Is functional information in DNA always conserved? (Part one)

_{Giuseppe Puccio

May 18, 2014

Intelligent Design}

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Conservation of sequence in the course of natural history has always been considered a sign of function. But does function always coincide with sequence conservation? And are there other important aspects which must be considered? This topic has been discussed recently with some passion here, so I will dedicate a series of two posts to it, in the hope that we can base our discussions on reliable data. I apologize in advance if some of the following discussion is necessarily rather technical.

In general, in evolutionary analysis, conservation is considered a sign of function. Protein coding genes which are more strictly conserved in the course of time are usually considered as having greater functional constraint than those genes which change more. The same is supposed to be true for non coding sequences, although the topic is much more controversial.

So, we start here considering how much of the human genome is conserved, and how that conservation relates to function. These will be the first two points in the discussion.

1) How much of the human genome is made of conserved sequences?

Luckily, this is a point which is well understood. After all, conservation can be evaluated objectively aligning the genomes of different species, and that has already been done with enough precision.

However, it is important to remember that the result can be somewhat different according to how we define conservation, and according to the method we use to measure it. That is perfectly normal.

A very complete paper about sequence conservation in genomes is the following:

Adam Siepel, Gill Bejerano, Jakob S. Pedersen, et al.

”Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes”

In that paper, they evaluate conservation in vertebrate genomes. Just to make it short, they find about 4.3% of conservation in the human genome (referred to vertebrates), while allowing that:

These numbers are somewhat sensitive to the methods used for parameter estimation. Various different methods produced coverage estimates of 2.8% – 8.1% for the vertebrates, 36.9% – 53.1% for the insects, 18.4% – 36.6% for the worms, and 46.5% -67.6% for the yeasts (see Supplemental material). Note that the vertebrate coverage is similar to recent estimates of 5% – 8% for the share of the human genome that is under purifying selection (Chiaromonte et al. 2003; Roskinetal. 2003; Cooper et al. 2004), despite the use of quite different methods and datasets.

So, we can say that with most methods the percentage of the human genome which is conserved is about 3 – 8%.

If we look carefully at Figure 3 in the same paper, and in particular to the data about vertebrates, we find other interesting information:

a) Protein coding regions (exons, in red) are highly conserved, about 68%, but they are only 18% of the conserved regions.

b) Introns are less conserved, almost 5%, and they are 28.5% of the conserved regions.

c) Unannotated regions (the rest of non coding DNA) are even less conserved, about 2,5%, and they are 41.2% of the conserved regions.

Other gene associated sequences (5’ UTR, 3’ UTR, etc.) represent smaller fractions.

So, there is no doubt that non coding DNA is less conserved than coding DNA (less than 5% versus 68%), but there is no doubt that most of conserved DNA is non coding (about 70%).

Another important point is that we are discussing here general conservation. The same paper analyzes also highly conserved elements (HCEs). They cover only 0.14% of the human genome, a much smaller fraction: About 42% of these were in gene coding or gene associated regions, and about 58% in non coding regions.

Finally, there is an even more restricted category, ultra conserved elements (UCEs), with 100% identity, which is described in this paper:

G. Bejerano et al.: “Ultraconserved elements in the human genome”.

2004 May 28;304(5675):1321-5. Epub 2004 May 6.

There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.

This is an even smaller fraction of the genome.

2) Is there functional DNA which is not conserved, in the human genome?

Certainly, and a lot of it!

Everybody knows that the ENCODE project has found that most of human genome is transcribed. That does not necessarily mean that it is functional, as many have pointed out.

A very recent paper from the people at ENCODE discusses the problem of function. It is:

“Defining functional DNA elements in the human genome”

The authors in that paper use three different approaches to infer function in the human genome:

a) Evolutionary approach. That means conservation. They start with what we have already discussed at point 1, but they refer to mammalian conservation, which can be expected to be somewhat higher than vertebrate conservation. They comment:

The lower bound estimate that 5% of the human genome has been under evolutionary constraint was based on the excess conservation observed in mammalian alignments (2, 3, 87) relative to a neutral reference (typically ancestral repeats, small introns, or fourfold degenerate codon positions). However, estimates that incorporate alternate references, shape-based constraint (88), evolutionary turnover (89), or lineage-specific constraint (90) each suggests roughly two to three times more constraint than previously (12–15%), and their union might be even larger as they each correct different aspects of alignment-based excess constraint. Moreover, the mutation rate estimates of the human genome are still uncertain and surprisingly low (91) and not inconsistent with a larger fraction of the genome under relatively weaker constraint (92). Although still weakly powered, human population studies suggest that an additional 4–11% of the genome may be under lineage-specific constraint after specifically excluding protein coding regions (90, 92, 93), and these numbers may also increase as our ability to detect human constraint increases with additional human genomes. Thus, revised models, lineage-specific constraint, and additional datasets may further increase evolution-based estimates.

Now, let’s look at Fig. 1 in the paper, a Venn diagram which sums up the results of a detailed analysis of available data. I have checked the exact numbers on which the figure is based in the Supporting Information file. the purple circle is the protein coding fraction in the genome, about 1.25%. The evolutionary conserved fraction of human genome is the red circle, and it is 7.38% of the whole genome. The greater part of it (6.33%) is non coding DNA. That is in good accord with what reported at point 1.

b) Genetic approach. With that, the authors mean proof of modifications in phenotype with genetic alterations of the sequence. This is the “gold standard” of function. It means that function is certainly there.

The subset of genome for which there is genetic confirmation of function is the green area. I have not found the exact numbers for it in the paper, but I would say that it is about 15%. It can be seen that it somewhat overlaps the conserved circle, but at least 50% of it is not conserved and is not protein coding. As this is the gold standard, we have here a significant portion of non coding DNA which is not conserved while being certainly functional.

c) Biochemical approach. This is the traditional ENCODE approach, the one with indicates possible function in 80% of the genome. It is based on many biochemical evidences, which are explained in the paper.The blue areas indeed include about 80% of the whole genome.

However, the authors divided the blue area in three subsets, according to the level of activity detected. The dark blue area is the area with high level of activity. So, let’s consider only that subsets, leaving the other two as controversial, at present.

For the dark blue area (15.56%), evidence at transcription level and at other biochemical levels is very high. So, the inference of function can be considered very reliable. As can be seen, the dark blue area overlaps the green area and the red circle, but still about two thirds of it are out of both.

If we consider the union of these three different subsets (red circle, green area, dark blue area) we have the total portion of the genome for which there is convincing evidence of function, at the present state. It is about 24%, and most of it is non coding.

Moreover, the percentage of functional genome can only increase in time. While the red circle (conserved elements) and the purple circle (protein coding genes) are more or less final, the green area (gold standard) can only expand, and it can potentially confirm the function of parts of the blue areas (including those with lower activity).

So, to sum up:

– At the present state of knowledge, function is extremely likely for 24% of the human genome.

– For about 15% (green area) it is certain.

– Most of that functional genome (about 95% of it) is non coding.

– Most of that functional genome (about 70% of it) is not conserved.

But that is not all. There are two other important points which must be addressed, and which are even more intriguing. They are:

3) Conserved function which does not imply conserved sequence.

4) Function which requires non conservation of sequence.

I will deal with them in the second part of this discussion.

