Junk DNA

The ciliate protozoans are very large cells with incredible internal complexity and morphology. They may have whole “organ systems” contained inside a single reproductive unit. Correlated with large size they have a large macronucleus and typically one micronucleus which is diploid. The macronucleus originates by endomitotic duplication of the micronucleus. When the cell divides the micronucleus divides mitotically but the macronucleus just pinches in two without producing identical products. This leads to a physiological unbalance which has to be restored by making a new macronucleus. A new macronucleus is periodically produced by a series of mitotic duplications of the micronucleus (endomitosis). Otherwise the animal will degenerate and die. Cells which are prevented from doing this give rise to degenerating lines doomed to ultimate extinction.

I always thought this might have something to do with junk DNA because when the macronuclei divide amititically they must lose their genetic specificity in the process. The macronucleus, when first restored by approximately 10 endomitiotic replications which make it 1024 ploid, it is perfectly balanced and only gradually becomes unbalanced with subsequent amitotic replications. The micronucleus ALWAYS reproduces mitotically and accordingly genetically faithfully. The junk DNA may just be DNA that failed to replicate properly and the cells just had to find a way to get it out of the way.

Years ago Barry Commoner published a paper about what he called the “nuclear wastebasket theory.” The idea was that the cell had to get rid of its DNA somehow so it stuck it in the nucleus. I was his colleague at Washington University at the time, he in Botany, I in Zoology and everybody thought he was crazy, everybody except me that is! Of course everybody thought I was crazy too, so Barry and I always hit it off rather well.

The ciliate protozoa are extremely advanced creatures in many ways which I take to be support for the PEH. There is a picture of one, Diplodinium ecaudatum, which lives in huge numbers in the rumen of cattle, in section VII-2 of the Manifesto along with a key to its incredible intracellular structure. Leo Berg called this sort of thing “phylogenetic acceleration.” I call it “phylogenetic derepression,” That it could occur in a protozoan is compatible with a “prescribed evolution,” being simply a premature demonstration of it. A true placenta in certain sharks is another example. The ciliate protozoa may provide a model for the “Junk DNA” notion. I just don’t know.

“A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

There certainly have been a few ID theorists who have placed a lot of weight on the hypothesis that much/most of the junk DNA will prove to be useful. Most noteably, not because he is a central theorist, but because of the strength of his statement, is Denton. In Nature’s Destiny, pp 289,290 Denton says:

If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serious challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary evvents, when it would not in a strict sense be junk in any case, could the finding be reconsiled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited.

First of all, let me point out that I know nothing of DNA so my thoughts here should be taken with copious amounts of salt. It’s all idle speculation from a run of the mill programmer’s perspective and not intended as criticism.

It seems to me that a designer who front-loaded information into ancester DNA and went to
great trouble to ensure that different bits of code got activated at prescribed times, might also arrange for any junk to be systematically discarded as he went along if it was going to incur costs. That’s what I always tried to do when allocating and freeing memory in a C program. Maybe that’s an argument against a front-loading designer, or maybe it means that the cost isn’t so great after all.

If instead he were to use a garbage collector then he would need to mark the DNA as junk
as soon as it’s appropriate. Otherwise a garbage collector wouldn’t know if a particular segment of DNA was pure junk, coding DNA or DNA that didn’t code for anything but did influence something else somewhere along the line. One way a garbage collector running on a computer identifies junk is to traverse all of the memory still in use, marking valid objects as non-junk and then assuming everything no so marked is junk. However, in this case not-junk is defined as referenced by some extant object, the not-junk memory might still be random garbage. Also it should be noted that you need to allocate additional memory to store flags (or a generation number etc.) for the use of the garbage collector.

I’m not sure how a cell’s replicating mechanisms could decide if non-coding DNA might be “referenced” by which I mean it either had a useful effect in the past (and therefore needed for the next generation) or is likely to have a useful effect for the current organism sometime in the future. Again, the clever old designer probably would be the one to take care
of that.

I don’t see how a RM+NS model could handle a build up of junk. If it is all conveniently located
in one place, there is a change that it a fair chunk of it could be eliminated in one go providing an advantage. If, OTOH, the DNA is fragmented with junk here, there and everywhere, then getting one or two small pieces is probably not going to make a difference to the organism’s survival. Getting lot’s of non-contiguous sequences would involve lots of mutations with potential for a lot of harm done as well and the likelyhood of the introduction of new junk at the same time.

Also, I wonder if some things might work out differently if there wasn’t genuine junk, affecting timings.

Finally, the idea of garbage collection is that the system frees up memory from time to time, or when memory use reaches a certain level, not every time a mutation produces some new junk. Would you have the GC() run, say, every 1000 generations or when junk content reached a particular percentage of the total?

Junk DNA will remin Junk DNA until a function is demonstrated for it. I am also at a loss to understand what future evolutionary events might be expected. I see none on the horizon as I indicate with my signature. What do others expect I wonder? All is see is extinction myself, lots of it.

“A past evolution is undeniable, a present evoluton undemonstrable.”
John A. Davison
.

I misspoke in my earlier message . Commoner felt it was the nucleotides that had to be gotten rid of and replication of the DNA was the way the cell had of getting rid of them with the nucleus functioning as a kind of garbage disposal. Kind of far out eh?

“A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

Front Loading~ Cascading genetic changes~ mutational functions gained lossed= Left over? or maybe Junk DNA does have a function?

Sounds like the jurry is out on this one!

Let me also address the issue of junk DNA from the perspective of a programmer. When I write a “hello world” program, and compile it up, the result is an executable that is around a megabyte in size. I could write the same thing in optimized machine language in a kilobyte or so. So it seems clear to me that modern programming methods produce significant quantities of “junk code”. Therefore I personally do not find it unreasonable for an intelligent designer to produce junk code.

