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New information, Genetic entropy and Junk DNA blablabla

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New information, Genetic entropy and Junk DNA blablabla
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Nesslig20User avatarPosts: 280Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post New information, Genetic entropy and Junk DNA blablabla

I have come in contact with a creationist youtuber Standing For Truth (SfT) and he wants to have a talk with me and others in the near future, although I have yet to get a response from him to know exactly when he wants to talk. I have listened to him multiple conversations with people like Jackson Wheat, Crispr and Scientist Sam and I can summarise his tactic of discourse as such:
JAQing off (short for "Just-asking-questions")
It’s a way to phrase claims as questions in such a way that completely disregards the answers that could be given and is only intended to influence the views of spectators. For example, if an 9/11 truther asks questions about how you can explain their perceived evidence of a controlled demolition, it implies that IF you or someone else is unable to answer the question on the spot then they are seemingly winning the point automatically, hence it WAS evidence of a controlled demolition. It’s a clever way to shift the burden of proof. So SfT often asks questions with claims and assertion hidden within them. That's one thing to watch out for. SfT also employs changing topic constantly by asking new questions immediately after previous one is answers and once he is pinned into a corner (the opponent won't let him change the subject), he apparently begins to freak out and starts spouting a string of nonsense all at once just to flabbergast the opponent and distract them with this steaming pile of BS. A discussion with him would be quite some experience. And I believe that his tactic would work more effectively with people who aren’t prepared to answer his loaded/leading questions, so here I have prepared some answers/rebuttals to his questions/assertions.

One of his main talking points is new genetic information, in which he seems to define as “new functional DNA popping out of nothing”. Note the “out of nothing” caveat. It doesn’t matter if you have a completely new gene forming from non-coding DNA which previously didn’t do anything, it doesn’t count as new information since the template was already there. Of course, Evolution doesn’t entail nor require that things pop out of thing air. Evolution is more like tinkering. Rather than inventing new things it uses old stuff and modifies it to make the new. A good example of this is the GPCR (G-coupled Protein receptors) superfamily. They bind to molecules outside the cell and when that happens they activate an internal signal transduction pathway. It is an extremely fast way for cells to respond to external stimuli. The first GPCR got duplicated, and the duplicated version got duplicated in turn, and so forth, creating this protein super family.
Image
Each duplicated version was slightly modified such that they would react to different molecules. This produced a wide variety of different GPCRs with completely different functions in many systems. There are those that bind to hormones, regulate the immune system and inflammation, some are involved in our sense of smell and taste because they bind to flavour and odour molecules. Some GPCRs even got modified such that they could react to light and are now the opsins in the rod cells of our eyes. It's rather odd that creationists are asking us to show new information, i.e. show how DNA can pop into existence from nothing.
That’s the creationists view, God making things from nothing. So they should be asking this question to themselves, not us.
It also shows that they have this conception that these biological systems just HAD to come from nothing. They couldn't have evolved gradually by slight modification of existing systems, but the example above is just one example that completely discredits this notion.

The second talking point of his is the idea of genetic entropy. SfT thinks that the genome is somehow under influence of the second law of thermodynamics so it should break down over time, even though the genome is part of an open system and it doesn’t have anything to do with the “order” of a system. Thermodynamic entropy has to do with the amount of energy that is able to do work. This doesn't apply to the "order" or "disorder" of DNA.

The man behind genetic entropy is John Sanford, who is the scientist that co-invented the gene gun, which makes him a respectable scientists in the field of plant genetics. Though, that doesn’t mean all of his ideas are respectable. There are many scientists with ground breaking ideas like Lynn Margulis (Carl Sagan’s first wive) who proposed endosymbiosis, but she was also an HIV denials and 9/11 truther. Likewise Sanford has also some wacky ideas that aren’t supported, like genetic entropy. Sanford claims that genomes are deteriorating over time. This is because in every individual of every generation, there are numerous small deleterious mutations, a good fraction of which have almost no influence on fitness such that selection is ineffective to weed them out. Thus these small harmful mutations will accumulate due to genetic drift, generation by generation. This would inevitably deteriorate the genome over time and populations could never increase in fitness. They will always decrease in fitness. You might think “what about beneficial mutations? Wouldn't they cause an increase in fitness and counter act this "genetic entropy"?” Well, John Sanford simply dismisses the influence of of beneficial mutations, because he thinks that they are too rare and practically all of them are also effectively invisible to selection. He also claims that because of this, beneficial mutations cannot play the role in evolution according to the scientific consensus. More on that later.

One of the things that discredits genetic entropy is by pointing out that most mutations are completely neutral since most stretches of the genome is non-functional. But then, of course, SfT brings up ENCODE to claim that 80% of the human is functional and not junk DNA. However, most of the human genome is actually not functional (don’t have any effect on phenotype or fitness). SciShow did a recent video on this:

ENCODE defined “functional” as any region of DNA that interacted with a binding protein of some sort. It doesn’t matter if anything else happened. If something sticked to the DNA, the DNA is functional according to that ENCODE paper. It’s like (as Jackson Wheat put it) saying that a piece of gum on the ground is functional to your shoe because it can stick to the bottom of your shoe. The genome is a large molecular chain(s) of four different monomers. Simply by change, there would be large sections of DNA that are very similar to protein binding sites. Not entirely identical but similar enough such that proteins will occasionally bind to them and nothing else happens. And when we actually define functional as “DNA that has an effect on fitness or at least the phenotype of the organism” which is more reasonable and useful, we see that the majority of our genome is not functional. But whenever someone explains this SfT he begins to assert that we just assume that the DNA doesn’t have any function simply because we don’t know what it does. That’s not true, we can look at the DNA tell what they do and determine whether they do anything, and we have for most of the genome.

