The Emerging Complexity of the Genome

_{Paul Nelson

September 24, 2007

Intelligent Design}

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Recently, a friend who thinks about (and has published on) the nature of the eukaryotic genome, said to me, “Paul, no one really knows what the genome is any more.” He went on to explain that the picture most biologists carry around in their heads, of the relationship of genes to organismal form and function — indeed, the very concept of the “gene” itself — had been seriously challenged by discoveries in comparative genomics and molecular biology within the past few years. How all this will shake out eventually, he said, is anyone’s guess. But the theory of evolution, he concluded, cannot escape the coming turbulence.

For an overview of some of the discoveries my friend had in mind, see this article from today’s Boston Globe. [Registration may be required.]

And welcome to the Golden Age of Biology. Without question, it’s now the most exciting science going. Unfolding astonishing vistas of puzzling data, theory nowhere in sight, hard creative thinking required.

Comments

ReligionProf, There are hundreds, possibly thousand of research projects every year that are ID oriented. They just do not state ID expected results in their introduction, results, discussions or conclusions. If an ID proponent could examine the research proposal prior to execution of the study, ID predictions could be included and evaluated by the findings. In present day science this would never happen as the study would probably be de-funded or made to exclude any ID relevant predictions and conclusions. You mention that Behe is a legitimate ID scientist and he has recently pointed out how current and recent research has supported ID conclusions while the research itself would never admit it had anything to do with supporting ID.jerry_{September 26, 2007
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ID redefine science? What's the definition you're working with? Are you equating "Science" with a particular philosophy? Many ID proponents do take issue with people imposing a preferred philosophy upon science, but not all ID proponents seem to consider this subject a matter to fight over.Patrick_{September 26, 2007
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Janice, I hope I am at least clever enough to know that attempting to carry on a conversation in the tone you have adopted will not be very profitable. As for what science is, I am simply repeating the views of mainstream scientists. Proponents of Intelligent Design are pretty open about wanting to redefine science, and so perhaps instead of engaging in insulting rhetoric, you should actually read some of the writings of the proponents of ID and see if you have in fact understood what they are saying. The Wedge document says nowhere that it will TEST the HYPOTHESIS of design in the hundreds of peer-reviewed articles it aims to see published. The message is clear - this is not about testing a hypothesis scientifically, but promoting an ideology. Personally, I opt for the view of the mainstream of scientists who are persuaded that neither religious nor materialistic worldviews are required results of using the scientific method to investigate the natural world. I wish I could wish you well on the journey, Janice, but it sounds like you are not on a journey. You sound very much like me in my teenage years - certain you are right, with no room for anyone, even God, to get through to you and teach you something. I hope he manages to in spite of your attitude, as he did with me.ReligionProf_{September 26, 2007
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ReligionProf, At your blog you wrote,
Michael Behe is one of the few people in the intelligent design movement with qualifications in a relevant field.
You also wrote,
[T]here is no room for actually testing and assessing the validity of [ID's] "hypothesis" in its 20-year strategic plan. This isn't science.
So despite the fact that philosophers of science have largely given up on trying to distinguish science from non-science or pseudo-science you, an assistant professor of religion, feel qualified to determine what is, and what is not, science. Dear me. Your qualifications aren't in a relevant field. Maybe you should be more circumspect with your assertions. You also wrote,
Anyone who has read the "Wedge Strategy" document will know one thing for certain about intelligent design: it has its mind made up from the outset.