Dr. Davison, I recognize your position that evolution is complete. You certainly have made a significant case for your claim. I wonder, however, if I understand your position, the first primate had within it all of the information necessary to differentiate into a human and into a chimp. If so, could it be possible that the chimp still contains remnants of the DNA that would have made it human if it had followed the other path? If segments of “this is human DNA” are found in a chimp, would that not offer significant support for your hypothesis, and seriously challenge the status quo view — NDE?

Two comments pertaining to DaveScot’s blog entry.

When I’ve made this argument in the past the counter argument was that it’s really not that much extra burden in eukaryote cells because they are so big and have such slow reproductive rates to begin with regardless of how much DNA they have to replicate in the process of making a new cell. Prokayrotes have virtually no junk DNA in comparison and their reproductive success is largely due to how rapidly they can reproduce in great numbers. It’s a good counter argument but I’m not sure I buy it.

I think a better way to think about it is to consider the resources that a cell devotes to the maintenance and replication of its genome. It turns out that these resources are a rather small fraction of those spent by the cell or organism - small enough that natural selection probably would not promote either a smaller or larger genome. At least on this basis.

What really raises a red flag about how much junk is really in all our junk DNA is a how much information is required to build an organism as complex as a human. If every single bit of information in all 3 billion bases was being used for some purpose I still find it incredible that the schematics (or recipe) for a human can be contained in a gigabyte (a gigabyte is roughly how much information is in 3B bases). To posit that it can be contained in 20 megabytes (2% of one gigabyte) stretches the limit of credulity far beyond the breaking point.

This argument doesn’t make much sense to me.

Consider a very generous, if simple, scheme, whereby each and every cell in the human body is specified by a unique combination of transcription factors, each of which is either present or absent. How many such factors would suffice to uniquely specify each and every cell? Less than 50.

Given that we have many more transcription factors than this, and given that control is not a binary proposition (on or off, present or absent), I think the resources present in a very modest genome easily suffice to account for, not just human life, but all life.

Look at things another way - how many unique combinations of a subset of, say, 10,000 of the 30,000 genes in a human genome are there? Well, obviously, there are essentially innumerable combinations. Far more than the numbers of human cells on earth. And easily enough to account for the perceived complexity of a human, or orchid, or rainforest, or …..

IMO, 1 gigabyte of protein coding sequence can go a long way.

bfast, if you were to set out to write a “Hello World” problem from scratch, would you start out by writing a load of standard library functions which your program doesn’t need? AIUI, the standard libraries provide for a wide variety of programming needs. Their presense suggests that there are a load of other programs already out there which are using some or all of the other functions.

Also those standard libaries contain recognisable instructions similar to the ones your program makes use of (after compilation). It should be possible to produce a disassembly listing of those routines similar to the one you produce the the “Hello World” part.

That’s not always the case. Some of the entries to the obfuscated C contests have blocks of apparent junk which turn out to be compressed data, and the main program turns out to be a implemention of a decompression algorithm. Such programs can’t survive even a single mutation. In others, the decompression occurs coutesy of the preprocessor (also very sensitive to mutations, and which, in any case, I don’t think we need to consider here - TTBOMK, DNA is not a high level language processed by a succession of external preprocessors and compilers).
OTOH maybe human DNA could be some sort of introductory student exercise in how to use the compiler. It may alienate some of the “humans are special” tent occupents.

ds: “If it could be done faster, using less energy, and fewer raw materials that should be a strong selection factor in getting rid of stuff that isn’t used. Yet there’s a ton of it there.”

The amount of apparently “tolerated junk dna” in higher eukaryotes remains an enigma. The official amount of human repetitive DNA, largely derived from mobile elements, etc, is around 50%. This is rather conservative as much of it has mutated beyond our ability to recognize it as mobile element/ viral/ pseudogene derived. Somewhere between that 50% and the 98% figure you mentioned is the actual fraction. I suspect it is closer to 98% of dna that is “junkish” in origin (i.e. from transposons, etc); that is not to say it remains useless. A fraction of that supposed junk sequence has been established to have been co-opted by the organism for something useful. I suspect that fraction will continue to grow as we find out more. Like DS, I think that the ability of junk DNA to modulate the physical structure/size of DNA molecules, along with when and where various parts of the DNA molecule interact with the nuclear matrix, will turn out to be important. In conjunction with epigenetic regulation, there may be layers of complexity we haven’t even imagined. One of the concerns always in the back of my mind is that the complexity is ultimately such that it may be fundamentallybeyond our intellectual capacities to wrap our heads around it. That said, the incorporation of “junk” dna for useful ends does not entail a teleological purpose for that DNA as junk DNA. Even many evolutionary biologists get confused on this point. Just because something gets incorporated into a functional component here or there doesn’t mean its original appearance was teleological in nature. I might use an old tree stump for a chair, but few would argue that the stump was brought into existence to serve as my chair.

Now, as to why a ton of this stuff is in say, mammals, as opposed to bacteria. Part of the NDE theory, as indicated above, is that it has been coopted in mammals for thus far unknown purposes. (Also there’s the low-cost argument, which I don’t altogether buy) Another important piece of the puzzle, though, lies in the details of DNA repair mechanisms and how they differ between these two types of organisms. Mammals repair their dna in such a way that they can tolerate a great deal more interspersed repetitive sequence; bacteria and lower eukaryotes can not. of course, this brings up a chicken and egg issue. It’s plausible that the repetitive element proliferation (due to the lower population sizes of higher eukaryotes) forced this dna repair alterations in these lineages; this resulted in the tolerance of even *more* transposon proliferation, etc, leading to the stupendous amounts of “junk” sequence we observe.
In support of the above, there’s rapidly growing evidence that the primary cost associated with junk dna proliferation in many taxa is nonallelic (ectopic) recombination as opposed to insertional mutagenesis.