In the functional category we have:
Functional parts of protein coding genes, non-coding RNAs, regulatory sequences, SARs, Origins of replication, centromeres, telomeres, and conserved sequences of unknown function is about 8.7% (essential/functional). Non-functional includes transposable elements, viral DNA, pseudogenes and introns is about 65% (non-functional Junk). The remaining 26.3% is non-conserved intergenic regions of unknown function (probably mostly junk too).

Note: There are very few exceptions such as co-opted viral or pseudo genes that have acquired a new function secondarily, but these are just a fraction of a percentage of all these categories. Creationists will often jump on these exceptions which only account for less than 0.0001% of the genome and use that to claim that the entire genome is functional, which is like cherry picking one cherry on a tree and then claiming that the entire tree is edible. And there are also fractions of a percentage on the functional categories that are actually non-functional, so these small differences won’t change these overall percentages.

So 65% is KNOWN to be non-functional, but we can actually determine how much is likely to be non-functional by other means. There is this thing called genetic load, which sounds similar to the idea of genetic entropy but it is different. It’s real for one thing. The principle behind this is the fact that a population can only tolerate a finite number of deleterious mutations. And it is not like if we went beyond this limit, we would slowly deteriorate (even while increasing our population size) like according to genetic entropy. No, the population couldn’t increase in or maintain its size. We would go into extinction much quicker if we only had four couples (each man related to the same father), like with Noah’s family, because there there is almost nothing that increases the genetic load MORE than incestious inbreeding. But somehow, genetic entropy doesn’t apply with Noah’s family allowing them to produce thousands of offspring in a few generations without deteriorating because….reasons. Anyway..... a paper by Dan Graur published in genome biology and evolution shows how he calculated that we can only have 25% of our genome to be functional at the upper limit. But even this is absurdly generous. A more reasonable value is 10-15%, which is roughly correspond to the previous figure of 8.7% that is known to be functional. Remember, if it was functional over this limit, we would’ve dwindled into extinction a long time ago. Simply of this reason, most of our mutations would be within non-functional regions of the genome and be entirely neutral.

So what more does John Sanford use to support genetic entropy. He often cites various scientists like Michael Lynch and James F. Crow who supposedly all agree that the human genome (or any genome in general) is deteriorating (just like Sanford does):
J. Sanford wrote:“Subsequently, they realise that genetic information is currently being lost, which must eventually result in reduced fitness of our species. This decline unfitness is believed to be occurring at 1-2% per generation (Crow 1997)”
“The most definitive findings were published in 2010 in the Proceedings of the National Academy of Science by Lynch. That paper indicates human fitness is declining at 3–5% per generation.”

However, Sanford is misrepresenting the views of these scientists. Crow, Lynch and other scientists who are similarly quoted by Sanford are concerned with what is called “Relaxed natural selection”. In order for natural selection to fully operate, populations must produce lots of offspring only some of which would survive and reproduce. But when there are only few offspring per individual and each offspring is kept alive through artificial means, there is little opportunity for deleterious mutations to be purged or beneficial mutation to be rewarded and the fitness of the population declines for this reason. When we observe populations with large individuals and differential reproduction, fitness holds up just fine due to selection having full effect. But when selection is shut down, fitness and genomes deteriorate. And this is what Lynch and Crow are publishing about regarding human populations in industrialised societies which have few offspring per family and each offspring largely being kept alive by medial intervention.
James F. Crow wrote:“However efficient natural selection was in eliminating harmful mutations in the past, it is no longer so in much of the world. In the wealthy nations, natural selection for differential mortality is greatly reduced. A newborn infant now has a large probability of surviving past the reproducing years. There are fertility differences, to be sure, but they are clearly not distributed in such a way as to eliminate mutations efficiently. Except for pre-natal mortality, natural selection for effective mutation removal has been greatly reduced.”

Michael Lynch wrote:“the mean phenotypes of the residents of industrialised nations are likely to be rather different in just two or three centuries, with significant incapacitation at the morphological, physiological, and neurobiological levels. Ironically, the genetic future of mankind may reside predominantly in the gene pools of the least industrialised segments of society.”

But this doesn’t support Sanford’s claims. Sanford is specifically claiming that even natural selection cannot prevent genetic entropy. Obviously, the work of Lynch and Crow specifically apply to situations without natural selection, but the way Sanford cites these scientists is grossly misleading, such that it sounds like they are saying that the human genome is deteriorating regardless of selection. And there are other researches that shows evidence against the notion that humans are deteriorating due to a lack of selection, which is obviously ignored by Sanford and his ilk.