Really? Anyone? Or just you and those who, like you, perceive what they want to perceive and believe what they want to believe? To the best of my knowledge few science faculties teach logic to their undergraduate students as a matter of course and this is one reason why so many "scientific" research papers aren't worth the paper they're printed on or the bandwidth they consume. Now you have given me just one more reason to believe that the same shortcoming affects theology faculties too. So which are you? A whited sepulchre full of dead men's bones, one of a brood of vipers, or just a foolish person who has only a vague understanding of what he's talking about? You want to be a teacher? Think about millstones, necks and the depths of the sea and then get your act in order if you can - if, that is, you've been chosen since before the foundation of the world. Otherwise just enjoy the rewards you have now because they're all you're going to have. If you'd called yourself JoeBlogs or JohnDoe, I wouldn't feel so angry towards you. But you call yourself ReligionProf! Proud of what you've accomplished in this dying world, are you? Oooh! I have an assistant professorship! What a clever person am I! Go away, young man. Stop talking rot and grow up. After you've grown up come back and tell us what you've learned. I wish you well on the journey.Janice_{September 26, 2007
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ReligionProf: I have read your linked article. I don't want to seem rude, but frankly I must say that you seem to understand nothing of the matter when you speak about monkeys, probabilities, etc. It would be too long to open again this discussion from scratch (plese, just read something from Dembski or Behe, trying to understand what they say), so I will only comment briefly your post here. You say: "For some, the apparent inexplicability of such aspects of our existence is a pointer towards God. For others, the fact that we can understand, and that simple laws of nature give rise to great complexity, points towards God. The problem with treating these things as ‘proof’ is that, as Van Till points out, this is a ‘heads I win, tails you lose’ situation." But what do you mean? Both the sense of wonder for the complexity of things and the fundamental fact that the universe seems to be mathematically understandable can be valid arguments, for different reasons, in the context of a philosophical discussion about the possible existence of God. Indeed, you are not giving here, not addressing in any way, any kind of philosophical argument in a real context. But both the points you mention have nothing, absolutely nothing to do with science and with ID. Although I am a little bit tired, like many others here, of repeating the same things, ID is a scientific theory about the interpretation of available data, including a tight demonstration of the complete inadeguacy of the currently accepted theory (darwinian evolution). ID has no need to rely on "the apparent inexplicability of such aspects of our existence". ID relies on the obvious inexplicability of biological beings in a darwinian scenario, and on its possible explanation in a ID scenario. ID has no need to rely on "the fact that we can understand, and that simple laws of nature give rise to great complexity". That point is simply one fundamental "working hypothesis" of the whole scientific framework, and as such it naturally applies to ID. ID relies, strongly, on the demonstration, given many times and in many different ways, that no known law, either simple or complex, can explain the kind of complexity observed in living beings, while the working hypothesis of a designer certainly can. So, there is no "heads I win, tails you lose’ situation" here, just simple and very, very valid scientific arguments, which can be understood or not, but are absolutely true.gpuccio_{September 26, 2007
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For some, the apparent inexplicability of such aspects of our existence is a pointer towards God. For others, the fact that we can understand, and that simple laws of nature give rise to great complexity, points towards God. The problem with treating these things as 'proof' is that, as Van Till points out, this is a 'heads I win, tails you lose' situation. http://exploringourmatrix.blogspot.com/2007/09/monkeys-and-typewriters-on-edge-of.htmlReligionProf_{September 25, 2007
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How can it be in non-conserved “junk” DNA?
Indeed. Junk DNA doesn't just contain a single class of sequences - there are certainly sequences that regulate gene expression, but there are also sequences that are transposons, dead transposons, pseudo-genes, centromeres, telomeres, retrovisuses and probably all sorts of other weird things. Some is functional, and we've been aware of this for a long time. Some is also probably genuine rubbish that has just accumulated. And no doubt there is the digital sequence of one of Slartibartfast's colleagues (although not in humans, obviously). BobBob O'H_{September 25, 2007