The status quo, NDE as you call it, hasn’t got a leg to stand on and never did. There is no need to challenge myths. As for chimps and humans we are practically identical at the DNA level anyway. The most obvious difference between us at the chromosome level is about a dozen recombinations of preexisting chromosome segments. There is not a shred of evidence that any new information was required for our differences to now exist. Until such information is forthcoming, I will assume it doesn’t exist and probably never did. At present I regard Primate evolution as largely and possibly entirely a matter of position effect.

I am sure this will not be accepted by many but it represents my present posture nevertheless.

A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

In support of the above, there’s rapidly growing evidence that the primary cost associated with junk dna proliferation in many taxa is nonallelic (ectopic) recombination as opposed to insertional mutagenesis.

Here’s where I suddenly realise that I’m really out of my depth and should stick to writing buggy software.

sorry steveh, that last bit was a bit jargon-heavy as I was in a rush. To paraphrase, there has been a running debate as to whether the process of creating new junk dna insertions (mobile element copies) in the genome is what is primarily harmful to the host—since it can disrupt genetic coding regions (and hence this is why mobile elements are often found to be repressed) OR whether the most harmful consequence of mobile elements is that the cell machinery gets “confused” when repairing or recombining DNA, and accidentally recombines similar-looking repetitive DNA from different locations, resulting in genetic loss/translocations/duplications, etc. Publications are increasingly pointing to the latter effect as being the more significant of the two. That’s not to say that the insertional/disruptional effect is not important at all. There are a number of human diseases resulting from mobile element insertion. But basically, the fact the misalligned repair/recombination looks like its the most significant consequence of “junk” dna argues that the extent to which the DNA repair system or recombination system allows for such confusion will determine how detrimental the presence of repetitive/junk sequence will be. In mammals, which have a pretty good screening system for avoiding such recombinations–it’s by no means perfect–the negative effects of interspersed repetitive sequence is greatly mitigated, allowing the tolerance of more of it.

As the old saying goes, one man’s junk is another man’s treasure. How does this relate? Heck if I know.

Seriously now. I spent a few minutes today pondering the difficulty in factoring large numbers. Some of you probably know about the RSA challenge. $200,000 to the first one who factors the 2048 bit sub-prime. (http://www.rsasecurity.com/rsalabs/node.asp?id=2093). Well, quite frankly I could use the money. Who couldn’t. Anyway, the random thought came to me that humans can’t factor 1024 bit numbers very easily. Why does anyone suppose they know how the DNA system came to exist? This seems to be a problem several orders of magnitude beyond factoring numbers. Is this my intuition gone haywire? Or do I sense a real arrogance on the part of some who think they know?

Pardon this post. It’s from the part of my brain that thinks in red-neck logic.

Allelic mutations never had anything to do with creative evolution. Neither did natural selection, Mendelian genetics nor obligatory sexual reproduction, all of which are purely conservative, anti-evolutionary processes that serve only to maintain the status quo as long as possible. For the vast majority of all organisms, past and present, that has proven to be a losing proposition, leading inexorably to extinction. The era of creative evolution ended long ago. We are now in the age of extinction.

It is impossible to imagine an hypothesis more completely divorced from reality than neoDarwinism.

“Orthodoxy means not thinking - not needing to think. Orthodoxy is unconsciousness.”
George Orwell, 1984

“It is undesirable to believe a proposition when there is no ground whatsoever for believing it to be true.”
Bertrand Russell

“An hypothesis does not cease to be an hypothesis when a lot of people believe it.”
Boris Ephrussi

“A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

There is really a lot of evidence that non coding DNA has a great importance. Apart from molecular evidence of messenger RNA with regulatory functions only (that is, completely unrelated to protein synthesis), there is the classic argument made, for example, by Mattick, that the non-coding/coding ratio is the only quantitative data which correlates well enough with species complexity. Humans, with a non-coding percent higher than 98, are indeed the most complex species, but there is a rather continuos increase of the non-coding percent passing from prokaryotes to one-celled eukaryotes, and then fungi, invertebrates and so on. You can find the details, along with the corresponding article in Scientific American, on Mattick’s site (www.noncodingDNA.com).
I think there can be no doubt that we still understand very little of how DNA works. The “genetic code”, certainly an important step in understanding that, but widely overrated in the general opinion, is only a specific code to synthetyze proteins, that is the ultimate effectors of biological information, but there is no reason to believe that it is the only way information is stored in DNA or anywhere else. DaveScot has stressed very well what we could call “the information problem” in biological beings: less than 1 GB of total information, less than 20 MB of supposed useful information (protein coding). And in that, we should have all the information necessary to build a human being from a single cell, to orderly differentiate billions of billions of cells in thousands of different patterns and states, each of them derived from a special, very fine tuned, “interpretation” of the same basic genome, from a specal regulation of which and how many genes have to be translated at a certain moment, and how much each of them has to be translated.
In those 20 MB (or 1GB) we have also to find the necessary information about the space and time structure of the macroscopic human being, the pattern of tissues and organs, the pattern of neuronal connections, of humoral network regulatory systems destined to connect cells at a distance, or to fine-tune the immune response, and so on.
I understand that the information in DNA, or epigenetic, or wherever it is, is certainly very efficient. I am sure, also because I do believe that it was very intelligently designed, that it is not certainly written in some kind of visual basic counterpart, but rather in the most synthetic biological machine language. But still, I can’t believe that 20 MB will do, and I still have great problems with 1 GB.
Perhaps we must admit a few things:
1) The protein coding information is only a tiny part of the information which must be available to the cell.
2) At present, we have no idea of where and how the missing information (the real “code” of life) is stored.
3) Non coding DNA must have an important regulatory function, which at present is only partly understood.
4) May be an important part of the information is not in the form we think (that is, in the base sequence intended as digital bits). Recent observations about the importance of non coding sequences to modify DNA space structure are very interesting.
5) We have still only few ideas of how DNA transcription (the key element in cell individualization and differentiation) works, and no idea at all of how transcription regulation is guided and regulated.
6) Maybe the new science of biophysics could give, in the next few years, some of the answers which biochemistry cannot at present give.