Sanford also likes to cite his own adapted figure for the frequency distribution of mutations and their effect on fitness from the 1979 paper of Motoo Kimura, here below, to argue for why beneficial mutations are too rare and too low impact to be selected for and counter genetic entropy
Image
Here is the figure of the original article, figure 1.
Image
His “adapted” figure is fudged in a subtle way. The “no selection zone” is significantly enlarged in his graph, as sanford boundary is closer to the -0.001 mark while the original is closer to the 0.00 mark. There is also the fact that the original doesn’t show anything on the positive (beneficial mutation) side of the fitness scale, while Sanford has added a tiny curve on the right to represent the beneficial mutations, which are apparently infrequent and always inside the “no selection zone”, just as he claims. If John presented this figure as his own speculative hypothesis, to illustrate his ideas, it would be fine. But no, he claimed that this tiny curve also represent what Kimura would have put in for beneficial mutations:
Sanford wrote:“In Kimura’s figure, he does not show any mutations to the right of zero – i.e. there are zero beneficial mutations shown. He obviously considered beneficial mutations so rare as to be outside of consideration.”
“So selection could never favor any such beneficial mutations, and they would essentially all drift out of the population. No wonder that Kimura preferred not to represent the distribution of the favorable mutations!”
"Kimura does not show the beneficial distribution, which is essential to the question of net gain versus net loss! When I show the beneficial distribution (while Kimura did not do this, I suspect he would have drawn it much as I did), anyone can see the problem: the vast majority of beneficial mutations will be un-selectable"

But what does Kimura actually say in the article?
Well….
Motoo Kimura wrote:“Note that in this formulation, we disregard beneficial mutants, and restrict our consideration only to deleterious and neutral mutations. Admittedly, this is an oversimplification, but as I shal show later, a model assuming that beneficial mutations also arise at a constant rate independent of environmental changes leads to unrealistic results.”
“Under the present model, effectively neutral, but, in fact, very slightly deleterious mutants accumulate continuously in every species. The selective disadvantage of such mutant (in terms of an individual’s survival and reproduction - i.e., in Darwinian fitness) is likely to be of the order of 10^-5 or less, but with 10^4 loci per genome coding for various proteins and each accumulating the mutants at the rate of 10^-6 per generation, the rate of loss of fitness per generation may amount to 10^-7 per generation. Whether such a small rate of deterioration in fitness constitutes a threat to the survival and welfare of the species (not to the individual) is a moot point, but this can easily be taken care of by adaptive gene substitutions that must occur from time to time, say once every few hundred generations.”

Thus Kimura actually believed that there would be selectable beneficial mutations that compensate for the accumulation of deleterious mutations. So if he did draw a line for beneficial mutations, the curve would extend beyond the non selection zone. The reason why Kimura omitted beneficial mutations in his figure is that, in his primitive mathematical model, the presence of any beneficial mutation would make it blow up, i.e. he omitted them NOT because (as Sanford claims) Kimura believe they were negligible, but because their effect was too strong. (See citations: 11 and 12)
So what does Sanford have left to speak about? Are there laboratory experiments with populations that show clear genetic entropy (regardless of selection)?

John Sanford wrote:“It is true that most lab experiments do not show clear degeneration. But Scott should realize that anything alive today must have been degenerating slowly enough to still be here, even in a young earth scenario. All three of the downward decay curves I show in my book indicate that degeneration slows dramatically as it becomes more advanced. If a species is alive today and has been around for thousands of years, the rate of degeneration must be very slow (too subtle to measure in most cases). Obviously, genetic degeneration is not going to be clearly visible in most lab experiments.”

The answer seems to be “no” at least not most experiments. But we do have an interesting caveat here. Genomes are relentlessly deteriorating, yet at the same time it is happening so slowly that we cannot detect it? Notice that the “slowness” of entropy is added just to explain away how species could have survived thousands of years of genetic entropy (especially considering that they all started from just an incestious gene pool right after the flood 4000 years ago). Trying to have your cake and eat it too it seems. About the “downward decay curves” that he cites in his book, I have no better response to this than Dr. Scott Buchanan.
Scott Buchanan wrote:"The claim here is that genomes are relentlessly deteriorating, but we cannot detect it. I’m sure that genetics simulation programs can be adjusted to show that the fitness of all sorts of organisms, from bacteria to elephants, starting from some idealized mutation-free state, could fall dramatically from 4000 B.C to say around 500 B.C., then almost level out. I do not find that compelling support for genetic entropy."

In his book (fourth edition), Sanford makes an attempt to support his claims with actual data (emphasis on "attempt"). He compared his figure 14 (results of Sanford’s mendel’s accountant algorithm, that models his genetic entropy, showing a fitness decline over time) and compares it to figure 15, the data of is comes from influenza viruses from the paper by Simonsen et al a rare example of Sanford referencing to real world data. He presents that figure as - “Actual biological data, showing mutation accumulation and fitness decline in human influenza virus”.
John Sanford wrote:“This graph illustrates the pathogenicity (i.e., fitness) of the H1N1 strain, as well as the other two pandemic-causing strains during the last century.”

But this is, just like with the Kimura figure, completely misrepresenting the original figure 1 from Simonsen et al. That figure doesn’t quantify pathogenicity nor fitness like Sanford is claiming. As Gerard Jellison said in his review on Amazon:
Gerard Jellison wrote:“…the figure shows a ratio: the number of influenza-caused deaths of people under 65, divided by the total number of deaths. The point of the paper is that the flu epidemic of 1918-1919 was unusual in that it killed mostly young people. The authors studied how this ratio varied with time, and modeled the results in terms of different immunity in the two age cohorts. Thus, the curves in Sanford’s plot merely show that, as time goes on, flu strains kill a greater proportion of elderly people. This makes sense, since young people have more vigorous immune systems [….] Sanford’s Figure 15 is invalid, since it does not illustrate declining viral “fitness” at all. This blunder is an absurd misuse and/or misunderstanding of scientific data.”