Comments

Piotr:
I have given you one such thing.
No you haven't. You have simply listed an observed fact of nature. There isn't anything in evolutionary theory that would allow us to predict or expect one way or another. Eric Anderson

Piotr, I have explained why some organisms have more DNA than others. Your willful ignorance is very telling. If a designer starts with a bird that can fly and then wants to get a bird that cannot, there is most likely more regulation required which requires more DNA. No coincidence at all. Joe

Nonsense. Not the facts; the “not surprisingly” statement. There isn’t a single thing in evolutionary theory that would argue for organism X to have a larger genome than organism Y. There wouldn’t be any “surprise” if the facts were precisely the opposite of what they are. Whatever it is, it is.
I have given you one such thing. So it's pure coincidence that crocodiles have 2-3 times as much DNA as birds, and bats have genomes 0.5-0.6 times the typical mammalian size; and among the birds high C-value are correlated with flightlessness. Yeah, it could be "precisely the opposite" -- but somehow it isn't. Piotr

Piotr:
Not surprisingly, flightless ratites have bigger genomes . . .
Nonsense. Not the facts; the "not surprisingly" statement. There isn't a single thing in evolutionary theory that would argue for organism X to have a larger genome than organism Y. There wouldn't be any "surprise" if the facts were precisely the opposite of what they are. Whatever it is, it is.
The cost of DNA maintenance and replication is low. Larger than zero, of course, but not large enough for negative selection to override drift.
As I said, the junk DNA proponent can always fall back to the circular argument . . . -----
Yep, but it wasn’t designed by engineers (which is probably just as well).
Well, that's precisely the question at issue, isn't it. Of course we could always just assert -- as a matter of philosophical preference -- that the systems in question weren't designed. And we could "explain" the existence of such systems by saying that some stuff works and sticks around, other stuff doesn't work and doesn't stick around, yet other stuff doesn't work but still sticks around. The Great Evolutionary Explanation: Stuff Happens. Eric Anderson

The number of genes isn't as important as the number of gene products. Alternative gene splicing can do more with less. Overlapping genes can also do more with less. Naturally organisms that don't have that designed into their system would have more DNA. I bet ENIAC had far more components than a smart phone. Joe

The whole idea that the most complex functional systems we know of consist of small islands of meaning swimming in a vast sea of chaos and nonsense should strike any engineer as preposterous.
Yep, but it wasn't designed by engineers (which is probably just as well). Piotr

In some species selection against junk is strong enough to get rid of most of it (e.g. high metabolism, hence reduced cell size, hence a pressure to reduce the genome size as well). And guess what? The species in question thrive without it. Birds and bats have roughly the same number of genes as humans, but less than 50% of the DNA. It isn't because they require fewer regulatory sequences; its just because they fly. Not surprisingly, flightless ratites have bigger genomes -- ostriches more than twice as big as hummingbirds. The cost of DNA maintenance and replication is low. Larger than zero, of course, but not large enough for negative selection to override drift. Unless you are a prokaryote (in which case even a minimal cost is important), some extra pressure is necessary to effectively select for a smaller genome and remove the junk. Piotr

Eric: Absolutely! You have put it perfectly. :) gpuccio

jerry @94:
However, the higher the number that is functional the harder it is for any natural process to integrate/cooridinate this functionality in an organism.
Maybe. But one could certainly make a reasonable argument that having a bunch of junk would bring the system to a grinding halt and that it would be even more difficult for a complex functional system to continue operating with precision while swimming in a chaotic sea of junk. If one takes the view that the great majority of DNA is junk, then they are essentially saying that the functional aspects are islands swimming in a sea of chaotic junk. We have never seen anything like that in any complex functional system. Indeed, it is rather preposterous that such a system could function for any length of time without failing. That alone should give us considerable pause. Furthermore, if all this DNA is junk, then there are a lot of wasted resources being used keeping it around. Anything the cell spends time and energy and resources on other than function is -- by definition -- deleterious. Oh, sure, the junk DNA proponent can always fall back to vague and general claims that (i) the selection pressure isn't strong enough to eliminate all the junk (a circular argument), or (ii) there hasn't been enough time yet to eliminate all the junk (a questionable assertion, rather than demonstrated fact). The whole idea that the most complex functional systems we know of consist of small islands of meaning swimming in a vast sea of chaos and nonsense should strike any engineer as preposterous. Could it be true? Sure, from a purely logical standpoint. But it would come with its own set of additional recognition and coordination problems that have never been properly acknowledged or thought through by junk DNA proponents, much less explained. At the very least the whole idea of significant amounts of junk DNA should strike us as unlikely and should give us considerable pause. Eric Anderson

Piotr: I like it when you are mean. When you are politically correct, you risk to be boring. So, please, attack! :) gpuccio

Piotr and jerry: "Nothing much depends on the exact number anyway." I am not sure I agree with that. Let me explain, I don't think that if it is X we win, and if it is Y they win. That is certainly not the point. The point is to recognize the procedures in non coding DNA, and to understand if other procedures are in other places (epigenetic or else). IOWs, we need to understand how things happen, where is the software which makes them happen in a certain way. We need to understand the algorithmic origin of transcriptomes in metazoa. We need to distinguish adaptation from genuine new design. And so on. Non coding DNA is a precious resource for that, because certainly much of that happens there. So, the ideological need to minimize its importance because many people think that it could help creationists, or some other noble reasoning of that kind, is a serious scientific error. gpuccio

Piotr: There is no downward trend. "80% or more" is referred to the transcriptional evidence found by ENCODE. That evidence has not changed. My "at least 20%" is a cautious evaluation which limits the present total to the part fro which transcriptional evidence is very strong. As I will try to discuss later, indeed there is no need for transcriptional evidence to be strong fro refined unction to exists, so it is perfectly possible that "80% or more" will be true, in the end. I remain cautious about the final percentage of the genome which could be functional, not because I think that a great part of it can really be "junk". Indeed, I believe that, while truly useless parts of the genome can exist, they will be shown to be really small. The real problem is the vast part of the genome which is very repetitive, IOWs the transposonic elements. Now, while as you know I am a big fan of transposons, I think that this transposonic part could well be a potential resource, not necessarily active functionally at all times or in all species. For example, transposons could have a fundamental role in directing evolution and speciation, or in adaptational processes. So, what we recognize as function can well depend on how we define function, and on our window of observation in time and space. But I do believe that most of our genome is there for some purpose, and that sooner or later we will understand those purposes. Take it as a personal prediction. gpuccio

Nothing much depends on the exact number anyway.
I agree. However, the higher the number that is functional the harder it is for any natural process to integrate/cooridinate this functionality in an organism. The eukaryote cell is incredibly complex with extremely precise coordinated processes and we know very little about how this complexity came about and what does the actual coordination. jerry

And wrt to "junk DNA", until the design is fully understood only fools would hazard guesses to the $ of real junk. Joe

Piotr, The mutation doesn't have to know anything. If the organism's program produced the mutation due to some environmental cue, then it ain't random. Joe

Joe @86, BA77 Hotspots of mutations, dependence of mutation rate on environmental stresses, etc -- it's all old news. Mutations are not distributed randomly in the sense that every locus can be affected with the same probability. None of it changes the fact that when a mutation happens it may turn out to be beneficial or deleterious, but it doesn't "know" what consequences it's going to have for the phenotype. Piotr

Gpuccio: If I wanted to be mean, I'd say that it was "80% or more" two years ago, and "20% or more" today, so the trend is clearly a downward one. Let's wait and see what they say when the dust settles. Nothing much depends on the exact number anyway. Piotr

Piotr: I was hoping to hear something more specific from you. I appreciate your loyalty to standard ideas of the scientific community, but I expected more excitement! :) gpuccio

Piotr: Why not "at least"? 20% is the part for which we already have convincing evidence. New evidence is accumulating almost daily. My (semi-)educated guess is 40 - 60%. Or even more. gpuccio

Whatever is good enough gets through the filter of natural selection. And that can be just about anything- shorter, longer, taller, fatter, slimmer, faster, slower, better sight, no sight, legs, no legs, gills and fins, lungs and legs, wings to fly, wings to swim, wings that just hang there, color, no color, stripes, spots, sharp teeth, grinding molars, loud, quiet, camouflage, no camo, smart, stupid- whatever. Joe

Piotr:
Mutations are copying errors.
That is debatable, however that is the evo propaganda.
They are random at least in the sense that they happen irrespective of their potential adaptive value
That is the propaganda, however James Shapiro has presented evidence to the contrary. Joe

