Wednesday, August 28, 2013

The Dark Matter of ENCODE.


Now for something a bit different.

I suppose the latest advances in molecular biology and genetics are not really subject of interest to the majority of the manosphere. But, for its more religious and traditionalist members, some of the recent findings of the ENCODE project look like they will have more than just scientific significance.

One of the curious paradoxes of modern genetics is that most of genome seems to be composed of of what appeared to be non-functional "junk" . Roughly, mainstream scientific wisdom has determined that about 4% of genetic material codes for the proteins that build up our body, the rest of the stuff.............well....... we don't know. Scientists, in attempting to work out what this DNA does have performed experiements where they have "knocked out" some of this junk DNA, with the  offspring animals not seeming to suffer any ill effects from the deletion, confirming the notion of junk DNA.  Molecular Darwinism too,  is Ok with the idea, since it the random nature of genetic mutations would imply that not all our DNA be functional. My understanding of the matter is that mathematical models of Darwinian evolution predict fifteen percent of DNA to be "functional" and the rest to be junk.

Indeed, our favorite mass-man/cognitive miser evolutionary theoretician Richard Dawkins loved junk DNA. He used its existence to bash away at those who supported some from of intelligent design. Thundering from the pulpit, in 2009 he said;
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us... 
Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes."
Now, this idea of junk DNA has always struck me as odd. One thing that struck me in my undergraduate years in biology was the notion that there was still so much to learn about, especially with regard to genetics, and that any definitve pronouncements on the matter were likely to be rash. But medicine and science have a good tradition of confidently pronouncing on subjects they woefully ignorant in. In the old days, when doctors didn't know about the functioning of the spleen or thymus, they declared these organs vestigial and non-functional and removed them with abandon; it was only years later that they were discovered to be vital for the development of immunity and the protection against certain types of the disease. My studies left me with the impression, which I still hold to this day, that there is very little waste when it comes to molecular machinery and that the system is very efficient.

Some other people must have had this notion as well and they decided to go "poking around" this junk DNA. In 2007 the U.S. National Human Genome Project Research Institute started and investigation called ENCODE program. It involved over four hundred scientists and its findings, released late last year, are simply stunning. Roughly 80% of the junk is "functional". (The other 20% was "silent" most likely, in my opinion, due to technical limitations and in due time will eventually be found to be "functional"). It appears from the project that  there is very little "junk." and the "junk DNA is responsible for the regulation of our genes through through a variety of mechanisms. One of the major ones being the the production  non coding RNA, a class of molecules whose significance has only appreciated recently.

The findings have unleashed some uncharacteristically sarcastic and bitter responses from the Darwinian pit bulls, such as is not seen in the clinical and staid world of molecular genetics. But they have a point, and the point concerns the definition of "functionality".  The Darwinians assert that the only thing that the ENCODE project have discovered is biochemical activity in bits of the junk DNA and not actual biochemical function. What they are arguing is that the discovered activity is nothing more than "transcriptional noise" or random biochemical activity. What's really surprising is the vehemence with which they are making their claims. The ENCODE scientists concede that they haven't demonstrate "function" as yet but it's very likely that the activity is functional.

But the data is beginning to surge in.

Prader Willi Syndrome and some variants of autism have now been found to be due to defects in the production of long non coding RNA as have other illnesses. Long non coding RNA seems to determine our brain architecture and neurological functioning.  As well as our embryonic development. Several cancers have now been linked to abnormalities of ncRNA expression.

More importantly, what appears to be one of the most damning papers for the Darwinians has just been released. (You're at the cutting edge of science here!) It appears to strongly vindicate the researchers of ENCODE and the abstract deserves to be quoted in full:
Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional. Here we directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project. Furthermore, using de novo transcriptome assembly of this RNA-seq data, we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell, significantly expanding upon prior lincRNA annotation sets. These lincRNAs are specifically regulated and conserved rather than being the product of transcriptional noise [ED]. In addition, lincRNAs are strongly enriched for trait-associated SNPs suggesting a new mechanism by which intergenic trait-associated regions may function. These findings will enable the discovery and interrogation of novel intergenic functional elements.
Game. Set. Match.