To make matters even worse for Sanford, there are experimental data that actually disproves the idea of genetic entropy. The most famous one is the long Long Term Evolution Experiment by Lenski et al. wherein in one paper they show that even after 50.000 generations, all 12 separate populations still increased in fitness relative to their ancestors following a power law model. This shows that surprisingly fitness can increase indefinitely (or at least for a very long time) even in a constant environment. This flies completely in the face of genetic entropy which says that populations must always decline in fitness over time. In other studies, they also show that beneficial mutations with the same effect occur independently in different populations. (see citations 15 and 16) So these beneficial mutations aren’t too rare nor are they invisible to selection. And of course, the most famous beneficial mutation of the LTEE experiment led to a completely new phenotype in one of the 12 populations. The ability to utilise citrate when oxygen is present.

Now creationist like SfT like to downplay the significance behind this mutations by claiming that it already could digest citrate so it is not “new information” and sometimes go as far to claim that it is actually a decrease in information (SfT specifically said it is a loss of "control") since it now lost its specificity to express these genes only when no oxygen is present. Now it is "unspecific" or "uncontrolled" such that the genes are active all the time. But that is all wrong. The ability to digest citrate under aerobic conditions wasn’t present before, so the phenotype is NEW by any reasonable definition of what count as new. It is also not the case that genetic information was lost since the mutation that was responsible for this new phenotype was a duplication. Well, now you can already hear the creationists yelling “duplications aren’t new information!!!”, but this duplication DID create something new, see diagram here below
Image
Picture from this
The section that was duplicated included the CitT (the gene which produces a membrane transporter that allows citrate into the cell) at one end and the RNK promotor (which expresses the RNK gene when oxygen is present). The duplication was tandem, meaning the duplicated section was directly put next to the original section. This ended up with a duplicated CitT gene being controlled under a duplicated RNK promotor. Notice that the original genes are still there and still being controlled by the same promoters. There is still a CitT gene controlled by a promoter that is activated when no oxygen is present and there is still an RNK gene controlled by a promoter that activates when oxygen is present. Hence NOTHING WAS LOST. What was gained was a novel regulatory module.

First you had these regulatory modules:
1. Promotor (activate when no oxygen is present) —> CitT
2. Promotor (activate when oxygen is present) —> RNK

After the duplication, you have:
1. Promotor (activate when no oxygen is present) —> CitT
2. Promotor (activate when oxygen is present) —> RNK

3. promotor (activate when oxygen is present) —> CitT
It’s an novel (new) module. No specificity was lost, no loss of control. Control and specificity was gained at the molecular level and a novelty was gained at the phenotype level.

Now I am done. I think that this pretty much shows that Genetic Entropy is complete bollocks as well as other talking points of creationists like “there is no junk DNA” and “no new information”. The sum of the sources are here below.

SOURCES:
1. Stevens, Raymond C., et al. "The GPCR Network: a large-scale collaboration to determine human GPCR structure and function." Nature reviews Drug discovery 12.1 (2013): 25.
2. Sandwalk: What's In Your Genome? - The Pie Chart
3. Sandwalk: Theme: Genomes & Junk DNA
4. Graur, Dan. "An upper limit on the functional fraction of the human genome." Genome biology and evolution 9.7 (2017): 1880-1885.
5. http://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
6. http://sandwalk.blogspot.com/2009/11/genetic-load-neutral-theory-and-junk.html
7. Rands, Chris M., et al. "8.2% of the human genome is constrained: variation in rates of turnover across functional element classes in the human lineage." PLoS genetics 10.7 (2014): e1004525.
8. Dr. Scott Buchanan "Letters to creationists" Junk_DNA_Design
9. Crow, James F. "The high spontaneous mutation rate: is it a health risk?." Proceedings of the National Academy of Sciences 94.16 (1997): 8380-8386.
10. Lynch, Michael. "Rate, molecular spectrum, and consequences of human mutation." Proceedings of the National Academy of Sciences 107.3 (2010): 961-968.
11. Dr. Scott Buchanan "Letters to creationists" Gen_Entropy
12. Gerard Jellison - Amazon Customer Review for the book "Genetic Entropy" by J. Sanford
13. Simonsen, Lone, et al. "Pandemic versus epidemic influenza mortality: a pattern of changing age distribution." Journal of infectious diseases 178.1 (1998): 53-60.
14. Lenski, Richard E., et al. "Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli." Proc. R. Soc. B 282.1821 (2015): 20152292.
15. Cooper, Tim F., Daniel E. Rozen, and Richard E. Lenski. "Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli." Proceedings of the National Academy of Sciences 100.3 (2003): 1072-1077.
16. Cooper, Tim F., et al. "Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli." PLoS Genetics 4.2 (2008): e35.
17. Blount, Zachary D., et al. "Genomic analysis of a key innovation in an experimental Escherichia coli population." Nature 489.7417 (2012): 513.
18. A Duplication Mutation and a New Arrangement: E.coli Cit+ phenotype
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Last edited by Nesslig20 on Fri Oct 05, 2018 10:53 am, edited 9 times in total.
Sat Sep 29, 2018 11:05 pm
RumraketUser avatarPosts: 1256Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: New information, Genetic entropy and Junk DNA blablabla