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idnet.com.au (#18): "“We are working on the alternative hypothesis that the majority of the genomes of complex organisms is devoted to the regulation of development and that most of this information is transacted by noncoding RNAs. Both logic and the available evidence suggest that these RNAs form a highly parallel digital network that integrates complex suites of gene expression and controls the programmed responses required for the autopoeitic development of multicellular organisms. If this is correct, our current conceptions of the genomic information content and programming of complex organisms will have to be radically reassessed, with implications well beyond biology.”" (Mattick) This seems in the right direction to me. Intricate interconnected parallel control of multiple gene expressions must be one of the major, if not the most important techniques by which the incredibly complex biological designs of higher organisms are built. Assuming instinctual behaviors are ultimately the function of specific neuronal structures in the brain, these instincts would just be one of many physical designs built up during embryonic development. But the apparently non-conserved nature of most of the "junk" DNA is still a major problem with this picture. It's interesting that Mattick carefully ignores the issue. If the junk DNA actually somehow specifies organismal structure in great detail, we would expect much of the developmental design description data to be conserved between classes and genera in mammals, for instance. The design data for the liver, heart, kidney, etc. would be expected to be mostly the same between mouse and man. Even the brain design data would be much the same in having the same basic overall structure and microstructure. This part of the information would need to be conserved between lineages. How can it be in non-conserved "junk" DNA? I wonder if there can be a form of data encoding on DNA sequences that works like digital data encryption, where much of the information can be the same between two different messages, but the two message data strings are very different from each other because of the use of two different decryption "keys". Continuing the digital data transmission/storage analogy, then data compression schemes would be a possibility, perhaps dealing with some of the problems of apparently insufficient base pairs in the genome for the total data. Another conceptual model would be successive holograms of similar but different objects (like an Edsel, a Pinto and a Fairlane). The data detailing the interference fringes of the different holograms would be completely different between images, but the 3-dimensional object information encoded by this data would have great generic similarities.magnan_{September 25, 2007
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gpuccio: I understand fully your reservation at that much data compression in the genome,So i will reiterate this "educated" look at the complexity we are actually looking at in the genome. Here is a quote on the poly-functional nature of the DNA from renowned Cornell Geneticist and inventor Dr. John Sanford from his landmark book, “Genetic Entropy”: There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). Dr. John Sanford (PhD in Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents! If you ate today you probably ate some food that has been touched by his work in manipulating the genetics of food crops!)bornagain77_{September 25, 2007
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I'm just so happy that research is emerging to warrant re-evaluation of Darwinian Theory. Opponents of Darwinism are basically regarded as lunatics! Hopefully this will all begin to change now.Tina_{September 25, 2007
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bornagain77: thank you for the link to Venter's paper, I was not aware of that information. Unfortunately, I could not access the whole text, because I think it would be extremely interesting. Anyway, I understand that it is rather new information, and probably it should be confirmed in further studies. That said, the concept is certainly relevant to our discussion. But, as Davescot has mentioned, bacteria are very different from eukariotes and from multicellular organisms. Although bacteria are certainly very complex, they are by far simpler than eukariotes. Besides, the almost completely lack non coding DNA, which was the subject of our initial discussion. And, like all single celled organisms, they don't need any program for specialized differentiation and body plan. So, not everything that applies to bacteria can propbably apply to more complex beings. Besides, if I understand the paper (from the abstract), the general model is similar to cloning (DNA transplanted in a cytoplasm), the only difference being that here two different "species" are involved (even if the concept of species is probably different in relation to bacteria). The fact that the final characteristics are those of the "DNA donor" should not surprise, because nobody has ever doubted that in cloning the final genetic characteristics are those of the nucleus donor. The point is that, anyway, we need a recipient cytoplasm to be able to exploit the information in the DNA, and the role of epigenetic factors is probably greater than a simple role of protein synthesis. Regarding the huge amount of information necessary in principle to build up a complex organism, like a human, I perfectly agree with you: it is certainly huge beyond our conception. That's why I can't believe that it is all in DNA, or at least not in DNA merely as a base sequence. Although I share with you the faith in the supreme intelligence of a Creator, I think that, in the science of information as we presently understand it, there are limits to how much information can be compressed, especially in a digital form, like a base sequence. With all my goodwill, I don't believe that such a great amount of information could be compressed in less than 1 gigabyte, even with multiple encriptions and codes. I prefer to think that, if that information is all in the DNA molecule (which I am not sure of), it is probably stored in other ways, and not only in the base sequence. DNA is a very complex molecule from the biophysic point of view, and one possibility could be that much information could be stored in biophysic properties of the molecule, independently, at least in part, from the base sequence. Information could be stored at a quntum level, just to make an example. Although these are extreme suppositions, we must also consider that the problem we are facing is really extreme (unless, like the darwinists, one chooses to shut one's eyes and to believe that 18000 genes can do the trick).gpuccio_{September 25, 2007