I will bring up again the framework of Sean Carroll who believes that the area of the genome that is most responisble for morphological differences in species is not the genes but what he calls the dark matter. I gather this is everything but the genes and includes something he calls switches.

From what I have read these swithces control the proteins which he just calls the toolbox of the genome (the nuts, bolts, other parts necessary to build an organism) and there are tens of thousands of these switches which orchestrate the building of the organism during gestation and I guess afterwards too. Few organisms are finished at birth.

If anything appears to be similar to a computer program, it is the orchestration of these switches which control the expression of proteins, type of cells, placement in the developing embryo at very specific places and very specific times etc. The Time magazine article indicated that 2-3% of the genome are made up of these switches.

Am I wrong to think that this is the main area of the genome that really controls the morphology of a species and should be the real focus of research for the formation of species.

Duplication of genes, inversions, mutations, co-options etc. may be red herrings in this investigation and the real focus should be elsewhere.

“There must be a long series of possible mutations, each of which conferring a selective advantage on the organism so that natural selection can make it take over the population.”

“There must be a long series of possible mutations, each of which conferring a selective advantage on the organism so that natural selection can make it take over the population.”

Except that many of the mutations that will be involved will be intitially neutral.

“The chain must be continuous in that at each stage a change of a single base pair somewhere in the genome can lead to a more adaptive organism in some environmental context. That is, it should be possible to continue to climb an “adaptive” hill, one base change after another, without getting hung up on a local adaptive maximum. ”

This is wrong, mutations are not limited to single base pairs.

“Now one might say that if evolution were hung up on a local Maximum, a large genetic change like a recombination or a transposition could bring it to another higher peak. Large adaptive changes are, however, highly improbable.”

Mutations don’t have to be large at the DNA level to have an effect on the phenotype. It is quite possible for a single nucleotide mutation to move on an adaptive landscpae in the way he says.

“Moreover, as I have noted in my book, the large mutations such as recombinations and transpositions are mediated by special enzymes and are executed with precision - not the sort of doings one would expect of events that were supposed to be the products of chance.”

There certainly is a large degree of randomness involved, and duplications can be very random.

“But our inability to observe such series cannot be used as a justification for the assumption that the series Darwinian theory requires indeed exist.”

Or for the assumption that it doesn’t. I’ve never heard anyone say ‘we know that happened becuase we haven’t seen it happen’.

“Evolution requires a long series of steps each consisting of an adaptive mutation followed by natural selection. In this series, each mutation must have a higher selective value than the previous.”

Not really, see above.

“Thus, the evolving population moves across the adaptive landscape always rising toward higher adaptivity.”

Not necessarily, and especially not in a changing environment.

“This is particularly likely because the steps it takes are very small - only one nucleotide change at a time.”

Except it’s not.

“The problem is compounded by the lack of freedom of a single nucleotide substitution to cause a change in the encoded amino acid.”

However sinlge nucleotide changes can cause large phenotypic changes especially in places like promoter sequences.

“To get a triple change would take 1014, or a hundred trillion, years. ”

Im not sure, but I dont think anyone claiming that much apaptive evolution involves specific multiple bases changing simeltaneously and independently of each other.

I see Chrs Hyland continues to spout Darwinian pablum.

It is hard to believe isn’t it?

Why do I waste my time here?

“A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

jerry: “Am I wrong to think that this is the main area of the genome that really controls the morphology of a species and should be the real focus of research for the formation of species.”

Jerry, this “switch” notion, in one form or another, has been a popular hypothesis for years among biologists. At least it was at the time I was in graduate school. The idea being that it was a lot easier to play around with the switches to create large-scale changes in relatively short order. The problem, as in much of macroevolution, is that we still don’t have strong empirical data one way or the other so people haven’t really pushed the idea much lately. Point mutations, etc, in proteins are easier to detect right now b/c we know where the proteins are and (on occassion) what they do. Yet you’ll find no one who thinks this is the whole story. These switches (promoters, enhancers, chromatin regulators, splicing regulators, etc) we have a very poor handle on at the moment so it’s not easy to track how they’ve changed across taxa and, more importantly, what those changes produced in the organisms. One exception, possibly, is that there’s progress being made on determining the factors that have allowed the dog species to morph into all its current forms. It’s been a while since I read about it, so I won’t attempt to go into the details, but I’ll try to find the article again.

p. phillips,
I will have to read and respond to your lengthy quote–if I have something meaningful to say–after the day job is over.

“There were about five hundred stretches of DNA in the human genome that hadn’t changed at all in the millions and millions of years that separated the human from the mouse and the rat,” says Haussler. “I about fell off my chair. It’s very unusual to have such an amount of conservation continually over such a long stretch of DNA.”

Why, fall of his chair? Because, he bought into the a priori assumption of gradual change? And was astonished at the conservation of information?

“From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It’s a tiny, tiny fraction. It’s virtually impossible that this would happen by chance.”

oringally quoted from Science, 2004, research paper, funded byNHGRI, NCI, NIH HHMI. Research by David Haussler, director of the Center for Biomolecular Science and Engineering at the University of California at Santa Cruz.

http://www.sciencentral.com/ar.....=218392305

Why would the study of random mutations involve a school of Science and Engineering? Presumably because one wants to unravel the secret of life. But if life has a secret to unravel and it can be found thru complex scientific searches utilizing some of the largest computers with pattern recognition systems and complex mathematical precepts, then one must be looking for significant, repeatable and reconizeable structures. A system oriented informational construct pliable, yet conserved for survival.

