“Junk DNA”’s defender doesn’t “do politeness”?

_{Denyse O'Leary

May 8, 2014

'Junk DNA', Darwinism, News}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

The Darwinians do seem to be biting back, to judge from yesterday in Nature:

The latest ENCODE report drew wide attention on Twitter. The paper didn’t provide any estimates about the proportion of the human genome that is functional; instead, it laid out the case that any accurate inventory of the functional parts of the genome must include evolutionary, genetic and biochemical data.

Given the history, some Twitter users wondered how Graur would respond. He soon ended the suspense with a series of tweets blasting ENCODE’s statistics and methodology. In one, he wrote that “the recent half-hearted recantation of #ENCODE was published without a press release.” In his blog post, he wondered why the ENCODE consortium seemed so eager to back away from its “80%” claim. Through it all, he admittedly showed very little tact. “I believe science is a search for the truth, not a lesson in manners,” he says. “I don’t do politeness.”

Kellis says that ENCODE isn’t backing away from anything. The 80% claim, he says, was misunderstood and misreported. More. (paywall)

Actually, ENCODE was neither misunderstood nor misreported. Life just wasn’t doing what Darwin’s followers said it was supposed to, and ENCODE reported that fact.

For free highlights of the junk DNA uproar, see:

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

By the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening.

Follow UD News at Twitter!

Comments

Dr JDD, you make me want to haul out my books on immunology! What a fascinating subject. kf, indeed! What we have in the cell is a manufacturing process. Wouldn't it be amazing if it were found to follow kanban principles, lo1! Weren't AVS or Evolve claiming that the cell isn't like a computer? hogwash. Wetware: A Computer in Every Living Cell Yes, that Dennis Bray.Mung_{May 8, 2014
May
05
May
8
08
2014
05:09 PM
5
05
09
PM
PDT}

JDD, Cells are not in a race with themselves to divide as fast as possible or as efficiently as possible. As long as they can survive, metabolize and divide within the constraints of a given environment, cells wouldn't care how efficient those processes are. You're wrongly thinking that cellular processes are super-efficient. That's not the case. A good example of an inefficient process operating within the cell is pervasive transcription, which produces lots of RNA noise: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000625 You're constantly failing to realize that regardless of the efficiency of the process, unless it is detrimental to the survival of the cell, natural selection won't be able to "see" it and get rid of it from the population. The cost associated with replicating excess DNA does not prevent the cell's metabolism or division. So it is "invisible" to natural selection. Thus it persists. This explains a lot of observations. We can delete large chunks from a mammalian genome and have a fully normal animal (see the Nature paper I quoted above). How's that possible if there's no such thing as junk DNA? We've species with gigantic genomes that won't make any sense unless most of their genome is junk. The Norway Spruce Christmas tree has a genome that's six times larger than a human's: http://www.huffingtonpost.com/2012/12/13/christmas-tree-genome-new-dna-study-conifers_n_2294265.html Various salamander species also have huge genomes, much larger than yours or mine: http://www.biology.colostate.edu/seminars/making-it-big-extreme-genome-sizes-in-salamanders/ But all this is dwarfed by the genome of a Japanese plant: http://www.sciencedaily.com/releases/2010/10/101007120641.htm Will you argue that, since there's no junk DNA, Christmas trees, plants and salamanders are more complex than humans?Evolve_{May 8, 2014
May
05
May
8
08
2014
04:19 PM
4
04
19
PM
PDT}

Mung: Long time since I heard that word! Notice, the use of localised info -- codes! -- to control logistics flows and reduce inventory leading to lean manufacturing. KFkairosfocus_{May 8, 2014
May
05
May
8
08
2014
02:56 PM
2
02
56
PM
PDT}

l decided to do a quick search and in 30 sec found a paper addressing this very issue AVS: http://m.jasn.asnjournals.org/content/17/7/1807.full note how they say "might seem wasteful but..." I will say it again, my initial point was that naturalists claim IDists limit scientific advance but by claiming something is likely to have function advances science more than the naturalist view that it is just the wastefulness of evolution.Dr JDD_{May 8, 2014
May
05
May
8
08
2014
02:34 PM
2
02
34
PM
PDT}

