of the genomes of eukaryotic organisms currently appears to fall under no existing classification other than "junk". For example, one experiment removed 0.1% of the mouse genome with no detectable effect on the phenotype.[29] This result suggests that the removed DNA was largely nonfunctional. In addition, these sequences are enriched for the heterochromatic histone modification H3K9me3.[30]

en.wikipedia.org...


As for the OPs post, common descent is proven beyond any doubt. Courts use comparison of genomes to determine if someone is a parent of his child or not routinely. Evolution is proven the same way. You are only embarrasing yourself.

reply to post by addygrace

1) You have to make a leap to get back to common ancestors.
1A) Common ancestors have never been seen or found.
1B) Because 1A is a true statement, we must give common ancestors the same treatment evolution modelers give God. We must throw it out with the rest of the Dogma.
2) "junk" DNA is not useless to the animal with which it's in.
2A) Because 2 is a true statement, "junk" DNA can no longer, in and of itself, give credence to the evolution model.

1) No you don't...plenty of evidence, not only fossils, but also DNA evidence and migratory evidence.

1A) Actually, we have thousands of common ancestors as fossils

1B) No, science isn't religion

2) By its very definition, that DNA has no clearly observable use...so yeah, you could say it's useless.

2A) Wrong conclusion based on a flawed analysis...

reply to post by Maslo

reply to post by rhinoceros

maslo, those images and concepts are taken directly from my molecular bio classroom text, "Genomes 3" by T.A.Brown. rhinoceros, you totally misread my reply to you.

from the genomegov quoted text, the 5% they are referring to is the same as the 5% active transcription sites (with the remaining 95% being the junk, as you already know). this website has intentionally obscured the facts and withheld the data that i am showing you.

the reason that i put up that image is because it says something that is, IMHO, a HUGE information gap in bioinformatics. the image is showing that, in fact, the entire chromosome including "junk" sequences are transcribed into mRNA. i was shocked to learn this and in the classroom it was explained in hushed tones.

this is a shocking fact that geneticists will not admit to easily because existing transcription theory requires the complex coordinated actions of promoters, etc. but, as the image shows, even "junk" is transcribed. in fact, the majority of mRNA transcripts that are produced are of "junk" sequences. if you were to ask a molecular biologist to explain this fact, you would likely get a stupid look and a shrug.

dear OP,

do you think that i make long detailed posts for my health?

no. it is because a few posts back, you ASKED me for more details. and although my "ATS sense" told me that it would be a waste of time, i decided to not leave you hanging.

your lack of response is such poor etiquette.

may you and the rest of ATS drown in your ignorance: i will not help you deny it any longer.

reply to post by addygrace

Originally posted by addygrace
post by madnessinmysoul

 

You're right, lots of disinformation, like the idea that "junk DNA" doesn't support the evolutionary model. The presence of non-coding segments of our DNA actually supports evolution, but you've already heard that and haven't accepted it.

Non-coding segments of our DNA influences the behavior of the the coding DNA. So....how does that support evolution? The fact that these segments aren't coding means nothing for evolution, because they do have uses.

Except that they do. Non-coding DNA regulates the coding of other DNA. And the presence of DNA that's not really doing anything except acting as a spacer supports evolution because evolution predicts that there will be extraneous DNA.

Hell, there are portions of our DNA that simply regulate the order in which DNA is coded.

That would be called "junk" DNA, or non-coding DNA. They are the regulators of coded DNA.

Exactly. And that is actually just as useful as the coding stuff.

More anti-science nonsense all up in this thread.

How is this anti-science? I guess you would rather somebody say, "God did it". That way you wouldn't actually have to back up your claims, and you could dismiss it outright.

It's anti-science because you're clearly not taking the time to actually look at the evidence of evolution and you're using something you don't understand in a manner which shows you don't understand it.