When one unlocks such a secret of life, then they can utilize repeated patterns learned from this discovery to design new life forms and powerful new computer technology.

Another words, what good does it do someone like IBM to invest in the secret of life, if it’s all random and unpredictable? And why are they continuing to look for “patterns”?

And why when they look for patterns are they having success?

A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
http://www.cell.com/content/ar.....7406010993

“Intelligent Design is the study of patterns in nature that are best explained as the result of intelligence.”
— William A. Dembski

Does anyone know if experiments have been done, modifying or removing non-coding “junk” regions to see what effect it would actually have on ontogeny?

I’ve often thought the junk regions are spacers for the coding regions. After all, it’s not enough that proteins code. They have to code at the right time and in the right position. Maybe it’s the *length* of the “junk” sequences that matter, not their content. Seems to me that a smart designer might utilize such an approach because the length of a region would seems to be less susceptible to errors than the contents of a region. So where less neucleotide precision is required, use length, otherwise use specific nucleotide values. Moreover, when these non-coding regions are duplicated, it takes less effort to use random values since all that matters is their length, not their values.

mike1962
I don’t know of too many, but see:

M.A. Nobrega, Y. Zhu, I. Plajzer-Frick, V. Afzal and E.M. Rubin (2004). “Megabase deletions of gene deserts result in viable mice”. Nature 431 (7011): 988-993. DOI:10.1038/nature03022.

For an example of deleting several million non-coding base-pairs with no visible effects to mouse health.

(from http://en.wikipedia.org/wiki/J.....te-Nobrega)

From that same Wikipedia article: “A surprising recent finding was the discovery of nearly 500 ultraconserved elements[9], which are shared at extraordinarily high fidelity among the available vertebrate genomes, in what had previously been designated as junk DNA. The function of these sequences is currently under intense scrutiny, and there are preliminary indications[9][10][11] that some may play a regulatory role in vertebrate development from embryo to adult.”

Interesting

Curses! The *Spam* filter, better known as Denyse (kidding!) got me, so here is the Spetner link:

http://www.trueorigin.org/spetner1.asp

http://www.trueorigin.org/spetner2.asp

The most important point he makes, and I don’t see how NDE can combat it is below, and he has calculated the mathematical probabilities:

One must understand that at the heart of NDT lies chance and randomness. Mutations are random events. The occurrence of a beneficial mutation at any given time in any given population is governed by chance. Even natural selection, which carries the burden of being the directive force of evolution, is subject to the laws of chance. Selection coefficients are average values. What happens in any particular instance is a random event. A mutation, even one that confers adaptive benefit on the organism, is likely to be wiped out by chance events (see Chapter 3 of my book). There is a good chance that it will disappear before it can take over the population. The question is not if it can happen, but, with what probability will it happen?

NDT is a theory that is supposed to account for the natural development of all life from a simple beginning. I don’t know why we need such a theory, because the development of life from a simple beginning is not an observable. The theory is gratuitous; it comes to account for something that was never observed.

Actually, evolutionary thinking goes like this.

1. One observes present life.
2. One then assumes that it arose in a natural way.
3. One then concocts a theory (e.g., the NDT) to account for the observation, given the assumption.

I suppose that if the theory were really a good one, and could really explain well how life could have developed in a natural way, it would lend some credence to the assumption that life did indeed develop in a natural way. But it is not a good theory, and it does not account for what it is supposed to. Evolutionists, realizing this, have lately been reduced to arguing that if no one has a better theory that can account for the natural origin of life, then one must accept NDT. As you will see from some of Max’s comments below, he also adopts this approach. I don’t know why NDT merits the pedestal on which evolutionists have put it.

Now let’s get back to the probability of occurrence of one of those evolutionary steps of Max’s. Since they are chance events, we cannot say with any certainty that they will happen. The best we can do is to say with what probability such an event will occur. So, evolutionists have offered us a theory (NDT) that postulates a long string of random events to account for the existence of life, assuming it developed in a natural way. If the probability of those events were to turn out to be close to 1, then one could say that the theory accounts for the observation. On the other hand, if, according to the theory, the probability of those events were very low, one would have to say that the theory does not account for the observation. If a theory predicts observed events to be highly improbable, then one cannot justifiably say that the theory accounts for those events.

You would think that, since the issue of the probabilities of the evolutionary events is so crucial to the validity of the theory, the advocates of evolution would have calculated the necessary probabilities to make their case. But they haven’t. Since they have not made these calculations, Max is not entitled to assume that evolutionary steps can occur.

There is some difficulty in calculating these probabilities because the values of the relevant parameters are not all known. In my book, I addressed the problem of the probability of getting enough successful evolutionary steps to account for the evolution of the horse. In spite of the difficulties I just mentioned, I was able to calculate an important result. I found that either the probability of the horse evolving was impossibly low, or else convergent evolution cannot occur. This result refutes NDT, and with it Evolution A. Not only is Max’s point here not substantiated, it stands refuted.

Let me excerpt this on defining “Evolution A”:

At the outset, I shall establish an important and necessary guideline in this discussion of evolution. The word evolution is generally used in at least two different senses, and the distinction between them is important. On the one hand, the word evolution is used to denote the descent of all life from a putative single primitive source. It is the grand sweep of evolution that is supposed to have led from a simple beginning, something perhaps simpler than a bacterium, to all organisms living today, including humans. This descent is supposed to have occurred through purely natural means. Neo-Darwinian theory (NDT), which is the prevailing theory of evolution, teaches that this development occurred through random heritable variations in the organisms followed by natural selection. I shall denote the word evolution used in this sense as Evolution A. When evolution is discussed for popular consumption, it is most often Evolution A.