Typing on phone so autocorrect - "nene fit" should be benefit.Dr JDD_{May 8, 2014
May
05
May
8
08
2014
01:29 PM
1
01
29
PM
PDT}

Evolve I am not missing the point. You are. Let me rephrase it another way that you might understand it: Cellular energy and expendency is either linked to survival and reproduction or not. I am claiming it is - that we see generally a non-wasteful cell. It takes a lot of energy to copy a huge genome and when 98% is unnecessary, cutting that to 2% would be favourable to the cell as it could divide quicker thus favourable reproducibility trait. You happily admit that new genes can for by large reshuffling, duplications, extra fusions through chance with nene fit, yet you cannot envisage in that huge time period similar loss of non coding regions? If you cannot see how that could happen yet genes arise from seemingly nowhere, then you are more blind in your naturalistic religion than I thought. I will repeat what I said before - the junk in the garage is a poor analogy as you don't regularly remove and replace, or duplicate your garage. A cell does this lots. Perhaps extend your garage analogy then. What if you had to add new things to your garage - would you make it bigger or just remove the junk? Which requires more energy? That analogy is no worse than yours.Dr JDD_{May 8, 2014
May
05
May
8
08
2014
01:28 PM
1
01
28
PM
PDT}

I am not too sure why i am bothering with someone who cannot grasp what i am saying, but anyway, what I actually said: "There is good evidence many RNA transcripts are rapidly translated and turned over..." I was saying it in that way to emphasise I am talking about the fact en a transcripts are rapidly translated (to proteins) and then degraded by the proteosome for a functional reason yet you claim i am making assertions about how efficient proteosomal degradation is. I am not. As you clearly cannot grasp simple science let me break it down for you: You say the cell is wasteful because it makes proteins that it simply degrades straight away. I say actually, there is purpose in making a protein to be directly degraded (eg for HLA presentation) therefore your claim that it is inefficient for the cell to make protein to just degrade is invalid. i then conclude that just because the cell does something that appears to be inefficient because we cannot understand function does not mean it is - it is just not currently understood why the cell does that. You then conclude I don't know what processes degrade proteins (laughable as I have published in several high impact peer-reviewed journals on the subject) and that i am speaking to how efficient the degradation system is. I am not. Anyone with half a brain can see i was a dressing cellular purpose and efficiency in why the cell might translate rna to simply degrade that protein product. "Dr JDD_{May 8, 2014
May
05
May
8
08
2014
01:17 PM
1
01
17
PM
PDT}

KanbanMung_{May 8, 2014
May
05
May
8
08
2014
12:25 PM
12
12
25
PM
PDT}

AVS:
I am not saying that the degradation system itself is inefficient. I am saying that the overactivity of the degradation system produces inefficiency because it degrades proteins that should not be degraded. Yes the proteasome serves an important function in the immune system, but it also destroys correctly folded proteins that the cell just spent a good deal of energy synthesizing. This is a waste of energy = inefficiency.
How do you know that it degrades proteins that should not be degraded? How do you know that this is a waste of energy?Mung_{May 8, 2014
May
05
May
8
08
2014
12:23 PM
12
12
23
PM
PDT}

"That it’s not perfect, it doesn’t have a direction, and that there are trade-offs." Trade-off is a design term.Mung_{May 8, 2014
May
05
May
8
08
2014
12:15 PM
12
12
15
PM
PDT}

A Darwinist claimed in this post,,, "Nothing is 100% efficient in the cell" Yet: Thermodynamic efficiency and mechanochemical coupling of F1-ATPase - 2011 Excerpt:F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,, Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase. http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1 William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.htmlbornagain77_{May 8, 2014
May
05
May
8
08
2014
11:41 AM
11
11
41
AM
PDT}

Now if only your position could account for DNA in the first place...Joe_{May 8, 2014
May
05
May
8
08
2014
10:56 AM
10
10
56
AM
PDT}

See this Nature paper where they deleted 2.3 mb of DNA from a mouse's genome. And that didn't affect its viability! Megabase deletions of gene deserts result in viable mice. Abstract The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined1. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts2, 3, 4 can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals. http://www.nature.com/nature/journal/v431/n7011/full/nature03022.htmlEvolve_{May 8, 2014
May
05
May
8
08
2014
10:46 AM
10
10
46
AM
PDT}