Piotr, You really are squirming trying to avoid the issue. What created the beneficial innovation? Natural selection may have preserved it, what created it? Was it blind dumb chaos or not? By your definition of beneficial, anything that is alive has received a beneficial innovation. Being born with one leg, or a hole in your heart is beneficial, because as long as you are able to reproduce, its beneficial. Albinoism is beneficial. Dwarfism is a beneficial innovation. Cystic Fibrosis is a beneficial innovation, because people pass it on. Huntington's disease, hemophilia..... I guess those individuals just had good dumb blind luck. phoodoo

Phoodoo: Mutations are just that -- copying errors. Natural selection manifests itself as a bias against some of them and in favour of others. If there is no selective pressure, there is no reason to regard a mutation as beneficial (or deleterious). Piotr

Piotr, I asked you where the beneficial innovation came from. Your answer is that mutations are copying errors. So is that your answer as to where the beneficial innovations came from? I sense you being slippery with language again, and wanting to go back to natural selection, when the beneficial innovations don't come from NS. They may last due to NS, but they certainly don't come from NS. So does beneficial innovation come from anywhere other than the blind dumb luck of accidental replicators? phoodoo

Piotr claims that: Mutations are copying errors. Yet it is now known that the vast majority of 'mutations' to the genome are directed not 'random': Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 moreover, New Research Elucidates Directed Mutation Mechanisms - Cornelius Hunter - January 7, 2013 Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,, These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,, http://darwins-god.blogspot.com/2013/01/news-research-elucidates-directed.html etc.. etc... bornagain77

Phoodoo @79 Mutations are copying errors. They are random at least in the sense that they happen irrespective of their potential adaptive value; but the filter of natural selection leads to the preferential survival of some of them -- those we call "beneficial". Piotr

I am happy that you set the threshold of junk at 80%. So, you agree with my assessment of at least 20% functional genome. Good to know. wd400 seemed to be less convinced even of that.
I see little justification for the "at least" part. "About" 20% is my (semi-)educated guess.
About our taxon being “high”: I expected someone would not agree, that’s why I added “if we agree to call humans that way”. However, we are at least the more recent, or among the most recent, I suppose.
All extant species are equally recent, from the humblest bacterium to the blue whale and the redwood tree, and all are products of almost 4 billion years of evolution.
Don’t you think that there is increasing complexity in the course of natural history? Just to know.
Since life started out as rather simple, it's quite natural that it should have tended to expand towards increasing complexity. But I don't think evolution necessarily makes living things more complex. Bacteria and Archaea reached a certain (apparently optimal) level of complexity very early and the vast majority of their lineages have remained there for billions of years. The rise of Eukaryota (and, it seems, sexual reproduction) made more complex organisms possible, eventually leading to multicellularity. But at every stage only some lineages evolved greater complexity; in fact, some organisms are less complex than their ancestors. Greater complexity doesn't always mean an adaptive edge. Are humans more complex than other animals? I won't deny that our intelligence is exceptional (and that my brain is one of my favourite organs), but how would you measure overall complexity? I don't even know if there is a theoretical limit of complexity, and if so, how close to it (or how far from it) we are. Piotr

But Piotr, where does the beneficial innovation you talk of come from? That is the whole crux of the issue. Evolutionists would just love to sweep it under the rug of, well, its HGT, or its neutral, or its random mutations, or its, its, whatever, doesn't matter. Ultimately the theory has to say whether it is a luck of random chaos, or it is intended for survival. Your side wants to stick with the idea that's its completely random lucky chaos of dust, while steadfastly trying to downplay the role of blind luck. phoodoo

Phoodoo:
In the case of evolution, Darwinists continually confuse the public by claiming that natural selection causes changes in organisms, which it most certainly does not.
Can you offer a quotation from a "Darwinist" who says so? I am sure that no evolutionary biologist worth his salt would put it like that. Natural selection affects the frequency of alleles in an evolving population by imposing a statistical bias in favour of some of them. It can't cause any changes in individual organisms.
And by doing so, it allows them to then claim that Darwinian evolution is not a random process, which is a complete ruse.
It's isn't a blind drunkard's walk, at any rate. The presence of a nearby adaptive peak gives it a tendency.
they do this, because they realize how absurd it is to consider all of the elegant solutions to life as being totally random events. So they confuse by clever word play such as yours.
It seems to me you are tilting your lance at a straw man. Evolution isn't what you probably think it is.
but the theory nonetheless is predicated on completely random events, and there is no process.
Everything in this complex universe is contingent on chance events. The asteroid impact that caused the extinction of some 75% of species on Earth 66 million years ago was a non-biological accident, but it surely had macroevolutionary consequences. No matter how fit you get, adaptive evolution cannot prepare you for such disasters.
It may not even be true that the fittest survive. It may simply be that the luckiest survive.
In a finite-size population there's always a larger-than-zero chance that a beneficial innovation will be eliminated by drift before it manages to spread thanks to positive selection. The probability of such an elimination is small if the population is large, but even so the first and only carrier of the beneficial mutation may fall ill and die (or become somebody's lunch) before reaching reproductive maturity. We all need a bit of luck to get on in life. Piotr

Piotr, I agree with you that there is no need to be pedantic about word use, except where it completely changes the ideas being presented. In the case of evolution, Darwinists continually confuse the public by claiming that natural selection causes changes in organisms, which it most certainly does not. And by doing so, it allows them to then claim that Darwinian evolution is not a random process, which is a complete ruse. they do this, because they realize how absurd it is to consider all of the elegant solutions to life as being totally random events. So they confuse by clever word play such as yours. So all over the internet they say, natural selection is not random, and people buy this, without even debunking the idea that natural selection does not do anything! Its is simply an observation of what happens to the changes in generations. Its an important distinction, natural selection is most definitely NOT a mechanism. Whatever the mechanism is for the adaptation of life on earth, we still haven't got a clue. Your side claims its this process, (not really random, because that sounds ridiculous) but the theory nonetheless is predicated on completely random events, and there is no process. It may not even be true that the fittest survive. It may simply be that the luckiest survive. phoodoo

Whether the genome is 98% non-functional or 0% non-functional is not a deal breaker for ID. Obviously the lower the percentage that is non functional the more credence it gives to the ID position. But even if the number is closer to 98% it does little to invalidate the ID position. I view the percentage of non functional DNA as a red herring in the debate. It makes interesting conversation but is not very relevant to the overall debate. I do not mean that it should not be pursued. Everything should be looked into. But it should be kept in perspective. We seem to spend an excessive amount of time on it when it has probably little relevance to the validity of ID or not. As an aside, the repair function is definitely something that supports ID but if it should repair non-functional DNA as well as functional DNA is irrelevant to whether ID is valid or not. jerry

Piotr: I am happy that you set the threshold of junk at 80%. So, you agree with my assessment of at least 20% functional genome. Good to know. wd400 seemed to be less convinced even of that. About our taxon being "high": I expected someone would not agree, that's why I added "if we agree to call humans that way". However, we are at least the more recent, or among the most recent, I suppose. Don't you think that there is increasing complexity in the course of natural history? Just to know. gpuccio