The vehemence which the Darwinian Atheists have attacked the ENCODE project is more than just a matter of defending a competing hypothesis, rather, what perceptive players have recognised is that deep philosophical issues are at stake here. Make no mistake, this is a Galileo moment.

John Mattick, a world renowned Australian researcher at the forefront of non-coding RNA research replied to the critics of ENCODE:
There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase “evolution-free gospel” in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006). [Ed] This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011). 
and
In any case, that our understanding of the remarkably complex processes underlying the molecular evolution of life, including the likely evolution of evolvability (Mattick 2009c), is incomplete should not be surprising. With the emergence of transformative technologies, such as massively parallel sequencing, which provide tools to view the inner molecular workings of the genome that were inconceivable less than a decade ago, it is as important as ever that we as scientists remain open to observations that challenge even the most fundamental paradigms that exist within biology today [Ed]
Mattick is not a creationist, he believes that these new findings are compatible with the "broad tenants" of evolutionary theory, but he does recognise the current Darwinian evolutionary understandings are seriously flawed. Make no mistake, one of the foundations of modernism has been seriously undermined by the latest findings in molecular genetics.

And what of our friend Mr Dawkins, what's his take on the new findings with regard to junk DNA?
"I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that's awkward for Darwinism. Quite the contrary it's exactly what a Darwinist would hope for[ED: See above quote], to find usefulness in the living world....

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it's doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk."
Seriously, sometimes you've just got to stand back and let them hang themselves.

HT: Egnorance blog for the Dawkins quotes

Finally, this post is dedicated to Simon Grey who feels there may be a bit of defeatism in my recent writings. Rest assured. There's still some fight in the old bastard.

Bonus.  John Mattick on Vimeo

19 comments:

Mark In Mayenne said...

Yep, the idea of junk DNA has always struck me as odd too.

Igniss said...

Just poking some holes in evolutionary theory doesn't in any way prove or even indicate intelligent design. There is still the contest of one theory that has explained almost everything vs. the other theory that has explained almost nothing. Which should we be inclined to believe, even if a hundred things staples like junk DNA were successfully disproved?

The Social Pathologist said...

Igniss

This isn't a little hole that they've poked into the theory. They've virtually torn it to shreds.

To quote Dan Graur, one of the fiercest critics of ENCODE,

"Two problems: (1)If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long undirected evolutionary process, cannot explain the human genome. If, on the other hand, organisms are designed, the all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right then Evolution is wrong."

Even the critics of ENCODE recognise its significance if true which is looking increasingly like it is. I'm not laying the hyperbole when I say this is a huge paradigm shift in human knowledge. This is a Galileo moment.

Evolutionary theory has been able to thrive in our ignorance of basic genetic process and crude biochemistry. For years we were taught that chimpanzees and humans had heaps of common DNA and yet microanalysis of DNA yeild this

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653425/

We see that the chimpanzee and human Y Chromosomes are "markedly divergent in structure and gene content". The theory predicts similarities not differences.

None of this, btw proves intelligent design right what it does prove however, that mainstream understanding of evolution is wrong.

Anonymous said...

Seems counterintuitive that the theory of evolution would require an excess. Everything in the universe subject to various opposing forces tends towards a minimal "perfect balance". I also wouldn't expect any theory about the history of the species to be adequate until we have a much more thorough understanding of the organism right in front of us. There was no point making hypotheses about "junk DNA" until the matter was thoroughly investigated

Drew said...

The point of science and theory is to make useful predictions. New theories and explanations gain favor when they make several correct predictions in a row, that the current accepted knowledge completely misses.

I remember the ID guys years and years ago making a prediction that "junk DNA" will turn out to be functional.