DJDD, ///Evolve that is a poor example. Garages do not replicate. Replication requires energy and if 98% is unnecessary that is hugely inefficient for replication. I do not accept that as a good explanation and completely stand by what I said. We are to believe evolution can produce incredibly complex machineries like the 150+ protein complex spliceosome but just ignores the 98% of the genome of no use to it does not seem rational at all to a scientific mind./// It's not a poor example. You're failing to grasp the point that anything that doesn't affect the survival and reproduction of the cell will be ignored by selection and won't be weeded out. So while the cell may have to spend a bit more energy to replicate junk DNA, as long as that extra energy doesn't affect the cell's energy budget, it won't care.Evolve_{May 8, 2014
May
05
May
8
08
2014
10:38 AM
10
10
38
AM
PDT}

"I said it degrades rna transcripts that had been translated." That's like saying "I drove my four wheels and a motor that has been assembled by Honda, to their house"AVS_{May 8, 2014
May
05
May
8
08
2014
10:33 AM
10
10
33
AM
PDT}

"I did not say it degrades rna transcripts I said it degrades rna transcripts" Right. If you had knew what you were talking about you would have said it "degrades nascent polypeptide strands." You are completely missing my point. I am not saying that the degradation system itself is inefficient. I am saying that the overactivity of the degradation system produces inefficiency because it degrades proteins that should not be degraded. Yes the proteasome serves an important function in the immune system, but it also destroys correctly folded proteins that the cell just spent a good deal of energy synthesizing. This is a waste of energy = inefficiency.AVS_{May 8, 2014
May
05
May
8
08
2014
10:21 AM
10
10
21
AM
PDT}

AVS please read what I said. I did not say it degrades rna transcripts I said it degrades rna transcripts that had been translated. And to be properly processed into the correct nonamers or octamers or decamers or whatever nmer the peptide is it likely has to be translated to a fully functional protein otherwise you might get peptides the thymus didn't display to T-cells and the immune system would see that cell as non-self and kill it. I just gave one example of why it may not be inefficient and again I stand by that example as a good, necessary example to balance recognising self and non-self by the immune system. My point remains - you see wastefulness where I see unknown function as yet. Which advances a investment more? That is my point with supposed junk DNA. It is also my point about the evolutionary outlook. In fact, as we advance our understanding I see in science that we show more and more function where it was previously assumed non-function. These processes simply add to that story. That is the trend we are observing therefore the rational extension is that where we have unknown function, we are most likely to expect it is simply unknown as of yet rather than no function and wasteful evolutionary processes. I get your resistance to that thinking though as accepting that puts a dent in the evidence an evolutionist likes to use. So i naturally expect such resistance from you over this point.Dr JDD_{May 8, 2014
May
05
May
8
08
2014
10:10 AM
10
10
10
AM
PDT}

Yes, JDD, obviously there is a function for protein degradation. But the fact that this machinery often ends up degrading proteins that have just been correctly and fully synthesized by the cell, is an example of inefficiency. And the fact that this is continuously happening in trillions of cells many times per minute in each cell adds up to a large degree of inefficiency. Also, the proteasome does not degrade RNA transcripts as you said, that would be the various nucleases within the cell.AVS_{May 8, 2014
May
05
May
8
08
2014
09:57 AM
9
09
57
AM
PDT}

Evolve that is a poor example. Garages do not replicate. Replication requires energy and if 98% is unnecessary that is hugely inefficient for replication. I do not accept that as a good explanation and completely stand by what I said. We are to believe evolution can produce incredibly complex machineries like the 150+ protein complex spliceosome but just ignores the 98% of the genome of no use to it does not seem rational at all to a scientific mind.Dr JDD_{May 8, 2014
May
05
May
8
08
2014
09:35 AM
9
09
35
AM
PDT}

Yes Evolve, unguided evolution is good at breaking things and collecting junk. Too bad it cannot account for DNA in the first place.Joe_{May 8, 2014
May
05
May
8
08
2014
09:35 AM
9
09
35
AM
PDT}

AVS:
At the nanoscale level these processes can approach 100% efficiency much more easily than at the macroscopic.
Ah, that's why we humans go on building inefficient macroscopic machines, and do not build cells. We like challenges, and we are bored of simple things! Now I understand.gpuccio_{May 8, 2014
May
05
May
8
08
2014
09:32 AM
9
09
32
AM
PDT}

