Sandwalk

While new discoveries of biological function are fascinating, I don't think it follows that we are overturning the idea of junk DNA (however the phrase was coined). More likely we are converging towards an understanding where most of the genome really is non-functional. Here's a recent accounting [1] of known function suggesting 90% is junk. I wonder how much this differs from our understanding of decades ago, it really may not have changed much at least in terms of broad accounting. Now the potential significance of those little fractional bits of recently uncovered function, well that's a different discussion and more aligned with the original article, which I don't think mentioned junk anyway. [1] https://sandwalk.blogspot.com/2021/11/whats-in-your-genome-2021.html

No one is saying evolution is all random, only mostly random. Natural selection obviously plays a role in shaping the direction of individual mutations - deleterious ones get purged relatively quickly. When those are culled, the vast majority of mutations are neutral or nearly neutral. >Brute forcing the genome to something better is clearly possible, but if you converted all of the matter in the visible universe into DNA and mutated every strand a trillion times a second for a trillion years, it's very possible you would never even encounter a viable strand of DNA for that organism. Yes, but consider the following. I just ran: >>> np.random.random() 0.8867453976799686 What were the odds that I ended with this specific 18-digit float in the whole set of floats in [0.0, 1.0)? And yet, here we are. The word you're looking for is contingency. Gould spoke much about "replaying life's tape" and how it would yield different results every time it was "replayed". Interestingly, people have actually attempted to put this thought experiment into practice at a very prosaic level [0] [1]. They find that although there are convergent patterns of adaptation, over the long term populations diverge considerably. [0] https://science.sciencemag.org/content/362/6415/eaam5979 [1] https://sandwalk.blogspot.com/2019/09/contingency-selection-and-long-t…

Despite your patronizing tone, I fear it may be you who is naive. I don't know what field it is that you've been in for the last 20 years, but I suggest you start reading up on genetics and biochemistry, as you've got a lot of catching up to do. In the meantime, here are a few questions for you to think about. You are already aware, of course, that 90% of the human genome is unconserved, that 50% of the genome consists of dead transposons and viruses, and that mice have been generated that are homozygous for megabase-scale deletions with no discernible effects? Perhaps you can come up with some hypotheses that could explain these facts that are consistent with your claim of functionality? You've heard of pseudogenes, right? Why do they look exactly like broken genes? What do they do? Why is there great variability in the sequences of repetitive DNA in many species, including humans? Why do some individuals have many more copies of these tandem repeats than others? Are the extra repeats functional? If so, why does the number of copies change rapidly and stochastically from generation to generation? Do you know anyone who thinks satellite DNA is functional? The links below will help you get started on the basics of genome biology. Good luck. http://www.genomicron.evolverzone.com/2007/04/word-about-junk-dna/ http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html

https://sandwalk.blogspot.com/2018/03/whats-in-your-genome-pie-chart.h… We don't need 1M copies of Alu: https://en.wikipedia.org/wiki/Alu_element A lot of the sequences are defective copies. These are often how new genes arise, but they are not useful to the individual.

You're refuting a strawman. The junk DNA claim is not, and as far as I can see never had been, that all non-coding DNA is junk. It's that most of our genome -- around 90% -- is junk[1][2]. But since the genome is over 98% non-coding, that implies that something like 8% is functional non-coding DNA, which is several times the amount of coding DNA. Finding small amounts of additional functional non-coding DNA does not significantly challenge this[3]. [1] https://sandwalk.blogspot.com/2022/08/junk-dna-vs-noncoding-dna.html [2] https://en.wikipedia.org/wiki/Junk_DNA#History [3] https://judgestarling.tumblr.com/post/154553548091/long-noncoding-rna-…

Still 90% junk. https://sandwalk.blogspot.com/2011/05/whats-in-your-genome.html

I don't think this article gives the pro-"Junk DNA" arguments fair treatment. Check out Larry Moran's blog [1, 2] if you want to to hear the other side of the story. He maintains that most of the human genome IS junk, and I find his arguments compelling. [1] A representative article: https://sandwalk.blogspot.com/2013/07/five-things-you-should-know-if-y… [2] Rabbit hole warning, all of his Junk DNA posts: https://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html

Seems like there are much more intuitive ways to show these differences, something like the plot on Dr. Moran's blog: http://sandwalk.blogspot.com/2012/01/whats-difference-between-human-an… Although the 3D plots are neat, they kind of feel like 3D barcharts: they add very little over a more straightforward representation (like a heatmap instead).

This is very interesting, given that ScienceDaily reported the discovery of the seventh and eighth bases in 2011! Did they forget how to count, or do they just republish press releases without any understanding of the subject matter or actual journalism? Source: http://sandwalk.blogspot.ie/2011/07/stop-press-scientists-discover-7th…

Personally I think the idea that life/prebiotic soup came to earth on a comet is suspect, for the reasons explained in these blog posts and the links therein: http://sandwalk.blogspot.ca/2011/11/nasa-confusion-about-origin-of-lif… http://sandwalk.blogspot.com/2009/04/can-watery-asteroids-explain-why-… Two problems with the 'organic asteroid' theory are the 'racemization problem' (how to explain why life only uses L isomers rather than both the L and D isomers present in meteorites), and the fact that the amount of organic matter in meteors is tiny. Compare that to the opportunities for life to arise on earth in its diverse chemical environments. See the calculations by Jeffrey Bada discussed in the second link.

I will join your movement. http://sandwalk.blogspot.co.il/2009/03/profzi-scheme.html

and large parts of our genome is bit-rotted and non functional Larry Moran has a lot of good material on this http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html