I, as well as others, hold that the existence of highly sophisticated repair mechanisms that repair 'random' mutations is a direct contradiction to neo-Darwinian claims. Yet Piotr claims that
The existence of repair mechanism is of little relevance.
These authors beg to differ:
The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - 2011 Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.” http://www.benthamscience.com/open/toevolj/articles/V005/1TOEVOLJ.pdf
The following paper is good for giving us a glimpse as to how extremely sophisticated the repair mechanisms in the cell are:
Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010 Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Our best computer programmers and systems engineers can only dream of approaching that level of sophistication. Yet, in direct contradiction to common sense, Piotr holds that, through selecting the most advantageous 'potholes', that the 'potholes' themselves somehow rose up and constructed such unfathomed complexity as is seen in a '40 team member pothole crew of "smart" machines'. Repairing random mutations in such a sophisticated fashion is not only in direct contradiction to Darwin's theory, and its reliance on random mutations in the first place, but it is also an insult to our intelligence to suggest that 'potholes' can build pothole repair machines. Surely Piotr must have some pretty impressive evidence to believe in such a preposterous notion??? Yet, as we would rightly suspect, we have no empirical evidence of 'advantageous potholes' that are on their way to building up functional complexity above and beyond that which is already present:
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
Thus while Piotr may personally imagine, against all common sense, that potholes can build extremely sophisticated pothole repair machines, he simply has no empirical evidence that it is even remotely feasible in reality. Piotr also claims
I never said 98% DNA was junk. I’d estimate its content at about 80%, give or take a few percent.
I wonder, if it were possible to do so, if Piotr would have the courage in his convictions to allow 80 percent of his genome to be removed?
Jonathan Wells on Darwinism, Science, and Junk DNA - November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
of related note:
Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. -- So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html
bornagain77

Piotr, Design is a natural process. My car did not appear via divine fiat. As for natural selection its process is differential reproduction due to heritable chance mutations. Joe

Phoodoo: If you insist that every word that happens to have a technical meaning should be used exclusively with that meaning, you'll make exchange of thoughts impossible. Natural languages always offer some leeway for the figurative use of words. Oops! Did I say "leeway"? Leeway has a precise nautical meaning:
The sideways drift of a ship to leeward of the desired course.
Does it mean that I can't use it as I did above? So, for clarity's sake: mechanism has also a less formal meaning, not restricted to any particular field (Oxford Dictionaries online):
A natural or established process by which something takes place or is brought about
... and this is what I meant. Can you accept that, or will you start nitpicking about the technical meaning of "natural" and "process"? Piotr

Piotr, Once again you use the word mechanism to describe natural selection. Here is what wikipedia says about the word mechanism for biology: In the science of biology, a mechanism is a system of causally interacting parts and processes that produce one or more effects. What exactly is the system, or parts or processes that are natural selection? phoodoo

98% of useless DNA
Are you confusing noncoding DNA with useless DNA? I never said 98% DNA was junk. I'd estimate its content at about 80%, give or take a few percent. I hope you don't take the infamous Dog's Ass Plot seriously.
highest taxon
We are the "highest" among other taxa only from our anthropocentrically biassed perspective. There's nothing special about our DNA. It's all about economy. If the accumulation of junk were costlier than it is, purifying selection would gradually clean it out, but the cost is so low that the junk doesn't really matter. Most eukaryotes, no matter whether "high" or "low", tolerate it as well. Piotr

Piotr: I anticipate you: I have messed my negations again. Should have been: "f you really can’t see that the accumulation of 98% useless DNA in the highest taxon (if we agree to call humans that way), in a biological context where a lot of error management software is present and so many refined functions are implemented, is a true problem," gpuccio

Piotr: You can rationalize it as you like, but if you really can't see that the accumulation of 98% useless DNA in the highest taxon (if we agree to call humans that way), in a biological context where a lot of error management software is present and so many refined functions are implemented, is no problem at all, I must say that there is something really wrong in your approach. gpuccio

Piotr believes that a large percentage of our genomes are junk. I pointed out that his belief contradicts the fact that highly sophisticated repair mechanisms are found in life. How exactly is that not relevant? Do you think that a direct contradiction to his reasoning is not there?
The existence of repair mechanism is of little relevance. Those mechanisms can repair many kinds of physical damage (structural defects) and cancel some base substitutions, but they are not perfect; otherwise copying errors wouldn't happen at all (making even microevolutionary variation impossible). Nearly neutral theory bases its models on the known (observable) rates of mutation, and so it takes into account the operation of repair mechanisms as well. Piotr

of note: I should point out that Sal was as guilty as Mung was of acting like a spoiled brat. bornagain77

Thanks gpuccio. ,,, Mung all personal dislike you may have for me aside. Exactly what is not relevant in post 34? https://uncommondescent.com/intelligent-design/is-functional-information-in-dna-always-conserved-part-one/#comment-500765 Piotr believes that a large percentage of our genomes are junk. I pointed out that his belief contradicts the fact that highly sophisticated repair mechanisms are found in life. How exactly is that not relevant? Do you think that a direct contradiction to his reasoning is not there? Just because you don't personally like me or my posting style is no reason to be dishonest towards the evidence mung!,,, Though I strongly disagree with you from time to time, Mung, I truly do appreciate your wit and references many times (which are as profuse as mine are). But, as with your ugly disagreement with Sal, mung, in which you frankly acted like a spoiled uncontrollable brat, it is clear that when you have a personal vendetta against someone, for whatever reason, that you don't care for truth so much and and that you will be petty to the point of neglecting truth. This is sad, for there is so much potential in you if you would only realize that it is not all about how you look mung but about what the truth actually is! bornagain77

Mung:
Are you referring to the theory/theories of Tomoko Ohta?
Yes, of course, the insights that we owe to Ohta, plus later developments. Piotr

Mung: There are circumstances in which evolution is strongly adaptive, and therefore selectionism is more or less an adequate model. And there are circumstances (like small effective populations) when it is not quite adequate. It doesn't mean that it stops working, only that other effects dominate the dynamics of the process. Neutral theory was not invented as an alternative to natural selection; the two mechanisms occur together and complement each other. It is important to understand why Darwin did not take random drift into account. In his times the mathematics of stochastic processes (even those of interest to physicists, such as Brownian motions) did not yet exist. It began to be applied to population genetics in the 1930s, and its results are somewhat counterintuitive (we humans are ill-equipped to deal with probabilities by intuition alone). Darwin realised that there were heritable fluctuations in the population, but he assumed -- naively, from our more enlightened modern point of view -- that such fluctuations were around a certain mean, and that they cancelled out in the long run in the absence of selective pressures. It's hard to blame him for not being a clairvoyant. He couldn't know about DNA either. His theory included as much as it realistically could at the time, but a good deal of progress has been made since, so the model has been extended in various ways. Piotr

Mung at #58: If a theory which declares to be true about facts is not true about facts, then it is logically false. Neo darwinism (pan selectionism) is false as an explanation of biological information. Neutralism, while true as a theory of random variation in biology, is false as an explanation of biological information. Non design thinkers are very able in shifting different levels of truth to escape scientific falsification. That's what makes their position so "adaptable". But, in the end, their position is false. Shifting the meaning of truth while pretending it remains the same is falsity. It's an adaptable falsity, but falsity just the same. gpuccio

Mung and Piotr: BA has his own style. You may like it or not, but it has its merits. I don't always agree with him (that is well known), but most times I do, and however I really appreciate his contributions. He has a real talent in finding sources, and providing them. OK, he accumulates them very much, and some of them are not sources I would sponsor. But many are. And there is always a sense in his accumulation, right or wrong that it may be. gpuccio

Mung: "Is it possible to be a non-Darwinian Theistic Evolutionist?" It is certainly possible, but you should explain better what you mean by it. Then I will say if it is a position I find reasonable, or not. In my statement, I referred mainly to darwinian TEs, or any way to "naturalistic" (whatever it means) TEs. And I suppose that "The Active Designer(s)" is fine. gpuccio

Piotr:
Nearly neutral theory explains why (and when) junk manages to accumulate in the genome and escape purifying selection.
Are you referring to the theory/theories of Tomoko Ohta? The Nearly Neutral Theory Of Molecular Evolution Mung