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I would love to see the data and/ or evidence that demonstrates that culled genetic accidents can cobble together command and control functions. We do have such data and evidence which demonstrates that intelligent agencies do so on a daily basis- that is design and implement command and control functions. Command and control is yet another hallmark of Intelligent Design.Joseph_{September 25, 2007
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Sorry for the long post IDNET.au, I didn't mean to be rude but I don't know how to attach as a pdf document right now. I will try to learn how to so as to avoid clogging blogs. I don't know what an edit to the post means but you are free to do it,,,but If you don't mind I would like to know exactly what that is. DaveScot, Thanks for the correction! I did put "gives tentative indication" in the sentence before Venter's link. I am not intimate with the similarities between the supporting structures of the different bacteria he used so I truthfully cannot say how much similarity is required for such transplants to be viable I still think this experiment of Venter's is a good starting point in finding the edge of how much information is required in support of a genome. And still feel that it gives weight to the fact that most of the "essential" information for "life" is indeed in the genome.bornagain77_{September 25, 2007
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bornagain Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together in just 3 billion base pairs of DNA code. That's not at all true for complex animals. You can't insert the nucleus from a duck egg into a frog egg and get either a viable duck or a viable frog. What you'll get is an unviable egg. The structures surrounding the nucleus must be from the same or very similar organism for such a genome transplant to work. Epigenetic factors are critical at least in metazoans.DaveScot_{September 25, 2007
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Bornagain 77 Long posts like that one should be published as a PDF and a link attached. They are too hard to read. May I put an edit of that post on idnet.com.au?idnet.com.au_{September 25, 2007
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First I would like to point out that Craig Venter's work in transplanting a genome from one bacteria into another bacteria gives tentative indication that much if not all of the information for "life" is encoded in the genome. Go here for overview: http://www.sciencemag.org/cgi/content/abstract/1144622 A little bit more on the complexity and wonder of the genome: To illustrate the complexity and wonder in the DNA of man, let's look at some of the work of Samuel Braunstein who is a quantum physicist at the Weizman Institute in Israel. Samuel Braustein was asked to present a talk to the science-fiction club in Rehover. What better topic, he thought, than quantum teleportation? Because of the limitations, imposed by the laws of physics, of ever teleporting any material object, Braunstein suggested the secret to teleportation would lie not in transporting people, or material objects, but would lie in teleporting the molecular information about whatever was to be teleported. Somehow, this Star Trek type teleporter must generate and transmit a parts list and blueprint of the object being teleported. This information could be used in reconstructing the object at its final destination. Presumably, the raw materials would be available to reconstruct the object at its final destination. Naturally this process raises a lot of questions that the script writers for Star Trek never answered. For example, just how much information would it take to describe how every molecule of a human body is put together? In a human body, millimeter accuracy isn't nearly good enough. A molecule a mere millimeter out of place can mean big trouble in your brain and most other parts of your body. A good teleportation machine must be able to put every atomic molecule back in precisely its proper place. That much information, Braunstein calculated, would require a billion trillion desktop computer hard drives, or a bundle of CD-ROM disks that would take up more space than the moon. It would also take about 100 million centuries to transmit the data for one human body from one spot to another. "It would be easier," Braunstein noted, "to walk." Yet the DNA of man contains the parts list and blueprint of how all these trillions upon trillions of protein molecules go together in just 3 billion base pairs of DNA code. As well, the DNA code contains the “self assembly instructions” that somehow tells all these countless trillions of proteins molecules how to put themselves together into the wonder of a human body. Yet far from the billion-trillion computer hard drives calculated by Braustein, these 3 billion letters of information in the DNA of man could easily fit onto the single hard drive of the computer I’m writing this article on with plenty of room left to spare! That ratio of a billion trillion hard drives reduced to one hard drive is truly an astonishing amount of data compression