Junk, or Not Junk, that is the Question

Competent engineers make kludge and junk all of the time.

You say that genomes should not have junk if they were designed. I think point out that 90% of the human genome is junk. So is that a falsification of ID, or not?

I always considered that to be a subjective opinion, not something that can be measured.

Then they are less than competent at the time.

That is being brought into question, I understand, and even if it were true, it could be analogous to the machinings scrap in the manufacture of a precision instrument.

So not.

That does not mean it does not exist, or even that it isn’t prevalent.

The broad consensus is that ~90% of the human genome is junk. I don’t see how “machining scrap” is a valid analogy since we already know where most of the junk comes from (e.g. transposon activity, pseudogenes). You don’t need all of that junk to make genes work, as shown by the tiny bladderwort genome that is 3% the size of the human genome but has about the same number of genes.

There’s that shift in the burden of proof again. Seems to be a common refrain among ID/creationists.

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Broad consensuses can change, and there is more to it than ‘making genes work’.

With respect to elegance, we are not, as you pointed out, talking about proof of anything.

What does ID tell us to expect? Is 90% junk lethal to ID theory?

Catch up on your reading, in this thread. I don’t subscribe to ‘ID theory’.

That can be said about every single theory in science. It’s really not a compelling argument.

I would also be curious what this “more” is that has to do with making genes work. We have the bladderwort with 0.082 billion bases in its genome. We have 3 billion bases. The onion has around 50 billion bases. There are single celled amoeba that have over 200 billion bases in their genome. The puffer fish has 0.6 billion bases. Except for the amoeba, those species have about the same number of genes. There isn’t any rhyme or reason as to why there are these big swings in genome size, other than the accumulation of junk DNA.

I was talking about empirical measurements, specifically. I think we all agree that humans have subjective opinions, such as beauty, elegance, and the such.

OK Dale. What does your working hypothesis suggest about the percentage of junk DNA in the human genome?

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Didn’t the ENCODE project call this consensus into question? This article goes all the way back to 2012. ENCODE Project Writes Eulogy for Junk DNA | Science

No. ENCODE tried (unsuccessfully) to blur the line between “does something” and “functional”.

This is the analogy I often use. Let’s say you go to the local big box store and buy a big TV. You take it home and after just an hour the screen goes blank, sparks fly out of the back of the TV, and it starts billowing out smoke. You take it back to the store and ask for a refund. The manager takes a look at it and says, “The TV is still functioning”. With a puzzled look on your face, you ask how he came to that strange conclusion. He says, “Look at the screen. It’s has dust on it. It is still functioning as a dust magnet”.

That’s the scam ENCODE tried to push on the scientific community. As long as a stretch of DNA bound to something or was part of some rare biochemical reaction then it was considered functional, even if that reaction was similar to dust sticking to a burned out TV.

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Are you saying you take a position different from the one taken by the article in Science mag? Or does the Science mag author and the authors of the 30 mentioned papers take one different from the consensus?

I take the position found in this peer reviewed paper:

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I don’t have the expertise to know which position is better supported, but it does appear that there are different ones.

And that’s all fine and well. I’m all for the freedom of scientists to debate and argue different positions. It does seem to call into question the use of the term “consensus” as if there is an authoritative nature to it.

Well, the key point is that this negative rule applies ONLY within scientific discourse. Outside science, we can infer divine design all we like.

I think Mount Everest was designed!

No one in science cares that I say this, because I’m NOT making that claim within scientific discourse. That is the key point. MN is not a worldview, it is just rules to play by with in the “scientific restaurant”. Violate that rule, people respond like you aren’t tipping the waiter, or worse, skipping on the bill.

No, ENCODE did not call this into question. The use of “Junk” is a misnomer, any ways, and was disputed long before ID and ENCODE, because it is often misunderstood.

That is right.

Scientists argue about use of words all the itme, even when we agree on the content. Case in point is @T_aquaticus and me right here. There is no such thing as Junk DNA, in my view, but ENCODE did horribly equivocates “something happens” with “something important happens.”

A lot happens in the genome, but most of it doesn’t matter. Wee know this because we see a large amount of variability in the parts that do not matter.

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I don’t think so. You can follow some of the discussion from Larry Moran’s blog (Encode articles here). His “Required reading for the junk DNA debate” is a very good list of articles. Carl Zimmer has a number of articles for the lay audience. I think his NYT Magazine article was pretty balanced. One needn’t be a expert to comprehend the arguments.

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I do have the expertise. Dan Graur et al. have the supported position. I would be happy to go through the paper (in a separate thread) with you and explain why Graur et al. are right.

There is a lot of truth in that. What matters is the evidence, and the evidence strongly supports ~90% of the human genome not having sequence dependent function (i.e. junk). Just to touch on one portion of the study, ENCODE claimed that 75% of the genome is transcribed. What they left out is the level of transcription. Junk DNA will be transcribed at really low levels because RNA transcriptase will bind to junk DNA now and then. Therefore, just because a stretch of DNA is turned into RNA does not mean the DNA has function. Just because DNA does something does not mean it has function.

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Might need to clarify ‘view’ for “no such thing as Junk DNA”. It’s not a perfect term but there seems to be plenty of stretches in many genomes where the term generally applies.

So what I am hearing and seeing is there is a diversity of points of view regarding ENCODE. Fine. I appreciate the linked articles. For my purposes right now, I’m content to note that there are different takes on it and leave it at that.

Thank you for noting that.

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“Junk” requires us to settle on a purpose, but people come to genomes wiht different purposes. One persons Junk is another’s Treasure. What you call “Junk” is a boon to population demographic inference, because it is the neutral part of the genome.

“Junk” is a term without scientific content because it is relative to purpose, the purpose is unstated, and we come to genomes with different purposes.

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Sure, but’s it quite unlike the ‘to-may-to’ vs. ‘to-mah-to’ controversy. And you might want to take what the Discovery Institute says about it with a grain of salt and some skepticism.

FWIW - Junk DNA, or whatever one chooses to call that general category, is neither proof for nor against, a designer. I don’t understand why the DI is so heavily invested in it’s particular position on the subject.

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