Piotr:
When I refer to a strictly “neo-Darwinian” point of view, I mean the pan-selectionist bias that emphasises the adaptive aspect of evolution and plays down the effects of random drift (and mutations). That’s why Richard Dawkins, a staunch Darwinist (and proud of it) was once so sceptical of any DNA being junk. Natural selection should not tolerate junk if its presence costs anything. But this is only true if you ignore other aspects of evolution.
Well, no. Neo-Darwinism (aka pan-selectionism) is only true if it's not false leaves out the possibility that it's just nonsense, that it can be both true and false or that it can be neither true nor false. So which is it? Is neo-Darwinism false, or is it just extremely "adaptable"? I opt for the latter. It's not falsifiable. It's rather obvious isn't it, that ignoring other aspects of evolution has not falsified the neo-darwinian theory, nor has taking into account other aspects of evolution falsified the neo-darwinian theory. Mung

Self-correction: I mean, thanks, Mung. Piotr

Thanks, Jerry, I appreciate that. I'll be happy to respond if BA77 offers more than another broadside. Piotr

jerry:
People who argue by mocking generally have little of substance to say. Otherwise they would not do it . In this case the mocking is validating BA.
Hardly. Here I will take Piotr's side. BA77's posting of numerous quotes and or links to numerous articles while failing to provide an actual argument makes it appear is if bornagain77 who has little of substance to say. Some people appreciate all BA77's quotes and links. No doubt there is some good material there to be had. But it's highly unreasonable to expect someone to wade through them all to try to find anything relevant while also being placed in the position of trying to infer whatever argument BA77 is making (if any) from all the posted material. Piotr has given his reasons for responding the way he does to BA77's link/quote spamming, so it's not fair to pretend like he hasn't. He gave fair warning. So yeah, mocking is probably the next best thing to ignoring. If BA77 chose to put forth an actual argument, I believe Piotr would respond. When faced with quotes and links in lieu of argument, I can't blame him for responding as he has. Mung

gpuccio:
You may know that I reject, on scientific ground, both the neo darwinian paradigm and any TE paradigm. I am absolutely convinced that the emergence of complex functional information, both at OOL and in the following evolution of species, absolutely requires active and multiple design interventions.
What do you call this view? The Continuing Creation? The Dabbling Designer? The Active Architect? The Evolving Engineer? Is it possible to be a non-Darwinian Theistic Evolutionist? Mung

CentralScrutinizer @ 52
Why don’t you show us what you’ve got and let’s see.
Here's a simple guideline to follow:
What is(are) the name(s) of that(those) protein(s)? How can it (they) arise? can provide link(s) to reliable source(s) for that info?
It certainly must be a very interesting process for many of us to study and learn from. Can’t wait to read about it. But most probably I won’t understand it well, so I will have to ask specific questions about it. Shouldn’t the description of such an interesting process be on a separate OP thread? Just a suggestion. Dionisio

Piotr: If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards?
Why don't you show us what you've got and let's see. CentralScrutinizer

Piotr, unguided evolution doesn't predict nor can it explain, eukaryotes. Joe

Curious Cat @40
However, in this specific case, you seem to hold these two theories as a kind of anything goes approach.
It's nothing of the kind. We know which process dominates depending on the circumstances. We can predict, for example, that prokaryotes will normally have very little junk DNA, and eukaryotes will have a lot of it (and the amount may vary significantly even between closely related taxa). If you find a eukaryotic species with an exceptionally small genome and surprisingly little junk DNA, like the humped bladderwort, Utricularia gibba, you need to explain that. The reason, in the case of the bladderwort, can't be a vast effective population. More than one competing explanations have been suggested and only time can tell which of them (if any) is correct. Piotr

Jerry, Australian indigenous people have separated from Africans for about 50.000 years. Is this enough time to look at which sections of the genome have “rotted” and which remain fairly constant. Not even close, I'm afriad. With 25 year generations you will end up with changes in about 1 out of 100 000 base pairs under neutrality. How much Neanderthal DNA is there? They supposedly left Africa 400-500 thousand years ago even if we assume Australia had been isolated all that time. Several whole genomes. It's still really too short a time to talk about conservation. Human and neanderthal genomes are only different in 0.03% of nucleotides (around the neutral expectation...) so it's going to be hard to tell which are conserved and which just haven't changed by chance. wd400

CuriousCat @40 You are apparently so accustomed to branding all your opponents "Darwinists" or "neo-Darwinists" that you forget these terms mean something specific in the context of evolutionary biology. When I refer to a strictly "neo-Darwinian" point of view, I mean the pan-selectionist bias that emphasises the adaptive aspect of evolution and plays down the effects of random drift (and mutations). That's why Richard Dawkins, a staunch Darwinist (and proud of it) was once so sceptical of any DNA being junk. Natural selection should not tolerate junk if its presence costs anything. But this is only true if you ignore other aspects of evolution. Nearly neutral theory explains why (and when) junk manages to accumulate in the genome and escape purifying selection. In some circumstances selection against excess DNA may still be strong enough to delete a lot of junk without any visible harm done to its owner. That's why some closely related organisms may exhibit several-fold differences in the amount of non-functional DNA in their genomes. In T. Ryan Gregory's classic example, one onion species, the ramson, Allium ursinum, has almost twice as much DNA as the common onion, A. cepa, and more than four times as amuch as A. altyncolicum. They are otherwise very similar and have similar amounts of very similar coding DNA (and before you ask, the difference is not due to polyploidy). Piotr

gpuccio @ 42
But the point is: functional complexity is the tool to infer design. It is the demonstration that only conscious understanding and conscious purpose can accomplish some well defined task, and generate some well defined result. If the concept works, it must work in the same way for simple proteins and for complex systems. IOWs, it must be true that complex functional information can only arise from a conscious designer. And it is true. For proteins, as much as for systems of them.
Accepted your convincing argument. Thank you. Actually, a separate thread could start with the above quote as the OP, if the moderators of this blog would agree. OT: You clearly use a very didactic style to describe difficult things. Do you lecture at a university or professional conferences? Dionisio

gpuccio @ 35
Yes. If presented with evidence that a new functional protein exhibiting new original dFSCI can arise naturally without intelligent design, I would agree that dFSCI admits false positives, and that would certainly redefine its value. So, yes.
Interesting, very logical reasoning. Thank you. What is(are) the name(s) of that(those) protein(s)? How can it (they) arise? It certainly must be a very interesting process for me to study and learn from. Can't wait to read about it. But most probably I won't understand it well, so I will have to ask specific questions about it. Shouldn't the description of such an interesting process be on a separate OP thread? Just a suggestion. Dionisio

CuriousCat: I essentially believe that the neo darwinian theory, in all its variants, can be falsified in a Popperian sense. So, it is a scientific theory, although a very bad one. But, as you imply, it's certainly very flexible in its attempts at avoiding falsification ! :) gpuccio

jerry: "I have a quick question. Just looking at the human genome, can we imply function by looking at sequences that are essentially the same across groups separated by long times?" I suppose that sequence conservation must be higher to be relevant, if the separation is shorter. "Conservation" is an indirect measure of a functional constraint. That's why we are interested in it. The idea is: sequences which have no function are free to change, and they will change because of neutral random variation. On the other hand, sequences which are functional will change less in the same time, because much of the variation in them will be deleterious, and will be eliminated by negative (purifying) selection. Now, the longer the time which separates two species, the higher in principle the neutral random variation in their genomes. So, if two sequences are highly conserved between Caenorhabditis elegans and humans, that is more significant (implies higher functional constraint) than if two sequences exhibit similar conservation between chimp and humans. That's why it is important to specify which type of conservation is being measured, as I have tried to point out. gpuccio

BA at #34: Good points. gpuccio

Dionisio: You say: "Even if ALL functional proteins could be shown to easily arise naturally, I would still require a detailed, step by step, complete, comprehensive, coherent, logical description of the origin of the systems I’m studying." OK, the complexity of systems is obviously much greater than the complexity of their individual parts. That's an aspect of the concept of irreducible complexity, for which we must be really grateful to Behe. But the point is: functional complexity is the tool to infer design. It is the demonstration that only conscious understanding and conscious purpose can accomplish some well defined task, and generate some well defined result. If the concept works, it must work in the same way for simple proteins and for complex systems. IOWs, it must be true that complex functional information can only arise from a conscious designer. And it is true. For proteins, as much as for systems of them. gpuccio