Here's a big win for the ID guys. Hopefully they can use ID framework to come up with additional useful theories and test them.

The Social Pathologist said...

Seems counterintuitive that the theory of evolution would require an excess.

Not really. If you consider random GATC combinations as noise, given enough a time a "signal" i.e a gene is bound to become randomly generated. Therefore, evolution predicts that amongst any signal there will be a fair amount of noise present. Therefore a low signal to noise ratio is the biochemical signature of evolution through random mutation.

Simon Grey said...

Well I'm glad to see there's still some fight left in you. I'd become a little worried when you were saying that the only options for a conservative revival were either nil or the apocalypse. At any rate, hope things are going well for you and that you can keep posting regularly, preferably with less doom and gloom ;)

candide3 said...

Pfui. There is no monopoly on stupidity. Lots of people have been spent their careers talking about junk DNA being junk, and now that they have been proved wrong, they have to recant? No way, they'll double down on the junk stuff and make all other evolutionists look silly. Anyway it has long been known in the scientific circles that some of the supposed "junk" has functions and that much of the other "junk" is probably functional too. It's the popularizers of science, that cursed breed, who promote drastically simplified versions of decades-old theories as the current state of the art. I still remember how my 80s geography schoolbook was based upon the geosyncline theory.

As for the Y chromosome, the abstract says We then compared the MSYs of the two species and found that they differ radically in sequence structure and gene content, implying rapid evolution during the past 6 million years. So primates have been evolving rapidly during the past 6 million years. This is news?

candide3 said...

Slumlord, you'd better read the whole text of that Y-chromosome article — it's available on pubmed for free — because it says i.a. we aligned and compared the nucleotide sequences of the chimpanzee and human MSYs. As expected, we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%)15. Surprisingly, however, > 30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa. In this respect the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks an homologous, alignable counterpart in humans, and vice versa. and we previously discovered that the chimpanzee X-degenerate regions had lost four of 16 genes through inactivating mutations, while the human X-degenerate regions had not lost any genes since the time of the last common ancestor9. We also reported that two X-transposed genes in the human MSY had been acquired since the time of the last common ancestor. This article won't bury "The Descent of Man", no it won't.

The Social Pathologist said...

@candide3

@It's not just the fact of the rate of change, rather the nature of the change itself. What we're seeing is not some gradual genetic changes selected for by enviormental pressures, but "churn and chop" of the genome.

But I guess you didn't get the significance of that paper. Why does only the Y Genome "churn and chop" and not the others? Are there two different evolutionary mechanisms at play or does evolution affect different chromosomes at different rates?

Oh, and as for that 98% thing.

98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%)

You see, the guys who ran that oft quoted study were only comparing monkey protein coding genes with human protein coding genes. They ignored the "junk" because, hey! it's junk and not that important.

(Also, if you read the study carefully, you will see that the the only chromosomes comprehensively mapped in both chimp and human are chromosome Y and 21, the detail of the rest hasn't been worked out.)

Anyway other bright sparks have had a look into the matter and in this paper;

http://www.mobilednajournal.com/content/2/1/13.

The researchers found considerable variation between human and chimp dna in the "junk" regions.

I'm not sure if you looked at the Mattick video I linked to, but Mattick describes what appears to be the new biological picture of life.

Basically, there are about 20,000 different types of proteins in the biosphere with quite a degree of similarity amongst species. Where they differ is in their gene expression as modulated by their junk dna.

Humans and sponges share a remarkable amount of similarity in their protein building blocks but not in how these blocks are arranged.

Mainstream Darwinism's days are numbered.

candide3 said...