that far exceeds the capacity of man to do as such. It is abundantly clear that all that required information for exactly how all the protein molecules of man are put together is somehow ingenuously encrypted in some kind of “super code” in the DNA of man. Amazingly, many evolutionary scientists “used” to say the majority of DNA that didn’t directly encode for proteins (genes) was leftover “junk” DNA from man’s falsely presumed evolutionary past. Now this blatantly simple-minded view of the required complexity that is inherent in the DNA of man has been solidly overturned. In June 2007, an international research consortium, named ENCODE, published a huge body of preliminary evidence that gives a glimpse into the world of the DNA’s complexity. This is a quote from a Science Daily article about the landmark study. In a group paper published in the June 14, 2007 issue of Nature and in 28 companion papers published in the June issue of Genome Research, the ENCyclopedia Of DNA Elements (ENCODE) consortium, which is organized by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported results of its exhaustive, four-year effort to build a parts list of all biologically functional elements in 1 percent of the human genome. Carried out by 35 groups from 80 organizations around the world, the research served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function. The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. The revelation of a complex interwoven network is a major blow to evolutionists. Now bear in mind, this is only a “feasibility study” of 1% of the Genome. The interwoven complexity is sure to be multiplied exponentially as the effort extends to decipher the remaining 99% of the DNA. This preliminary study, of how DNA is actually encoded, clearly indicates that most, if not the entire 100%, of the DNA is “poly-functional”. Poly-functional simply means the DNA exhibits extreme data compression in its character. “Poly-functional” DNA sequences will exhibit several different meanings on several different levels. For instance, if you were to write a (very large) book similar to the DNA code, you could read many parts of the book normally and it would have one meaning, you could read the same parts of the book backwards and it would have another completely understandable meaning. Yet then again, a third equally coherent meaning would be found by reading every other letter of the same parts. A fourth level of meaning could be found by using a simple encryption program to get yet another meaning. A fifth and sixth level of meaning could be found in the way you folded the parts of the book into specific two and three dimensional shapes. Please bear in mind, this is just the very beginning of the mind bending complexity scientists are finding in the DNA code. Indeed, a study by Trifonov in 1989 has shown that probably all DNA sequences in the genome encrypt for up to 12 different codes of encryption!! No sentence, paragraph, book or computer program man has ever written comes close to that staggering level of poly-functional encryption we find in the DNA code of man. Here is a quote on the poly-functional nature of the DNA from renowned Cornell Geneticist and inventor Dr. John Sanford from his landmark book, “Genetic Entropy”: There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). Dr. John Sanford (PhD in Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents! If you ate today you probably ate some food that has been touched by his work in manipulating the genetics of food crops!) Though the ENCODE consortium is about to undertake the task of deciphering the remaining 99% of the humane genome, I firmly believe that they, and all their super-computers, are soon to be dwarfed by the sheer and awesome complexity at which that much required information is encoded into the three billion letters of the DNA code of man. As a sidelight to this, it takes the most powerful super-computer in the world an entire year just to calculate how a single 100 amino acid protein sequence will fold into a 3-dimensional shape from its 1-dimensional starting point. Needless to say, this impressive endeavor by ENCODE to decipher the entire genome of man will be very, very interesting to watch. Hopefully ENDODE’s research will enable doctors to treat a majority of the over 3500 genetic diseases (mutational disorders) that afflict man without having to fully understand that much apparent complexity in the DNA of man. The only source for purely evolutionary change to DNA, that is available to the atheistic evolutionists, is the natural selection of copying errors that occur to DNA. This is commonly known as natural selection of random mutations to DNA. What evolutionists fail to ever mention is that natural selection is actually just some totally random selection of some hypothetical beneficial mutation that has never actually been clearly demonstrated to occur in the laboratory. For all practical purposes, All random mutations to DNA, that have been observed in the laboratory (we are talking millions of observations here), are either clearly detrimental or slightly detrimental, to the organism having the mutation. All mutations that are deemed to be somewhat beneficial to the organism, such as the anti-biotic resistance of bacteria, all turn out to involve loss of function in the genome. In fact, at least 99.9999% of the copying errors that do occur to DNA are proven to be somewhat harmful and/or to the organism having to mutation (Gerrish and Lenski, 1998). Evolution assumes a high level of beneficial flexibility for DNA. But alas for the atheistic evolutionists, the hard evidence of science indicates an astonishingly high level of