Joe: You say: "The problem with that is no one knows what the natural history was." Well, nobody has really observed directly natural history. All our ideas about it are indirect. The concept of conservation of sequences is obviously derived from comparisons in the existing proteome, and on some fundamental assumptions, especially Common Descent and the concept of negative (purifying) selection acting on variation of functional elements. I accept those assumptions, otherwise I would never discuss about conservation and its meaning. Anyone is free to reject those assumptions, and therefore reject my reasonings too. gpuccio

Piotr: Your first paragraph ends with this sentence.
So from a strictly “neo-Darwinian” point of view (if you insist on using such a term) any junk DNA should be eliminated from the genome.
Your second paragraph ends with this sentence:
For most eukaryotes it is insignificant — at any rate, not high enough for purifying selection to override the effects of neutral evolution, which allows junk to accumulate simply because it does no harm (and may even be occasionally co-opted for a function).
Your fourth paragraph reads:
So the presence of junk DNA, while predicted by nearly neutral theory, is not necessary .
I'm sorry but I cannot follow your logic. I'm pretty much Popperian when it comes to science, but, let alone a strict falsification, I sincerely cannot understand what evolution theory suggests vaguely in the view of what you have written. Furthermore, your first sentence any junk DNA should be eliminated from the genome is simply wrong. As you have pointed out in your second paragraph, selective pressure coming from the restrictions on energy is negligible for most of the eukaryotes, and other than that, there is no reason to expect the elimination of unnecessary products (genes, proteins, pathways) unless they cause a high burden. to the organism Let us also remember that appendix, wisdom teeth, etc. have been conventional textbook examples of "junk organs", which are explained in the light of Darwinian paradigm. Hence your sentence, if it were published in a biological journal, would be corrected to: So from a strictly “neo-Darwinian” point of view ~~any~~ junk DNA may be eliminated from the genome. There is a further problem in your logic. You use two theories (neutral theory and neo-Darwinian selection) in a complimentary way. There are some approaches which complement each other in science, I agree with that. However, in this specific case, you seem to hold these two theories as a kind of anything goes approach. If we encounter these type of observations, then here's the theory to explain it.. If we encounter just the opposite, no need to worry! We have another theory to explain it. Coming back to the basic question of this discussion, now, if junk DNA does not come out to be so junk, then there would be two problems at the same time: 1. How is possible that a random search algorithm with negligible selective pressure can come up with so many correct guesses? 2. Now that neutral theory will be nearly falsified, how is it possible that new functional folds arise (without an extensive search suggested by neutral theory)? CuriousCat

Piotr at #29: I think you are "jumping" too much (to borrow the concept from wd400). Your suggested explanation for junk DNA is far from being proven. Indeed, the whole concept of abundant junk DNA is far from being proven. I would say the opposite is true. First of all, the accumulation of non coding DNA in more complex beings has a much simpler explanation: non coding DNA has important regulatory functions. This whole post, and the one which will follow, are dedicated to that point. The explanation you present is really ad hoc to defend the theory of darwinian evolution with a little bit of its variant of neutralism. A good recipe, but not one that explains what we observe. The functions of non coding DNA are emerging at tremendous rate. To quote yourself, I have the impression that you have "swallowed" the hype of ENCODE's hype a little too early. You say: "it seems that the ENCODE leaders are now backing down from their inflated claims and trying to blame the 2012 hype on the press." I don't think it is true. The recent paper from ENCODE is based on exactly the same data as before. It just acknowledges the objections that were made, and intelligently discusses them. It remains true that about 80% of the human genome shows biochemical evidence of likely function. What the ENCODE people have done is to divide that set into three subsets, each with higher level of evidence. I have accepted, in my discussion here, to stick to the subset with the highest molecular evidence, because, as usual, I tend to be very generous with the enemy. :) In my next post, I will discuss why a lower level of transcription evidence is not necessarily a lower level of evidence for function. The part of non coding DNA which remains more controversial from the point of view of function is the transposonic part. And yet, strangely, darwinists are the first to admit its very important role in the evolution of genomes. You refer to that yourself, when you say that junk can "accumulate simply because it does no harm (and may even be occasionally co-opted for a function). (Emphasis mine). That's an understatement, if I ever saw one! Don't you find it strange that the part of the genome which should be complete junk is also the one which seems to be responsible for new functional proteins, and for many important re-definitions of genomic information? I think that I will never really understand how non design people think... :) gpuccio

""Boom! Boom! Take cover! It’s the dreaded Bornagain Broadside!
People who argue by mocking generally have little of substance to say. Otherwise they would not do it . In this case the mocking is validating BA. jerry

I have a quick question. Just looking at the human genome, can we imply function by looking at sequences that are essentially the same across groups separated by long times? Australian indigenous people have separated from Africans for about 50.000 years. Is this enough time to look at which sections of the genome have "rotted" and which remain fairly constant. How much Neanderthal DNA is there? They supposedly left Africa 400-500 thousand years ago. jerry

#34 Boom! Boom! Take cover! It's the dreaded Bornagain Broadside! Piotr

Piotr:
I do not want to distract you now, but since you are making a very strong claim, I’d like to ask a simple question. If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards?
Yes. If presented with evidence that a new functional protein exhibiting new original dFSCI can arise naturally without intelligent design, I would agree that dFSCI sdmits false positives, and that would certainly redefine its value. So, yes. gpuccio

Piotr, I have a honest question for you. Now you believe that multicellular organisms contain a large percentage of junk DNA. But if the genomes of higher life forms contain large percentages of junk, then why does the cell have such elaborate mechanisms for repairing random mutations to DNA:
Protein Researchers Unravel the Molecular Dance of DNA Repair - March 2012 Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, "We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications," Petra Beli says. "This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works." The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways. http://www.sciencedaily.com/releases/2012/03/120315123022.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm A Look at the Quality Control System in the Protein Factory - JonathanM - March 2012 Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed. http://www.evolutionnews.org/2012/03/a_look_at_the_q057791.html Researchers discover how key enzyme repairs sun-damaged DNA - July 2010 Excerpt: Ohio State University physicist and chemist Dongping Zhong and his colleagues describe how they were able to observe the enzyme, called photolyase, inject a single electron and proton into an injured strand of DNA. The two subatomic particles healed the damage in a few billionths of a second. "It sounds simple, but those two atomic particles actually initiated a very complex series of chemical reactions," said Zhong,,, "It all happened very fast, and the timing had to be just right." http://www.physorg.com/news199111045.html More DNA Repair Wonders Found - October 2010 Excerpt: This specialized enzyme may attract other repair enzymes to the site, and “speeds up the process by about 100 times.” The enzyme “uses several rod-like helical structures... to grab hold of DNA.”,,, On another DNA-repair front, today’s Nature described a “protein giant” named BRCA2 that is critically involved in DNA repair, specifically targeting the dangerous double-stranded breaks that can lead to serious health consequences http://www.creationsafaris.com/crev201010.htm#20101007a Extreme Genome Repair - 20 March 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal. http://www.sciencedirect.com/science/article/pii/S0092867409002657 Scientists Decipher Missing Piece Of First-responder DNA Repair Machine - Oct. 2009 Excerpt: The first-responder machine, a protein complex called Mre11-Rad50-Nbs1 (or MRN for short), homes in on the gravest kind of breaks in which both strands of a DNA double helix are cut. It then stops the cell from dividing and launches an error-free DNA repair process called homologous recombination, which replaces defective genes. per science daily Repair mechanisms in DNA include: A proofreading system that catches almost all errors A mismatch repair system to back up the proofreading system Photoreactivation (light repair) Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase Base excision repair Nucleotide excision repair Double-strand DNA break repair Recombination repair Error-prone bypass etc..
Moreover Piotr, why do Darwinists ignore the obvious problem that this presents to their/your hypothesis?
Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution) http://www.youtube.com/watch?v=dzh6Ct5cg1o The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011 Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic The Darwinism contradiction of repair systems Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/
bornagain77