Outstanding post Nesslig.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Sun Sep 30, 2018 12:27 am
RumraketUser avatarPosts: 1256Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: New information, Genetic entropy and Junk DNA blablabla

Nesslig20 wrote:To make matters even worse for Sanford, there are experimental data that actually disproves the idea of genetic entropy. The most famous one is the long Long Term Evolution Experiment by Lenski et al. wherein in [url]one paper they show that even after 50.000 generations, all 12 separate populations still increased in fitness relative to their ancestors following a power law model.[/url] This shows that surprisingly fitness can increase indefinitely (or at least for a very long time) even in a constant environment. This flies completely in the face of genetic entropy which says that populations must always decline in fitness over time.

Heh, this is also a point I've raised before to Sanford and his fans. You will find his response hilarious, paraphrasing: The ratio of beneficial to deleterious mutations in the particular species of bacteria used in the experiment under the unique experimental conditions, is different from humans and lots of other organisms where genetic entropy must be the case in the wild.

That's it, that's essentially his response. So basically he will just respond to evidence that contradicts his claim with special pleading.

So if you show evidence of fitness increase in experiments, he will just say this is consistent with a model where fitness can increase in response to selection in the particular species used and with the particular experimental environment(and then he'll try to deflect by pointing out that many of the mutations are "loss of function" mutations)*, but that his genetic entropy claims are still true for everything else in the wild.

So we have to basically prove him wrong with experiments for all 10 million species on Earth in conditions that are pretty much exactly equal to whatever it is in the wild, or he's going to keep claiming genetic entropy must be the case for everything. Essentially he's saying "here's how everything is in my view, prove me wrong". Not understanding that it's HIS job to prove his claims right. :roll:

* This one is his get-out-of-jail-free card. He operates with two significantly different senses of genetic entropy in mind, and will casually switch back and forth between them as he sees fit. In the one sense he will argue that
1. Genetic entropy means there are too many deleterious mutations for selection to ever be capable of countering their cumulative effects, and
2. In the other sense he will say that loss of function mutations (or even just nucleotide deletions) are also examples of genetic entropy, even if they have positive fitness effects. That way he has basically defined his position in very specious fashion so he will always be able to argue that what we're seeing is "genetic entropy". That's what he does in response to the LTEE, because the majority of the beneficial mutations in the experiment were either loss of function mutations or deletions.

It is extremely dishonest.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Sun Sep 30, 2018 12:45 am
Dragan GlasContributorUser avatarPosts: 3190Joined: Mon Dec 14, 2009 1:55 amLocation: Ireland Gender: Male

Post Re: New information, Genetic entropy and Junk DNA blablabla

Greetings,

I agree with Rumraket:, excellent post, Nesslig.

Given Sanford's claim regarding deleterious and beneficial mutations being "invisible" to evolution, this would place them in the "neutral' category. Of course, his claim that beneficial mutations are rare in comparison with deleterious ones, allows him to claim his idea is right. However, since he hasn't provided any positive evidence for this claim of genetic entropy, his claim can be held as unproven, if not dismissed outright as wrong.

Regarding Lynch's paper, and its misinterpretation/misrepresentation, this was used before in the Onceforgivennowfree thread.

Dandan had cited it - having first attempted to get me to agree that, if he could provide scientific evidence of his claim that deleterious mutations were more frequent than beneficial ones, would I admit I was wrong?

I initially dealt with it here - Inferno's two subsequent replies also dealt extensively with it. Aron and HWIN also addressed it - and DutchLiam pointed out that dandan's definition of "real science" was whatever he thought agreed with his own worldview, which may be what Sanford is doing!?

When it was pointed out by Inferno that dandan hadn't understood his own paper, and asked by myself if he'd read the three I cited in response, he admitted to not having read any of them.

I - along with others - attempted to point out that he'd failed to prove his claim here, and all he could do was complain that we weren't using his definition of "information" (Dembski's).

If you read that part of the discussion from the first post to which I linked, you'll get a good sense of what the problem is, along with some good information/answers from those taking part in the discussion.

Kindest regards,

James
Image
"The Word of God is the Creation we behold and it is in this Word, which no human invention can counterfeit or alter, that God speaketh universally to man."
The Age Of Reason
Sun Sep 30, 2018 1:28 pm
Nesslig20User avatarPosts: 280Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: New information, Genetic entropy and Junk DNA blablabla

So, yesterday I had a conversation with Crispr Cas9 about what I wrote here to check my mistakes. A few hours later Standing for Truth had his conversation with Immutable Destiny.

The conversation starts at 26:16


Standing for Truth then left a commont on my hangout, so I will respond here.