integrity in the DNA code! A code which Bill Gates, the founder of Microsoft, states is far, far more complex than any computer code ever written by man. Sometimes a mutation to the DNA is found to be the result of a “complex feedback” of preexisting information that seems to be somewhat beneficial to the organism at the macroscopic level (such as lactase persistence). Yet, even in these extremely rare examples of “beneficial” mutations, the questioned beneficial mutation never shows a violation of what is termed “Genetic Entropy”. Genetic Entropy is a fundamental principle of science that means functional information in the DNA cannot increase “above the level of parent species” without an outside source of intelligence putting the information in the DNA. To be absolutely clear about this, evolutionists have never proven a violation of genetic entropy in the laboratory (Sanford; Genetic Entropy, 2005), thus they have never even proven a gain in information in the DNA of organisms above the level of parent species, thus they have never conclusively proven evolution as a viable theory at the molecular level in the first place! To make matters worse for the evolutionists, even if a purely beneficial random mutation were to ever occur it would be of absolutely no use to the evolutionary scenario for it would be swallowed in a vast ocean of slightly detrimental mutations. Yet evolutionists act like evolution has been conclusively proven on the molecular level many times % DNA is extremely resilient in its ability to overcome copying errors to the DNA, yet, as stated earlier, evolutionary scientists claim that the copying errors in the DNA that do occasionally slip through are what are ultimately responsible for the sheer and awesome complexity we find in the DNA code of man. Contrary to their materialistic beliefs, mutations do not create stunning masterpieces! As well, the overwhelming “slightly detrimental” nature of all observed mutations to DNA in the laboratory has been thoroughly established by Dr. J.C. Sanford, in his book “Genetic Entropy”. He shows in his book that there is a indeed a slightly negative effect for the vast majority of mutations. These slightly detrimental mutations are not readily apparent at the macroscopic level of the organism. These slightly negative mutations accumulate over time in all higher species since they are below the power of natural selection to remove them from a genome. These “slightly negative” mutations accumulate in a higher species until “genetic meltdown” occurs in a species. Indeed, if mutation rates for higher species have stayed similar to what they currently are, throughout the history of complex life on earth, then genetic meltdown is the most reasonable cause for the numerous mysterious extinctions in the fossil record. Over 90% of extinctions in the fossil record have occurred by some unknown natural mechanism. The average time for “mysterious extinctions” is rather constant at about 4 million years per species in the fossil record (Van Valen; A new evolutionary law, 1973). Mysterious extinctions which are not part of any known major natural catastrophes in the history of the earth. I would like to point out that since the laws of physics have been clearly proven to have remained stable throughout the history of the universe, then, there is no compelling reason to suspect the naturally occurring mutations to DNA have change significantly from their present rate for any prolonged period of time. Thus the “genetic meltdown theory” is surprisingly strong as the solution to the fairly “constant rate” of mysterious extinctions of higher life-forms in the fossil record. I’ll end my paper with a bit of trivia. The capacity of the DNA molecule to store information is so efficient that all the information needed to specify an organism as complex as man weighs less than a few thousand-millionths of a gram. The information needed to specify the design of all species of organisms that have ever existed on earth (a number estimated to be one billion) could easily fit into a teaspoon with plenty of room left to spare for every book that has ever been written on the face of earth. Obviously, I am just barely touching the surface of the complexity that is apparent in the DNA of man. Yet even from this superficial examination, we find truly golden nuggets of astonishing evidence that we are indeed the handiwork of Almighty God. Psalm 139:14 I will praise You, for I am fearfully and wonderfully made;bornagain77_{September 25, 2007
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idnet: Working hypothesis is perfectly fine for me.gpuccio_{September 25, 2007
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gpuccio I favour the phrase "working hypothesis" to "assumption". The working hypothesis of ID is as important to biology, as the working hypothesis that the physical universe is mathematically structured, is to physics. Both hypotheses are constantly being verified by emerging data.idnet.com.au_{September 25, 2007