If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards?
Even if ALL functional proteins could be shown to easily arise naturally, I would still require a detailed, step by step, complete, comprehensive, coherent, logical description of the origin of the systems I'm studying. Note that -at this point- I'm not interested in the origin of the biological systems that I'm studying. I like serious philosophical discussions, because I love wisdom, but I'd rather leave that seemingly abstract 'origin' research to those who are more educated and have an 'acceptable' IQ (mine is comparable to my current age). I'm simply focused in on describing how some biological systems currently work, so that I could model and simulate them "in-silico". That's an overwhelmingly difficult task for me, because I'm not a biology scientist, but an engineer, who has worked for a number of years on software development projects for engineering design systems. The cellular and molecular biology information I'm interested in is widely disseminated all over the cyberspace, and a large portion of it -specially the most recent data- is behind paywalls, i.e., inaccessible to me, because I'm operating on a minimum budget. This makes the gathering of reliable information more difficult and slow. Please, keep in mind that vague explanations -which might sound impressive in some philosophical discussions- don't go too far in engineering software development projects. They are simply unacceptable. Regardless of how sophisticated it may sound, any description that fails the old Wendy's restaurant commercial question "where's the beef?", won't do well in engineering software development projects. Biologists should be well aware of the fact that more engineers and computer scientists are joining this revolutionary field of research. In other threads I provided a couple of specific examples of engineers and computer scientists who lead biology-related research works at some universities. There's an obvious reason why this is happening these days. Dionisio

Junk DNA- there is no way, at present, to determine how much, if any, DNA is truly junk. I would love to see this alleged prediction of junk DNA wrt the neutral theory... Joe

Piotr:
What is the “function” of brown eyes, for example, or the ability to roll your tongue (no just-so stories, please)?
Sexual selection, Piotr. Ever heard of that? Joe

gpuccio:
Conservation of sequence in the course of natural history has always been considered a sign of function.
The problem with that is no one knows what the natural history was. Joe

Curious Cat: The existence of junk DNA incurs some slight metabolic cost, so you could expect purifying selection against keeping superfluous DNA even if its sequence doesn't do anything deleterious. So from a strictly "neo-Darwinian" point of view (if you insist on using such a term) any junk DNA should be eliminated from the genome. But the cost will be different for different organisms, depending on their way of life, typical population size, etc. For most eukaryotes it is insignificant -- at any rate, not high enough for purifying selection to override the effects of neutral evolution, which allows junk to accumulate simply because it does no harm (and may even be occasionally co-opted for a function). Note that prokaryotes, which have immense effective populations and are therefore susceptible even to very slight selective pressures, keep little if any junk DNA. Also, for various other reasons, some eukaryotes have downsized genomes with little junk DNA compared to humans (not to mention onions and lungfish). So the presence of junk DNA, while predicted by nearly neutral theory, is not necessary. On the other hand, the administrators of this very forum have boasted that ID makes the following "testable prediction":
Non-functionality of “junk DNA” was predicted by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980), Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. By contrast, predictions of functionality of “junk DNA” were made based on teleological bases by Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004). These Intelligent Design predictions are being confirmed. e.g., ENCODE’s June 2007 results show substantial functionality across the genome in such “junk” DNA regions, including pseudogenes. In short, it is a matter of simple fact that scientists working in the ID paradigm – despite harassment, slander and even outright career-busting — carry out and publish research, and that they have made significant and successful ID-based predictions. ...
Leaving factual errors asside (some of the publication referred to above don't deal with junk DNA, and Dawkins, in particular, was in fact speptical of the idea, as opposed to "selfish" DNA), it seems that the ENCODE leaders are now backing down from their inflated claims and trying to blame the 2012 hype on the press. Where does that leave ID theorists with their "scientific predictions"? Piotr

Piotr:
If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards?
Yes, if said protein arose in an environment that didn't have any proteins to begin with. Joe

Piotr, sure! He is more than capable of defending himself in this matter and I am sure he will,,,, I'm just curious, don't you think Darwinists should be held to the same standard as you are holding gpuccio to? Or does evidence even matter to you? If not why not? Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013 http://www.evolutionnews.org/2013/08/hopeless_matzke075631.html "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences." http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/ bornagain77

BA77: Will you please let Gpuccio speak for himself? Piotr

Piotr @20: I said
a high signal to noise ratio (SNR) in the genes would make the Darwinist interpretation of evolution pretty much difficult to accept.
and you asked
I wonder why. Can you explain it to me?
My reasoning is as follows. Now that Darwinian mechanism is based on essentially random events (I emphasize this "essentiality" to distinguish Darwinian evolution from a certain type of teleogical evolution, which, more or less, suggests that indivial events/paths can be directed -or chosen- by God, but the whole ensemble/sequence obeys a certain probability distribution), all the evolutionary paths (chosen or not chosen) and DNA sequences are random (or random within the frame defined by fundamental physical laws). Only those sequences (signal) that are advantageous locally within a certain time frame are selected by the nature, but those that are not functional (however you define this) will be accumulated as wrong guesses/junk/noise. Since the sequence space is much much larger than the function space (Maybe we cannot agree on the exact definitions of these, but it's pretty much obvious that this holds. If you do not agree with this suggestion, I've got another design argument in my pocket .)), and a random process is more likely to produce the outcome with the higher probability (law of large numbers), it is inevitable that the resulting genome should have a very high amount of noise. CuriousCat

Piotr you ask:
If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards?
gpuccio has been waiting on that 'if presented with evidence' bit for a long time, and has ably defended against each example put forward.,,, Care to present any evidence he has not seen before? Moreover, when you are shown why your purported example falls short, will you admit the whole Darwinian concept is a house of cards? Or does evidence even matter to you? bornagain77

As I believe that even one single complex protein commands a design inference, you can understand how much more that is true for the whole functional genome.
I do not want to distract you now, but since you are making a very strong claim, I'd like to ask a simple question. If presented with evidence that a new functional protein can arise naturally without intelligent design, would you agree that the whole concept of dFSCI is a house of cards? Piotr

CuriousCat: Thank you. In this post I do not deal directly with the design inference, but it is obvious that the more information we find in the genome, the more strict the design inference for biological beings becomes. As I believe that even one single complex protein commands a design inference, you can understand how much more that is true for the whole functional genome. You may know that I reject, on scientific ground, both the neo darwinian paradigm and any TE paradigm. I am absolutely convinced that the emergence of complex functional information, both at OOL and in the following evolution of species, absolutely requires active and multiple design interventions. Your "SNR" is the equivalent of my concept of dFSCI. I don't know what darwinists are capable to accept (probably nothing). Frankly, I don't care. I am only interested in what is reasonable and scientific. And a design paradigm is the only reasonable and scientific answer for complex biological information, however much it is. But obviously, the more the better! :) gpuccio

Dionisio: Thank you for your comments, and for the very interesting link. It is amazing how complex and at the same time robust and functionally redundant the spindle organization is! gpuccio

Curious Cat:
a high signal to noise ratio (SNR) in the genes would make the Darwinist interpretation of evolution pretty much difficult to accept.
I wonder why. Can you explain it to me? Piotr

UB: Thank you. Part two is already in my mind, I most only find the time to put it down. I chose to divide the discussion in two parts to avoid excessive length in the OP. gpuccio