Standing For Truth wrote:Here's what I stated in my discussion tonight with Immutable Destiny and Crispr, and I will say it again. We know AND agree that genomes of several organisms have been sequenced. We also know and hopefully agree that only a small portion of the human genome is used to code for proteins. And so here is the question: what does the remaining “non-coding” DNA do?
If you would read my previous comment, you'll see that I already answered this question.
I wrote:In the functional category we have: Functional parts of protein coding genes, non-coding RNAs, regulatory sequences, SARs, Origins of replication, centromeres, telomeres, and conserved sequences of unknown function is about 8.7% (essential/functional). Non-functional includes transposable elements, viral DNA, pseudogenes and introns is about 65% (non-functional Junk). The remaining 26.3% is non-conserved intergenic regions of unknown function (probably mostly junk too).
Note: There are very few exceptions such as co-opted viral or pseudo genes that have acquired a new function secondarily, but these are just a fraction of a percentage of all these categories. Creationists will often jump on these exceptions which only account for less than 0.0001% of the genome and use that to claim that the entire genome is functional, which is like cherry picking one cherry on a tree and then claiming that the entire tree is edible. And there are also fractions of a percentage on the functional categories that are actually non-functional, so these small differences won’t change these overall percentages.
So 65% is KNOWN to be non-functional...
About 1.0-1.8 % is protein coding DNA, which is part of the larger 8.7% portion that contains non-coding RNA's, regulatory sequences, etc. So we know that there are "non-coding" DNA that do have function (nobody is saying that all non-coding DNA is non functional), but these still amount to just 8.7%. 65% is KNOWN to be non-functional, and the remaining 26.3% is largely unknown. And as the paper by Dan Graur) shows, the genome can only be (at the upper limit) 25% functional, otherwise we would've gone extinct due to genetic load a long time ago. And that is still being very generous. It's most likely just 10-15% functional.


Standing For Truth wrote:I think it's quite evident that evolutionists have assumed and stated that it was inactive, redundant, or left over from the evolutionary process.
That's complete nonsense and a blatant straw man. No scientist has said that all non-coding DNA was non-functional. Junk DNA was never used as a synonym for non-coding DNA.


Standing For Truth wrote:I have also stated many times that based on pre-existing heterozygosity and built in designed variation or built in genetic algorithms, some genes are activated by environmental conditions and not typically expressed. This is evidence of the handiwork of our Creator.
First, you are starting with an assumed conclusion, i.e. there is "build in designed variation or built in genetic algorithms", and then you conclude with your assumed conclusion, i.e. "This is evidence of the handiwork of our creator".That's called Circular Reasoning. You are already beginning with the assumption that there is design to argue for design. That's not evidence at all, except for your poor reasoning skills. Also, how can anything be evidence of a magical man's handiwork? Think about it. God can do literally anything for any reason, meaning there is no possible scenario were we can say "Oh, this wasn't the handiwork of God". This means that God is an unfalsifiable hypothesis, and something that is unfalsifiable can't make specific prediction. Thus, saying that something is evidence for God is utterly meaningless since ANYTHING can be evidence for God by simply stating "That's just how god Didit". That doesn't mean you can't believe that there is a god or that there isn't a god or that god didn't do anything, it's just means that we cannot have evidence for it.


Standing For Truth wrote:I also ask how scientists perform experiments to conclude what functions some genes may have. The answer is that they do "knock-out" experiments. What does this mean? Well, simply put, it means that sections of DNA are removed from the genome of an organism to see what effect its removal will have. This will help us determine what sections of our DNA are doing, specifically in the non protein coding regions. Now here's what's MOST important: We know that extensive knock-out experiments for a mammal have yet to be performed, so it is premature and arrogant to make the claim that the majority of non-coding DNA is non-functional (“junk”).
Now your are doing in the same that John Sanford is doing as Rumraket was describing in a previous post:
Rumraket wrote:So if you show evidence of fitness increase in experiments, he will just say this is consistent with a model where fitness can increase in response to selection in the particular species used and with the particular experimental environment(and then he'll try to deflect by pointing out that many of the mutations are "loss of function" mutations)*, but that his genetic entropy claims are still true for everything else in the wild. So we have to basically prove him wrong with experiments for all 10 million species on Earth in conditions that are pretty much exactly equal to whatever it is in the wild, or he's going to keep claiming genetic entropy must be the case for everything. Essentially he's saying "here's how everything is in my view, prove me wrong". Not understanding that it's HIS job to prove his claims right. :roll:
In response to the overwhelming evidence for the majority (75% at the upper limit) of of the human genome to be non-functional, now you are saying that you wouldn't be convinced that this is the cause UNLESS we do knock out experiments that covers a significant portion of mammalian genomes, completely disregarding other experiments that would demonstrate the same thing. This is an absurd demand to falsify your claim, which was probably the point since you don't want to be proven wrong. There are other means to determine functionality/non-functionality than just knock out experiments. For example, the majority (44%) of our genome consists of transposable elements: transposons, retrotransposons (SINES and LINES). These are easily recognisable and we know what they do, they just jump around the genome or they make copies of themselves. That's it. Most of these are just broken fragments of complete (active) transposable elements. A fraction are active, but they simply jump around. Occasionally, like <0.01%, a (fraction of a) transposable element is evolutionarily co-opted for a new purpose, like in the evolution of adaptive immune systems.
Image
But this doesn't support your assertions, because (1) coopted TE's consists of just a fraction of a percentage of the transposable elements and (2) it supports the evolutionary origins of these complex biological systems.