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Non coding DNA has always been one of my favourite subjects. So, allow me to add a few considerations to the very interesting discussion above. 1) Mattick was indeed one of the first researchers to really believe in the importance of non coding DNA, and to carry on serious research about that. One of the main points in Mattick's reasearch is the consideration that the rate of non coding DNA versus coding DNA is the main single feature which seems to correlate with the complexity of an organism. In that sense, it seems that it is probably our non coding DNA which makes us humans and not, say, rats. That would be consistent with the really disappointing homogeneity of the coding part, which seems to change very little between very different organisms, both as gene number and as gene quality. 2) The important thing to remember is that we really don't know where the biological code is, least of all how it works. What I mean is: genes, as we know them, are the final effectors constituting the biological machines. But the real code, the real information, is the sum of all the possible procedures, regulations, networks, which make life possible, and which make possible the astounding differentiation of each cell starting from the same genetic information, and which build and control the multicellular network, that is the from, both macroscopic and microscopic, of the organism. That "code" must certainly amount to a very huhe quntity of information, and I have real difficulties in beieving that it may be stored not only in the few megabytes of the coding genes, but even in the few hundreds of megabytes of the total genome. 2) In my opinion, non coding DNA has certainly a cery important role, but still we must understand that that role is really elusive if we look at the apparent structure of most of it: repetitive sequences, transposons, and similar. If the fundamental code is written there, it is certainly written in a way that defies all imagination. 3) Finally, I would like to mention again that it is not necessary that all the information may be found in the genome, or at least in DNA. We have some evidence of the importance of epigenetic factors. I think we should reevaluate the role of cytoplasm. After all, even in cloning experiments, we need two different factors to generate a new living being: the DNA, which in that case is taken from a somatic cell, and the enucleated ovum cell. As the somatic DNA is, in normal conditions, totally incapable to generate a living being, or even to de-differentiate, for instance, to the state of stem cell, it seems that something in the ovum cell has the power to reactivate the full potential of a genomic store which, in its present conditions, is differentiated and practically inert. 4) However we look at it, the present state of our biological knowledge is totally incompatible with any known theory. That's the beauty of it. The truth is that we don't understand, and we are daily facing a lot of apparent contradictions. And the more we know, the more contradictions arise. But, while the darwinian evolution hypothesis becomes every day more unthinkable, not to say totally impossible, the design scenario is totally compatible with the development of new hypotheses, and with the development of both empirical reasearch and theoretical understanding. The Intelligent Design framework, indeed, is not a single, specific hypothesis, but rather a fundamental theoretical assumption which allows rational hypotheses about the biological reality to be made. It is as important, in biology, as the assumption that the physical universe is mathematically structured, in physics. And both assumptions are constantly verified by known facts.gpuccio_{September 25, 2007
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Dave and bFast - what are the instinctive behaviours in cereal mildews? For their genomes are large and full of, err, junk. BobBob O'H_{September 24, 2007
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DaveScot, you are surely correct that DNA somehow encodes instinctive behavior. Further, there must be a back propogation system that allows life-patterns to become instincts. Is this the only reason why prokaryotes have virtually no non-coding DNA whereas eukaryotes have tons of the stuff? I suspect that it is only a very small piece of the reason. Eukaryotes, after all, are vastly more complex of creatures in many ways.bFast_{September 24, 2007
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I would also like to point out that since ENCODE found “an extensive overlapping network” for the human genome, this recently discovered fact clearly indicates that scientists are completely misinterpreting the genetic data from their preconceived evolutionary perspective, since the Evolution hypothesis requires that the genome be a “multiple independent collection of selectable genes”. Thus I predict all similarity based evidence culled from different genomes in support of the evolution hypothesis will have to be reinterpreted, from the proper engineering perspective, since it is now clearly impossible for the evolutionary scenario to overcome the the demonstrated poly-constrained nature of a poly-functional genome (Sanford Gentic Entropy; 2005)!!!bornagain77_{September 24, 2007
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You all might like to check out the work of John Mattick in Australia. "We are working on the alternative hypothesis that the majority of the genomes of complex organisms is devoted to the regulation of development and that most of this information is transacted by noncoding RNAs. Both logic and the available evidence suggest that these RNAs form a highly parallel digital network that integrates complex suites of gene expression and controls the programmed responses required for the autopoeitic development of multicellular organisms. If this is correct, our current conceptions of the genomic information content and programming of complex organisms will have to be radically reassessed, with implications well beyond biology." http://jsm-research.imb.uq.edu.au/jsmgroup/idnet.com.au_{September 24, 2007
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dacook:
I’ve said it before, and I’ll keep on saying it: Darwinists are “surprised and confounded” all the time by real-life findings.