The second sense in which the word evolution is used is to denote any kind of change of a population. The change can sometimes occur in response to environmental pressure (artificial or natural selection), and sometimes it can just be random (genetic drift). I shall denote the word used in this second sense as Evolution B. Evolution B has been observed. Evolution A is an inference, but is not observable. The distinction between these two meanings of evolution parallels the distinction between macroevolution and microevolution, but the two pairs of terms are not identical. Evolution A is certainly what is called macroevolution, but what is called macroevolution is not identical with Evolution A. In any case, I prefer to use the A and B to avoid having to carry whatever baggage might go with the macro/micro distinction.

The distinction between these two meanings of evolution is often ignored by the defenders of Neo-Darwinian evolution. But the distinction is critical. The claim is made for Evolution A, but the proof offered is often limited to Evolution B. The implication is that the observation of Evolution B is a substantiation of Evolution A. But this is not so. Since Evolution A is not an observable, it can only be substantiated by circumstantial evidence. This circumstantial evidence is principally the fossil record, amino-acid-sequence comparisons, and comparative anatomy. Circumstantial evidence must be accompanied by a theory of how it relates to what is to be proved. NDT is generally accepted to be that theory. The strength of the circumstantial evidence for Evolution A can therefore be no better than the strength of NDT.

The important claim of Neo-Darwinism is that it can account for Evolution A. The public perceives this claim as the core of the controversy over evolution. This claim is also the source of the contention by evolutionists that life is the result of purely natural processes, which ensue from well-known natural laws. I have examined this claim in my book Not By Chance!, and have found it to be empty.

Evolution A is the principle message of evolution, namely that all life descended with modification from a putative single primitive source. The mechanism offered for the process of modification is basically the Darwinian one of a long series of steps of random variation, each followed by natural selection. The variation is generally understood today to be random mutations in the DNA. That primitive source of life is assumed to be sufficiently simple that it could have arisen from nonliving material by chance. There is no theory today that can account for such an event, but I shall refrain from addressing that issue here. That is for another place and another time. What is relevant to this discussion is that the requirement that life arose spontaneously sets, at the very least, a stringent upper limit on the complexity and information content of the putative first organism that could reproduce itself, and thus serve as a vehicle from which to launch Darwinian evolution. The issue I address here is the alleged development of all life by the Neo-Darwinian process of random mutation and natural selection, starting from a sufficiently simple beginning.

Despite the insistence of evolutionists that evolution is a fact, it is really no more than an improbable story. No one has ever shown that the mechanism of NDT can result in Evolution A. Most evolutionists assume that long sequences of microevolutionary events can produce Evolution A, but no one has ever shown it to be so. (Those few evolutionists who hold that macroevolution is really different from microevolution have changed their story several times since they first came out with it, and their mechanism is so fuzzy that I have a hard time telling what it is.)

Organisms do not get to become adapted. They appear perfectly adapted at the moment of their first appearance. From that moment on it is all down hill toward an inevitable extinction. There is no evidence that any species ever underwent any improvement during its stay on earth. Quite the contrary it was for the vast majority of all creatures a period of what Schindewolf called typostasis, followed by typolysis and ultimate extinction. Adaptation to a changing environment is nothing but another Darwinian opium dream. Any capacity to change was intrinsic in the creature at the moment of its inception and was in no sense the result of random mutation and natural selection.

Continue with your fantasies folks. I prefer the real world myself, the world of the experimental laboratory which has never supported any aspect of the Darwinian fairy tale and never will.

How do you Darwimps like them heresies? I hope they give you the runs.

I love it so!

“A past evolution is undeniable, a present evolution undemonstrable.”
John A. Davison

John, you wrote (and I better type face before Dave Scot hits the “terminate” key):

Organisms do not get to become adapted. They appear perfectly adapted at the moment of their first appearance. From that moment on it is all down hill toward an inevitable extinction.

Doesn’t that statement contradict your signature line, and let me remind you since you are forgetful, “A past evolution is undeniable, a present evolution undemonstrable”?

What about the comments that the genetic code just doesn’t contain enough information?

If I do get terminated, it’s been sort of nice knowing you. Except for “great ape”. He must be a lawyer in his “day job” — he generates a lot of…I was going to say wind, but how about heat and no light!

I better type “fast” not face. I don’t believe in Freud either.

Can “Gorilla my dreams” or what’s his name, “Great Ape”, comprehend this?

Just in - The Spectator review today of Dawkins The God Delusion . You have to register to read the review, but I’ll provide the link and an excerpt. I have quoted Charles Moore, i.e., this essay:

http://www.telegraph.co.uk/opi.....do0801.xml

Now, on to his review, and as I just did, he quotes Shakespeare:

http://www.spectator.co.uk/the.....ness.thtml

There are many things in this entertaining book which should certainly give religious people pause. Dawkins makes powerful attacks on the shiftiness of many religious apologists, and gives good examples of the sheer absurdity of some deference to religious belief. Did you know, for instance, that in the United States the Reverend Green in Cluedo has been renamed ‘Mr Green’? His points about the abuse of power by religious leaders are not new, but that does not make them less telling.

Because Dawkins is an evangelical, however, he never does his opponents the justice of taking their position seriously. Just as the televangelist takes disagreement as showing sin, so Dawkins, as his book’s title states, speaks of belief in God as a ‘delusion’. This may be an appropriate word for those who died in the Jonestown massacre, but it simply does not tell you anything worth knowing about John Henry Newman, or George Herbert, or Thomas Aquinas.