Standing For Truth wrote:Now in regards to the ENCODE project that is being talked about in this hangout, the ENCODE project examined 1% of the non-coding DNA of the human genome for possible function. What did they find? They found that at least 80% of the noncoding DNA was transcribed into RNA, SUGGESTING function.
WRONG!! First, you are talking about the ENCODE pilot project that only examined 1% of the non-coding regions. The ENCODE project with that "80% functional" result examined essentially the entire genome. Second, even transcription doesn't suggest function. Random DNA sequences can easily become promotor like with a few mutations, which is a factor that causes spurious transcription. In fact, natural selection has to keep most of our DNA from being promotor like to avoid too much spurious transcription.
There are also many pseudogenes that are transcribed, like the human MYH16 gene, which is a broken primate gene that codes for jaw muscle proteins. It even makes a protein, but it's broken and it doesn't work (It's non functional), which is the reason why our jaw muscles are so pathetic compared to other primates (Rhetorical question: why would we have broken monkey genes?). So even though it is transcribed and even though it is translated, it is still non-functional. Secondly, Encode did not define functional as "anything that is transcribed into RNA". This was their definition of "biochemical function"
The ENCODE Project Consortium, 2012 wrote:Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).
Notice that in order to qualify as "functional" it doesn't necessarily have to be transcribed. As PZ Myers noted:
PZ Myers wrote:That isn’t function. That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.
And as Jackson Wheat said to you. It's like saying that a piece of gum under your shoe is functional with respect to your shoe, because it sticks to it. And there is good reason to think that the leaders of the ENCODE project deliberately used their misleading usage of "biochemical functional" as a PR stunt to get the attention of the journalists. And unfortunately, they were successful in getting that attention.
Laurence A. Moran wrote:See What did the ENCODE Consortium say in 2012? for more details on what the ENCODE Consortium leaders said, and did, when their papers came out. The bottom line is that these leaders knew exactly what they were doing and why. By saying they have assigned biochemical functions for 80% of the genome they knew that this would be the headline. They knew that journalists and publicists would interpret this to mean the end of junk DNA. Most of ENCODE leaders actually believed it. That's exactly what happened...aided and abetted by the ENCODE Consortium, the journals Nature and Science, and gullible science journalists all over the world.
In other words, don't read too much into this 80% functionality of ENCODE nonsense.


Standing For Truth wrote:It has been found that the non-coding regions of genomes correlate with biological complexity better than the protein coding regions, suggesting that the non-coding regions do indeed carry significant information, probably for regulatory activity.
Eh? I going to need a citation for that one....
EDIT after posting:
Thanks to someone called "Ration alMind" I got the paper that StandingForTruth is referring to. This is what he told me about it.
Ration alMind wrote:he’s referring to the finding of papers like this one by John Mattick, who publishes tirelessly to insist that huge swathes of our genome is functional. While it’s true that this correlation exists, it’s premature to say that this means that most or all of the non-coding regions are functional. For example, it could be that 10% of non-coding DNA is consistently functional, so in order to get an extra 1% functional non-coding DNA you have to increase your non-coding genome size by 10%. This would produce the same correlation. Another glaring gap in this paper and others like it is the failure to consider population dynamics at all. It seems likely that the reason more complex organisms have more non-coding DNA is because more complex organisms (e.g. humans) tend to have smaller population sizes and longer generation times that less complex ones (e.g. bacteria) - this places different pressures on the genome. Bacteria are able to reduce their genome size to the bare minimum to increase efficiency, since their population sizes can handle it. Humans don’t have the same luxury - the selection coefficients to remove non-coding DNA are too low to efficiently remove extraneous sequences, and as you’ve pointed out with Graur’s 2017 paper, we can’t have anywhere close to a 100% functional genome, so a lot of non-coding DNA is needed as a “buffer”.
....and it better be a good one since there are numerous indications that this is completely wrong. For example, another reason for why most of our DNA is most likely non-functional ("junk") (a reason I didn't touch because I thought my post was already overkill) is the cleverly named "onion test". It is named after the observation that among the onion genus (Allium) there are species that have 2 times the amount of DNA that humans, another one has 5 times the amount of DNA and another one has 9 times of the amount.
T. Ryan Gregory wrote:Image
Left, A. altyncolicum (7 pg = 2 times human DNA); centre, A. cepa (17 pg = 5 times human DNA); right, A. ursinum (31.5 pg = 9 times human DNA).
So the question is, if you think that most of the genome is functional and the amount is correlated with biological complexity, then why do some onions have several times more DNA than us? And if you think that onions are actually special, they do require that amount, then what explains this range in genome sizes from 7 pg to 31.5 pg among the species of the onion genus? Especially considering that these species belong to the same genus and are thus very similar to each other. And this conundrum is made even worse when we consider other species. Lungfishes have 40 times more DNA than us. Salamander genomes fall between a range of 4 to 35 times more DNA and some single celled eukaryotes have over 200 times the human genome. One the other extreme end, the puffer fish has almost no "Junk" DNA (transposable elements are rare in Fugu). If "junk DNA" like transposable elements are so important, then how can they survive without it?
Genome Size and “The Onion Test" wrote:There are several key points to be understood regarding genome size diversity among eukaryotes and its relationship to the concept of junk DNA. First, genome size varies enormously among species [18], [19]: at least 7,000-fold among animals and 350-fold even within vertebrates. Second, genome size varies independently of intuitive notions of organism complexity or presumed number of protein-coding genes (Figure 1). For example, a human genome contains eight times more DNA than that of a pufferfish but is 40 times smaller than that of a lungfish. Third, organisms that have very large genomes are not few in number or outliers—for example, of the >200 salamander genomes analyzed thus far, all are between four and 35 times larger than the human genome [18]. Fourth, even closely related species with very similar biological properties and the same ploidy level can differ significantly in genome size.
Image
Figure 1. Summary of haploid nuclear DNA contents (“genome sizes”) for various groups of eukaryotes.
This graph is based on data for about 10,000 species [18], [19]. There is a wide range in genome sizes even among developmentally similar species, and there is no correspondence between genome size and general organism complexity. Humans, which have an average-sized genome for a mammal, are indicated by a star. Note the logarithmic scale.
These observations pose an important challenge to any claim that most eukaryotic DNA is functional at the organism level. This logic is perhaps best illustrated by invoking “the onion test” [20]. The domestic onion, Allium cepa, is a diploid plant (2n = 16) with a haploid genome size of roughly 16 billion base pairs (16 Gbp), or about five times larger than humans. Although any number of species with large genomes could be chosen for such a comparison, the onion test simply asks: if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human? Importantly, the comparison is not restricted to onions versus humans. It could as easily be between pufferfish and lungfish, which differ by ∼350-fold, or members of the genus Allium, which have more than a 4-fold range in genome size that is not the result of polyploidy [21].
In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades [18].
The simple answer to all of this is that most of the genome is non-funciotnal.