On June 21, 2007 I noted in another thread that a Google search for “more complex than expected” +evolution returns almost 10,000 results. Today, only three months later, the same search returns 11,700 results. It would be interesting to continue tracking this to see what happens.sagebrush gardener_{September 24, 2007
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One should keep in mind that prokaryotes have precious little DNA that is not coding genes. Nor do they have introns which lead to polylayered encoding and transcription editing. They basically have none of the junk DNA so common in eukaryotes. Years ago I asked myself what is a primary difference between prokaryotes and complex eukaryotes. The answer I arrived at was instinctual behaviors. I believe a lot of the junk somehow encodes instinctive behaviors. It informs a bird how to build nests and sing songs characteristic of its species. It informs a human infant how to suckle and cry for attention. These are exceedingly complex coordinated behaviors that don't yield to being under the control of mechanical protein cascades. It might also explain why when experimentors recently cut a 1.5mbp swath of DNA highly conserved between mouse and man there was no adverse effect found in the GM mice. Maybe they cut out some instinctive behaviors like fear of snakes and birds that didn't subsequently show up in the lab-raised GM mice. A subsequent question, if it's true that instincts are encoded in non-coding DNA, how is that hard learned behaviors eventually find their way into DNA? Any mechanism that goes backward, from protein to DNA, goes against the core principle of molecular biology first put forward (I believe) by Crick and Watson - that information only flows one way from DNA to RNA to protein and never the reverse. DaveScot_{September 24, 2007
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idnet.com.idu (#7): "My take on junk DNA for many years has been that the so called genes code for the protein machines and building materials. That is relatively easy. They contain the hardware shop of the organism. The “junk DNA” contains the plans for constructing and maintaining organisms." This has also been my view, based just on the insufficient information carrying capacity of the protein coding portion of the genome. The recent ENCODE research clearly points in this direction. However, there seems to be a contradiction here that needs to be resolved, in the science findings from two types of research. Both the ENCODE data and necessary information content considerations mean much or most of the DNA code must be intricately interlinked, with many areas of deep multiple translations. Then random mutations changing the base sequences of most of the genome would be even more astronomically likely to be deleterious. Much of the non-coding DNA, if it is functional, would have to be "conserved" in evolution - that is, prevented from accumulation of random changes. However this seems to be contradicted by the other research findings that appear to establish that only approximately 15% of the genome is conserved. The vast majority of the genome is supposed to accumulate sequence changes proportionate to the time elapsed from when the lineages apparently diverged (this picture seems to be roughly true regardless of debates over the rates of sequence divergence). There must be some error in the data, or in the assumptions and reasoning from the data. Where is this error? One idea I have is that some of the changes accumulated in "non-conserved" regions are not really random, but actual design changes (mainly developmental regulation modifications).magnan_{September 24, 2007
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"The picture that's emerging is so immensely more complicated than anyone imagined, it's almost depressing," Rigoutsos said. I love it!idnet.com.au_{September 24, 2007
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I guess we're the few and the proud. ;) Also, when Craig Venter's genome sequence was published, geneticists were surprised at the number of differences--4.1 million!--between his and the "reference genome" of the Human Genome Project. Background on Wired. The Genome Sequence Itself The Full Paper Abstract:
Presented here is a genome sequence of an individual human. It was produced from ?32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.
Patrick_{September 24, 2007
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Thanks Paul, This article is gold: Just four years after scientists finished mapping the human genome - the full sequence of 3 billion DNA "letters" folded within every cell - they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined. Then they have the audacity to state: But few had predicted the complex orchestration of genes and nongenetic DNA suggested by the Encode research. Even more sunning was the Encode finding that most "junk DNA" is transcribed, or copied, into more RNA molecules than can be accounted for by most prevailing theories. Hey Guys, How about the all the ID proponents that have been predicting this development all along..bornagain77_{September 24, 2007
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TRoutMac:
But, and pardon me for being so slow to ask this question, is that an accurate description of the human genome project?
I believe that the mapping of the human genome is a complete mapping of every DNA base-pair in one sample human being. Call her Lucy if you will. (I am also sure that they have mapped significant segments of hundreds of other humans.) As far as generating a DNA/Gene correlation, well, I don't believe that this was the assignment of the human genome project.bFast_{September 24, 2007
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