Dr.JDD ///I would be interested to hear a rational explanation for junk DNA remaining in such vast quantities within the genome by a naturalist. I have yet to hear a convincing argument./// You're not thinking enough. Cells will accumulate junk DNA as long as they have little to no deleterious effect on the ability to survive and reproduce. Such DNA is essentially invisible to selection. So they'll persist. One can draw an analogy to the junk accumulating in your garage. You may ignore it for years because it doesn't affect your day-to-day life in any significant manner.Evolve_{May 8, 2014
May
05
May
8
08
2014
09:29 AM
9
09
29
AM
PDT}

The changes that are made are undirected, the changes that increase efficiency are kept in successive generations. Changes that increase efficiency would include perfectly functional proteins that have been synthesized. They why is this process not kept in successive generations? You noted earlier that it's one of the things that are problematic for cell biology. It is still illogical to believe that an undirected process will cause change for the better. Because obviously it's not doing that.Barb_{May 8, 2014
May
05
May
8
08
2014
09:24 AM
9
09
24
AM
PDT}

AVS - perhaps you are assuming inefficiency with again, misunderstanding a process. Perhaps I suggest, not definite. I am merely saying consider it. Many of the cellular machines we find hard to point to inefficiencies. Often where we see inefficiency we just don't understand. Take for example, the fish movement has recently been shown by engineers to rewrite our understanding of optimal speed, direction and manoeuvrability. Prior to this, it seemed inefficient. You quote making proteins to simply just degrade it off the top of your head. Have you considered there is purpose to this? Have you considered the immune system, which we barely understand (I think I have the right to say that as an Immunologist) has a purpose for this? Our body relies on presenting short peptide fragments on HLA molecules (MHC complex) to recognise as self. This is important in both evading foreign infection but also in things like avoiding cancer. There is good evidence many RNA transcripts are rapidly translated and turned over (degraded by the proteasome etc) to have peptides presented on the cell surface as a role in adaptive immunity. Again, to prove my point - you take a process, assume it has no function as you don't see function, so attribute it to wasteful evolution. Therefore the possibility there is function is ignored to advance your favoured OOL theory and once again, science does not progress. Yet the irony is you claim IDists hinder progress in science! Again I emphasise. Irony. JDDr JDD_{May 8, 2014
May
05
May
8
08
2014
09:24 AM
9
09
24
AM
PDT}

The fact that you think removing 50% of an organism's genome and it not being able to function, "falsifies evolution" tells us quite a bit about how you understand and perceive science phoo.AVS_{May 8, 2014
May
05
May
8
08
2014
09:12 AM
9
09
12
AM
PDT}

JLAfan2001, What does slight or medium function mean? Now you want to have an out by saying whilst we may find purpose to more of the genome, you can claim its not an important function? Ok then, simple, lets try removing 50% of any organisms genome, and see if it can still function at all. If it can't will you agree that Darwinian evolution has been falsified?phoodoo_{May 8, 2014
May
05
May
8
08
2014
09:05 AM
9
09
05
AM
PDT}

The changes that are made are undirected, the changes that increase efficiency are kept in successive generations. This is the simplest form of evolution. The fact that I have to explain this to you is telling. Although not surprising.AVS_{May 8, 2014
May
05
May
8
08
2014
09:03 AM
9
09
03
AM
PDT}

How can something be efficient, or work towards better efficiency if it's undirected? That is entirely illogical. That you refuse to acknowledge this point is telling.Barb_{May 8, 2014
May
05
May
8
08
2014
08:58 AM
8
08
58
AM
PDT}

That it's not perfect, it doesn't have a direction, and that there are trade-offs Barb, did you have a point?AVS_{May 8, 2014
May
05
May
8
08
2014
08:49 AM
8
08
49
AM
PDT}

degradation of perfectly functional proteins that have just been synthesized What does this say about the efficiency of evolution?Barb_{May 8, 2014
May
05
May
8
08
2014
08:46 AM
8
08
46
AM
PDT}

Prev 1 2 3 Next

You must be logged in to post a comment.

Leave a Reply