If Dawkins really wants readers like myself to check into the atheist equivalent of the Priory for what he calls ‘recovery’, he must first of all understand the condition which he seeks to relieve. He doesn’t. One of the things which sends him into paroxysms of fury, for example, is the idea that children should be brought up in a particular faith. He thinks that this turns them into ‘demented parrots’ and may make them suicide bombers. It is wrong to speak of a ‘Catholic child’, he says, or a ‘Muslim child’, because such a child can give no real consent. One should speak only of ‘a child of Catholic parents’.

The reason that Dawkins is so angry about this is that he conceives religion simply as a set of opinions: opinions, to be of value, must be genuinely, personally held, and children are not ready for this. (Actually, I don’t agree even with this: children can and must develop their opinions, and can and should be guided, though not coerced, in them by parents, and I bet Dawkins in practice thinks the same.) But religion is not, at root, a question of opinions. It is the collective (and personal) attempt to live life according to a belief about everything. The whole of each human life, from conception, is therefore part of it. Most, though not all, Christians hold that God’s grace is channelled through the sacraments, and that the sacrament of baptism makes a child a Christian — i.e. a member of Christ’s family, not a person with a set of views. It is the spiritual equivalent both of the polio vaccine and the birth certificate, and it would therefore be unnecessarily risky to withhold it. Dawkins would think this all rubbish, of course, but he ought to acknowledge that ‘brainwashing’ need not be involved. Most churches have a later rite (confirmation) which depends on the free assent to beliefs given by people judged old enough for that assent to be real.

Similarly, the story of the Fall of Man excites Dawkins’s contempt because he thinks the punishment of Adam and Eve incredibly ‘vindictive’ for the minor offence of what he calls ‘scrumping’. That wasn’t the offence: it was disobedience of the one prohibition God had given them, the eating of the fruit which bestowed the knowledge of good and evil that would lead to death. Dawkins should acknowledge the internal logic of what he does not believe. If the tree guaranteed all life, then the intrusion of death by man’s wilfulness was indeed the ultimate wrong.

It is interesting, however, that Dawkins’s devotion to Darwin’s theory of natural selection produces in him a simulacrum of religious belief. He describes the pity we feel for the unfortunate and the desire we feel for members of the opposite sex even when we cannot have children with them as ‘misfirings, Darwinian mistakes: blessed, precious mistakes’. This is the Dawkins version of the ‘felix culpa’ of Adam and Eve, ‘felix’ because it led to Christ’s incarnation as a man, and to his saving death and resurrection.

And what Darwin called the ‘daily and hourly scrutinising’ carried out always and everywhere by natural selection ‘working … at the improvement of each organic being’ is expressed just as absolutely, and just as much in terms of intention (though Dawkins denies this), as is any statement about the purposes of the all-seeing God. Darwin was a very great man, but Darwinism can turn into a Victorian faith as dated as the Clapham Sect.

It is important for Dawkins to deny a real distinction between ‘moderate’ religion and fundamentalist extremism. He needs the cannabis-leads-on-to-heroin argument so beloved of schoolmasters. Yes, there are lots of nice religious moderates, but they set children off on the slippery slope, he says. This reveals his misunderstanding of what he attacks. The difference between moderates and bigots in religion is just as vital as is the difference between liberals and fascists in politics. Moderates (inadequate word, but I haven’t got another) see man’s relationship to his creator differently from fanatics. Their religious belief in man’s sinfulness leads them to humility: how can fallen man, with his partial understanding of everything, kill in the name of God and thus arrogate Godlike powers to himself? The fanatic’s attitude is different not in degree, but in kind: God tells him to kill, he believes, and so he must.

Dawkins appears not to accept this distinction, and it leads him to the most extraordinary omission in his book — the failure to discuss, beyond a couple of perfunctory, derisive mentions, the belief in divine love. Such a belief, which is at the heart of Christianity, does not, in itself, refute atheism. But it does explain the other aspects of faith which Dawkins barely notices — the lives devoted to teaching, medicine, care for the poor, the visiting of prisoners, the abandonment of material things, the creation of beauty, the dying that others might live — which a pathologist inspecting the corpse of religion might see as even more marked than the cruelties inflicted in its name. To ignore it is Hamlet without the prince, or rather, Lear without Cordelia.

Dawkins does treat, briefly, of love. He links human ‘falling in love’ with religion, each being ‘an accidental by-product — a misfiring of something useful’. He is puzzled why the majority of the human race remains unpersuaded by such language. Could it be that this man, so clever, so confident, so scientific, so modern and so liberal, has nevertheless missed something? For all his advocacy of the inquiring mind, this is not a question that seems ever to have occurred to Professor Dawkins

P. Phillips,

I won’t be able to address every point by Spetner–the essay touches a range of issues– but I will highlight one or two key disagreements I have with his take on things. If you haven’t done so already, everyone here should consider reading the lengthy exchange between Spetner and Max at talkorigins (for Max’s synopsis) and at trueorigins (for spetner’s synopsis) to see this all in context. I largely agree with Max’s response there, as well as Chris’s points above, so I’ll try not to rehash them more than necessary. I will reiterate though, as Chris Hyland indicates above, that Spetner has an overly simplistic view of mutations, the shape and dimensionality of fitness landscapes, and how populations of organisms might be distributed and move about on those landscapes. His arguments about getting inevitably and irreversibly stuck on local maxima fail as a result. The system is immensely more complex and noisy than his depiction, peaks are broader, and more wandering in the landscape occurs than he suggests. Yet this isn’t Spetner’s main point, so I’ll leave it at that.