Standing For Truth wrote:Now why do I say that these regions do play important roles in the placenta and embryo? I talked about this tonight with Immutable Destiny, and therefore, I highly recommend watching it.
I have watched some of it and I am not impressed. For one thing, you presented a quote from Michael Ruse wherein he supposedly said that evolution is a religion. Later at this time stamp 1:00:26 You finally presented your source for this quote...and this is what it says:
Michael Ruse wrote:
Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion — a full-fledged alternative to Christianity, with meaning and morality. I am an ardent evolutionist and an ex-Christian, but I must admit that in this one complaint — and Mr. Gish [Duane T. Gish the Creation Scientist] is but one of many to make it — the literalists are absolutely right. Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today.
Well, what quote of yours do you want to have on your gravestone?!
I think this paragraph, the introduction to a book review (for which I was never paid) in a Canadian newspaper some 10 or so years ago, has received more attention and more repetition (especially on the Internet) than anything else I have ever written. More even than my claim that morality is an illusion put in place by the genes to make us social animals. No matter that I qualified it then and have qualified it before and ever since. “Ruse recants! Evolution is a religion! Read all about it!” Or more accurately, don’t read all about it, because then you might find that that is not quite all that I had to say.
How can you possibly quote mine someone, while that person is correcting the quote mine right in the next paragraph?. Remember what you said about creationists quote mining Darwin about the evolution of the eye and they ignored the piece he wrote right after? And remember when you were insisting that you aren't doing the same thing? Well, you did something that's even worse. What an embarrassment.


Standing For Truth wrote:But ENCODE did not look at the portions of the genome involved exclusively in development; such DNA would only have function then.The trajectory of discovery favors genome-wide functionality.
What trajectory of discovery? You don't cite any discovery. All you have done is parroting the nonsense of the ENCODE 80% functionality (point refuted a thousand times), and make numerous assertions that are not substantiated by anything and often easily proven to be erroneous.


Standing For Truth wrote:So what does all this mean? And why is this consistent with Biblical Creation and Common Design.
Once again, if you believe in a magical character that can literally do anything, then anything can be consistent with your pet beliefs. Whatever happens is just the way that God did it. This means that there is no meaning behind any of it.


Standing For Truth wrote:We can infer and conclude that non-coding DNA is probably involved in regulatory functions (when and how fast to make specific proteins), embryonic development, the timings of protein manufacture, stagings of proteins for construction of molecular machines, switches, etc. Some non-coding DNA is transcribed into short chain micro-RNA that binds to specific sites in DNA thereby regulating transcription of those sites. Some RNA is involved in the splicing of mRNA before it is translated in the ribosome.
An inference based on nothing is not worthy to be considered.


Standing For Truth wrote:We are just beginning to understand the development process, how coding and non-coding DNA coordinate when, where, and how structures are sequentially put in place to produce a fully functional organism. So all in all, this suggests that our genome is both Poly-functional AND Poly-Constrained. This means that any change no matter how small it is will ultimately be deleterious.
Considering fact that all the evidence that we have examined so far points towards the exact opposite conclusion that you are asserting here. And considering the fact that you are arguing in a circle, starting with an assumed conclusion. This means that all you have said so far is nothing but fallacious and unsupported nonsense or fallacious nonsense already disproved. For the most part, it is the latter.
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Last edited by Nesslig20 on Fri Oct 05, 2018 9:36 pm, edited 13 times in total.
Sun Sep 30, 2018 2:02 pm
SparhafocPosts: 2525Joined: Fri Jun 23, 2017 6:48 am

Post Re: New information, Genetic entropy and Junk DNA blablabla

Rumraket wrote:Outstanding post Nesslig.



High praise. Marking thread to read for when my head consists of more than 3 pounds of disparate mush.
"a reprehensible human being"
Beliefs are, by definition, things we don't know to be true.
Sun Sep 30, 2018 3:32 pm
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