> You see, the guys who ran that oft quoted study were only comparing monkey protein coding genes with human protein coding genes. They ignored the "junk" because, hey! it's junk and not that important.
You won't allow that they might have had other reasons? To name just a couple, 1) it is much, much simpler to compare coding regions, because they suffer much less from genomic rearrangements and 2) it is much, much simpler to identify their opposite parts in human vs animal genome. When faced with a complex problem, do the easy part first, then go on from there. Of course, some popularizers are apt to forget the latter part, and start demanding a UN seat for chimps on the basis of that 98.5% figure, or something equally stupid.
> Are there two different evolutionary mechanisms at play
Of course! Does the word "autosomal" ring a bell? The Y chromosome is special, since only males have it and it is inherited only in the male line. Same goes for mitochondrial genome, except it is inherited in the female line.
> does evolution affect different chromosomes at different rates?
Yes. Nothing new or secret about that. You can read about it on Wikipedia. The study you quote mentions it as well.
> Basically, there are about 20,000 different types of proteins in the biosphere with quite a degree of similarity amongst species. Where they differ is in their gene expression as modulated by their junk dna.
So what? Does natural selection work only on the proteins? Does mutation only occur in the coding regions? Pfui.
> Mainstream Darwinism's days are numbered.
Sorry to disappoint, but the thing you think of as "Mainstream Darwinism" has been pushing up the daisies for 50-60-70 years, if it ever existed at all. In particular, it has long been known that many, probably most, regulator sequences lie within non-coding regions, and not necessarily close to their coding regions either. Pick up any serious introductory biochemistry text, e.g. this one, it will be there. It is not revolutionary or anything, people have been exploring this for at least a couple of decades already. It is extremely difficult to figure out, though.

The Social Pathologist said...

@Candide

You won't allow that they might have had other reasons?

Yes I would, but it was a combox reply. I've got no problems with doing the simple first. But a lot of pro-Darwin biology seems to be doing a simplified experiment and then making comprehensive claims. The devil with this stuff is always in the details.


Of course! Does the word "autosomal" ring a bell?

I vaguely remember reading about it somewhere. Still, I can't remember the laws of physics or biochemistry only applying to certain chromosomes and not others.

So what? Does natural selection work only on the proteins? Does mutation only occur in the coding regions?

Maybe natural selection is not the predominant mechanism at play here.

Mainstream Darwinism" has been pushing up the daisies for 50-60-70 years

Dawkins et al would disagree with you.

candide3 said...

> But a lot of pro-Darwin biology seems to be doing a simplified experiment and then making comprehensive claims.
That's partly true about science in general; scientists are not saints and many love making comprehensive claims, the comprehensiver the better. It's an occupational hazard for senior applied physicists in minor colleges to start debunking relativity or quantum theory in their old age. However mostly it's the fault of inept popularizers, scientific marketers and public relations people. The former seem to think that showing the messy side of science to the laymen harms its prestige, and they are often not that great at their science too, repeating the (naturally) simplified stuff they learned in their 200-level courses decades ago. About the latter the less said the better.
>> Does the word "autosomal" ring a bell?
> I vaguely remember reading about it somewhere. Still, I can't remember the laws of physics or biochemistry only applying to certain chromosomes and not others.
Come on, you can't expect me to take this seriously. The laws of physics and biochemistry are the same, but so what? The same laws of physics apply to diamond and graphite, and yet diamond is not graphite. The same laws of biochemistry apply to tomatoes and cows, and yet tomatoes are not cows. If you are genuinely interested, look up "autosomal" and "Y chromosome" in the encyclopedia. For a teaser question, consider why most two-sex species (exclude those that care for their young) have a 1:1 sex ratio. Why does fish produce so many expensive males? For sperm production, 1:100 would be perfectly fine, as the many Wolbachia-dominated species of insects show.
>> So what? Does natural selection work only on the proteins? Does mutation only occur in the coding regions?
> Maybe natural selection is not the predominant mechanism at play here.
Occam's razor. What's so special about proteins?
> Dawkins et al would disagree with you.
To hell with Dawkins. I haven't read him anyway. I did read "The Molecular Biology of the Cell" though. It weighs enough to kill a man with.

Anonymous said...