Very good post gpuccio, thanks. Looking forward to the second part. I find this issue the MOST important point in Darwinian vs. teleological paradigms. After all, it is not unacceptable for a person who believes in design (not only confined to stronger sense of design -ID-, but design in a more general way) to accept common descent and take probabilistic mutations + natural selection as God's design of probability-function landscape. On the other hand, it is difficult to absorb the idea (from the design point of view) that evolution is not the result of a "specific" realization (which obeys the probabilistic rules) of this stochastic mechanism designed by God, but truly (essentially) random. There is also the other side of the coin. This point is also one of the very few observations that has the potential (almost, I should add, since Darwinian view can always find a way) to falsify the Darwinian paradigm: a high signal to noise ratio (SNR) in the genes would make the Darwinist interpretation of evolution pretty much difficult to accept. In this case, the present realization of evolution, itself, would be "fine-tuned", still random to our human eyes and mathematics, but not random in essence. Even if we agree on the definition of function (which I highly doubt, as far as it is seen in the above civilized discussion), there would still be the issue of how much SNR is acceptable in Darwinian (or teleological) view, on which, I wonder, how we will agree! So let's see where the discussion will lead... CuriousCat

Dionoso, OT My impression is that you are focused on a mostly singular item of interest, and will collect a whole root of information along the way. If that is true, then you and I are the same in that regard. My interest was the physical conditions of a representation. Glad you're here. cheers... Upright BiPed

Upright BiPed @ 14, [OT] I'm glad you are interested in the subject of my current studies. I plan to share the results of my search at some point. Also I have enjoyed reading your interesting comments in other threads, though sometimes the discussed subjects are difficult to me. Dionisio

I didn't mean to imply that you'd called me anything, gpuccio. Rather, even if you happily make the leap form "subject to function" to "is functional" you end up with much less of th genome being functional than most of your fellow travelers seem to think is the case. wd400

(Dionoso, OT, I am among those here who are enjoying your search.) Upright BiPed

gpuccio,
Let’s try to just discuss, and let the ideas speak for themselves.
Well stated. Caro Dottore, So glad to see your new post, which as usually, has started to generate interesting follow-up discussions within the same thread. Also as usually, most of these discussions seem way above and beyond my limited capacity to understand them, but I try to read them so I can learn something new, that somehow might be related to the subject I'm currently interested in. I continue to struggle with trying to compile a detailed step by step description of the mechanisms behind the cell fate determination, differentiation and migration within the first few weeks of human embryonic development. This slow studying has led me to the intrinsic* asymmetric cell division, which has taken me to the spindle apparatus mechanisms. At this point I'm looking at the mechanisms associated with the centrosome and everything that goes with it during the mitotic phases. Among the several sources of information I'm reviewing, I thought that perhaps the following quote slightly (indirectly) relate to the complex functionality issues you've been writing about lately? If not, then just disregard it. Please, note that the quoted paper seems to be pretty fresh out of the oven, which might confirm something you told me in another thread - that certain things in this area of science are not so well understood yet, which makes this whole studying experience even more exciting to me!
The mitotic spindle is defined by its organized, bipolar mass of microtubules, which drive chromosome alignment and segregation. Although different cells have been shown to use different molecular pathways to generate the microtubules required for spindle formation, how these pathways are coordinated within a single cell is poorly understood.
From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898610/ (*) have left the extrinsic ACD for later reviewing. Dionisio

Thanks GP. Looking forward to part two. Upright BiPed

wd400: I don't call you anything, I just think you are wrong. And you still have to make this jump from the idea that a sequence has not yet been proven functional beyond any doubt to the idea that it is not functional. Again, biological evidence for new and different functions of different parts of non coding DNA is accumulating quickly, and most of it is very recent. In your shoes, I would just be cautious in "stating it’s likely most of the human genome is junk". And you should see the things I’ve been called in other places for just existing! :) Let's try to just discuss, and let the ideas speak for themselves. gpuccio

Well, to get to 20% you still have to make this jump from the idea that a sequence is subject to biological function to the idea it is functional. And 20% is a far cry most, and you should see the things I've been called here for stating it's likely most of the human genome is junk. wd400

Piotr: If you knew how tentative are many "gold standards" in medicine! :) gpuccio

gpuccio:
Well, I took the “gold standard” concept from the paper itself.
I realise that much. Still, it's too proud a name for a somewhat tentative criterion.
“A coding-independent function of gene and pseudogene mRNAs regulates tumour biology”
I have no problem with this kind of "function". Piotr

wd400, @2 I deliberately mentioned a specific colour (and the "function" of the allele involved, supposing for the sake of argument that it isn't involved in much else). No disagreement about the locus. Piotr

wd400:
I also think functional elements will always be conserved – it’s just a question the gap across which the elements have been retained: there will be ape and human-specific functional elements, which may even double the proportion of functional DNA form the mamallian-wide conservation. But it still won’t add up to the “death of junk DNA” that many commentators here seem to think has happened.
I have said clearly that conservation can be measured differently. Mammalian conservation is certainly higher than vertebrate conservation, and primate conservation is certainly even higher. The Siepel paper data are about vertebrate conservation. The Kellis paper data are about mammalian conservation, and they are slightly higher. However, the two series of data are essentially in accord. Even if you do not consider the estimated green area in the reasoning, we still have about 20% of the human genome which is very probably functional (red circle + dark blue area), and 19% is non coding. I think the general concept does not change. The problem is not the "death" of junk DNA. You can keep some pieces of it, if that is of some consolation. :) The point is that we have much more non coding DNA than coding DNA in the functional subset, and it is destined to grow. Maybe it will not be 80% in the end, but it will be definitely more than 20% of the whole genome. Maybe much more. We will see. Moreover, wait for the other two "arguments". :) gpuccio

Piotr: Well, I took the "gold standard" concept from the paper itself: "Genetic approaches, which rely on sequence alterations to establish the biological relevance of a DNA segment, are often considered a gold standard for defining function." I suppose that if we really look at biologically relevant effects, then your objection can be met. For example, this paper: "A coding-independent function of gene and pseudogene mRNAs regulates tumour biology" http://www.nature.com/nature/journal/v465/n7301/full/nature09144.html is about a role of pseudogenes as interacting with tumor suppressor genes. That is certainly a relevant biological function. gpuccio

wd400: The figure legend says: "The green shaded domain conceptually represents DNA that produces a phenotype upon alteration, although we lack well-developed summary estimates for the amount of genetic evidence and its relationship with the other types. This summary of our understanding in early 2014 will likely evolve substantially with more data and more refined experimental and analytical methods." So, I suppose it is an estimate ("summary of our understanding"), but I would not say it is "summary of our understanding". I think they based it on some general review of present literature, even if not on "well-developed summary estimates". There are many papers in the literature which may have been considered in that estimate, but there is probably no general quantitative summary of them. So I agree that we must consider that quantification as more tentative, and not as a precise measure. But it certainly has its value. gpuccio

I also think functional elements will always be conserved - it's just a question the gap across which the elements have been retained: there will be ape and human-specific functional elements, which may even double the proportion of functional DNA form the mamallian-wide conservation. But it still won't add up to the "death of junk DNA" that many commentators here seem to think has happened. wd400

It's pretty clear form Fig 1 that the size and shape of the green region is made up - it's name even has a question mark. Piotr, Im not sure I agree. In the examples you mention the variants themselves have not obvious biological consequence, but if the sequences they were from did play a role in some biological function we wouldn't be able to measure the variation (and indeed the eye-colour locus will certainly be subject to purifying selection, even if eye-colour alleles are not under selection). There could be examples of phenotypes form usually non-functional sections of the genome (i.e. a derived allele for a non-functional locus could mess up some other functional system) but I doubt there would be many such cases. wd400

I'll be watching this with genuine interest, especially if you develop the last two points. Just one remark at this stage: the fact that the phenotype is somehow affected does not unquestionably imply a function, so I wouldn't call it the "gold standard". Phenotypes often vary in ways that are genomically conditioned but don't affect their fitness. What is the "function" of brown eyes, for example, or the ability to roll your tongue (no just-so stories, please)? This, of course, accounts for the fact that many of the sequences in question will not be conserved. Piotr

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1) How much of the human genome is made of conserved sequences?

2) Is there functional DNA which is not conserved, in the human genome?

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