Where I agree with Spetner is that no one has observed and/or demonstrated microevolution translating into macroevolution. Or in his terminology, evolution A resulting from evolution B. Point taken. Sometimes, either due to ignorance or disingenuousness, pro-evolution folks will speak as though this has been definitively established. It has not. It remains, as I suspect it will remain for the forseeable future, an inference from circumstantial evidence. An inference to what we believe, for various reasons, to be the best account of Evolution A’s mechanism.

Most of us here agree that Evolution A–whatever the driving mechanism–is an undeniable fact. And virtually all of us agree that Evolution B (microevolution) is a fact. It is the inference from one the other which produces most of the sound and fury. The central issue is just how plausible is the link between the sort of “random” processes we see in Evolution B and the remarkable productions of Evolution A.
Spetner writes, “Most evolutionists assume that long sequences of microevolutionary events can produce Evolution A, but no one has ever shown it to be so. ”

Sort of. Evolutionists infer this to be the case from several lines of circumstantial evidence. They may then use this inference as a premise/assumption for the purpose of conducting studies, etc. The inference goes something like this: 1. the fossil record and genetic archeology strongly indicate evolution A happened. 2. When we look around today, to the best of our ability, the types of changes we see are Evolution B (microevolutionary) in nature. 3. invoking of uniformitarianism, we surmise that the types of changes that lead to evolution A were microevolutionary in nature. Under this view, what occurs then is basically what occurs now and is what occurred at all timepoints in between.

At the heart of Spetner’s “not by chane” argument, as well as others, is that this relationship is simply not plausible. If we, for instance, consider the probability of the mutations that would have to occur to produce some given organism, the probabilities are astronomically low. Particularly given the lower population sizes and generation times as you move up the food chain.

And yet, as Spetner himself admits: “There is some difficulty in calculating these probabilities because the values of the relevant parameters are not all known.”

Agreed. So what ultimately happens is that some generous and/or reasonable values are assumed, the calculations are attempted, and they indicate that it is astronomically unlikely for RM+NS to have produced such and such evolutionary progression, etc. It all sounds pretty gloomy for darwinism’s prospects. And, save for one or two points, I’d be inclined to agree. Most of the parameters used are generous (conservative) enough, and one might quibble here and there but ultimately it wouldn’t matter much. The thing thats missing in my opinion, though, the elephant that is often swept under the rug, is the shape of the “adaptive landscape” itself. What forms of life are possible? What transitions between those forms possible? Is the adaptive landscape sparsely populated with little islands of habitability or is it filled with possibility. It may be ridiculously unlikely to get horseform#473 specifically, but if the fitness landscape includes 40 trillion potential horse-forms, the notion of ending up with *one* of them is less insane. If you don’t understand the landscape, you can do do all the probability calculations your heart desires, and you still won’t have any idea whatsover about the plausibility RM+NS leading to evolution A (macroevolution). Combined with the fact that evolution isn’t *aiming* at anything–it’s simply exploring the available space–this suggests to me that understanding the space its wandering is crucial to understanding the plausibility question.

And we know next to nothing about the possible pathways, the adaptive space, the possible adaptive landscapes of life. So I would argue the implausibility approach is hindered by this fundamental unknown, and this is the essence of my response to Spetner. In my opinion, what we’re left with is the relative strengths of the evolutionists’ inference [evolution B results evolution A] vs. the ID inference of design [design inferred from immense complexity]. And where one falls in these camps is tied to what one makes of the circumstantial evidence as well as one’s philosophy of science.

great_ape: “3. invoking of uniformitarianism, we surmise that the types of changes that lead to evolution A were microevolutionary in nature. Under this view, what occurs then is basically what occurs now and is what occurred at all timepoints in between.”

An ungrounded inference if there ever was one. What is uniformitarianism inferred from? The physical evidence. But appeals to evidence cannot prove uniformitarianism. Uniformitarianism has to be assumed before the evidence proves anything.

Thus uniformitarinism props up NDE, and NDE props up unformitarianism.

Round and round the circle goes.

mike1962: “An ungrounded inference if there ever was one. What is uniformitarianism inferred from?”

There are several reasons one might invoke uniformity–albeit an approximate uniformity– of process for evolution. Here are some of my own thoughts; there are probably others that could offer superior arguments.

For one, it is the simpler assumption and does not entail additional nonmaterial or intelligent influences that we do not witness presently affecting population genetics. In this view, it’s an extension of occam’s razor. This is in more or less the same spirit that Lyell applied uniformitarianism to geological formations 2) when we look at the genomes of various species, of different levels of kinship, the varieties of changes that separate them are the very same type of changes that we observe arising naturally in present populations. (duplications, point mutations, rearrangements, mobile element insertions, etc). So we have robust empirical evidence that the changes that do occur in macroevolution are in the repetoire of mutations currently occurring. Finally, philosophically, I am of the opinion that we should only abandon so-called “naturalistic” explanations only at last resort, after we have exhausted all other options. This philosophical position of mine is ultimately pragmatic in origin, and is based on the past success of sticking to naturalistic explanations during the history of science. Microevolution as the generator, ultimately, of macroevolution is the best contender we have for a naturalistic explanation for evolution, and I do not believe we have exhausted it as a explanation as yet. But since microevolution has not been definitely shown to be the source of macroevolution, the door remains open for it to be refuted convincingly. Until then, I place my bets and allegiance with the ND/RM+NS hypotheses. This comes with the extremely convenient benefit of not being crucified by my colleagues. The latter being an incidental perk and in no way influencing my thoughts on the matter.

DaveScot said (too long ago to recall, probably):

art2

That may be true in eukaryotes but in prokaryotes it’s not. You’ve essentially restated the counter argument others have given but without separating the cases for eukaryotes and prokaryotes. The practical absence of any junk in prokaryote genomes is testimony to it.

??

I think that, in prokaryotes as well as eukaryotes, the resources devoted to genome replication are pretty small. This is no explanation for the difference betweem prokar