Splendid article S.P., evolutionists consistently show themselves to be either fools, as in the case of those doctors who so confidently declared various organs to be vestigial; or else outright malicious liars, as in the case of those who loudly proclaimed the discovery of fossils supposedly belonging to so-called "ape-men" piltdown man, nebraska man &c., &c. They are worthy only of the mockery & contempt which they so liberally pour out upon the remnant of the faithful. May the Kingship of Our Lord Jesus Christ be set up over every nation.

mdavid said...

Mainstream Darwinism's days are numbered.

I don't see how junk DNA means anything to Darwinian theory. Darwinian evolution is as obvious as your children having blue eyes because you have blue eyes.

Junk DNA makes complete sense with random evolution, because it allows for much faster change. Personally, I'm surprised DNA hasn't more "information storage" options.

I find these discussions more amusing than anything else; lots of heat and little light from most atheists and a good many who claim to believe in God (but their lack of faith in His methods is disturbing). I can't see how Darwinian science says one peep about creation or God in any way (well, nothing except that God is clever but not malicious...). And I don't see how junk DNA says anything meaningful about the root process of evolution Darwin (and many others before and after) have developed. It's simple common sense.

The Social Pathologist said...

@Candide3

Come on, you can't expect me to take this seriously

It was some Australian irony. I know the difference between Autosomes and allosome (sex chromosomes)

Interesting bug wolbachia but a distraction from the main point. ie. is why is the human Y chromosome so different to the chimp one, especially when we are meant to be direct ancestors? DNA amongst close relatives should be quite alike (according to Darwinian theory), and yet it isn't.

What so special about the proteins?
I'm not sure what your getting at here, but the proteins themselves seem resistant to evolutionary change. Presumably because mutant protein forms aren't really compatible with survival or healthy functioning,........

or

perhaps mutation rate calculations are based on false assumptions. It may just be that mutation rates in non protein coding regions may express natural variability instead of deviation from the norm. I don't know, it's only speculation.

Anon, thanks.


mdavid.

Darwinian science provides a good explanation an origin of life without the necessity of a God. Darwin is huge buttress to atheism and the undermining of it undermines atheism as well. This is why these findings are so important.

Personally, I'm surprised DNA hasn't more "information storage" options.

We still know so little about the operation of the cell that I wouldn't be so definitive yet as to what DNA can or can't do. Interesting times ahead.

mdavid said...

SP, Darwinian science provides a good explanation an origin of life without the necessity of a God. Darwin is huge buttress to atheism and the undermining of it undermines atheism as well. This is why these findings are so important.

I'm lost at sea, again. Points:

1. Darwinian science shows how life changes, but how does that get one anywhere "explaining" creation or self awareness? That's like saying because the world is in orbit and we know when the sun will rise that speaks about God? It's a big mystery to me. I've never understood how anyone can think Darwinian science "explains"; it merely provides us with rules like any science. If anything, Darwinian evolution adds more complexity and wonder to the theory of a first cause, not less.

2. Darwinian science being a huge buttress to atheism is bizarre. Only really uneducated people could think so. My thought: why pay attention to idiots, be they atheist or theist?

3. I really don't get how the ...undermining of [Darwin] undermines atheism.... Darwin merely explored the material world and had nothing to say about God. At best, the concept of science as "rule based" seems to jive better with theism than atheism. But that's merely a spasm; Darwinism and all science I've seen is silent about God, one way or the other. IMO, God likes the idea of intelligent people having a free choice at faith.

Jack said...

Great post, Soc. Please do keep it up. I've been feeling a bit the defeatist myself of late.

I recall the 'golden mean' used as proof of intelligent design. See:

https://math.temple.edu/~reich/Fib/fibo.html

ElectricAngel said...

@SP,

Another recent article on epigenetics talks some about the usefulness of the "junk": http://www.psmag.com/health/the-social-life-of-genes-64616/

If you read chapters 3 and 24 of George Gilder's new book Knowledge and Power, you'll get an information-theory-based critique of materialist science that aligns with this post. Email me if you want them.