Uncommon Descent Serving The Intelligent Design Community

Cenes and Cnome


Eric Werner of the University of Oxford published a blog piece in PLOS which I have liberally edited below. I think it is an important development in thinking about design in biology.

“The chimp really started people wondering if genes can account for the difference between humans and animals. Since the genes of chimps and humans are 98.8% identical, the differences between chimps and humans cannot be the result of the information in those few different genes.

Humans, chimps and mice are very different even if made of the many of the same parts. The information for construction and structure lies not in the information that describes the parts, rather in an architectural plan that is used by agents to construct the organism.

The information resides in the genome, but not in the genes. It is in the network architecture that consists of coding and non coding areas that determine the timing and spatial patterning of cells that ultimately results in the development of the organism.

Many traits are the result of the mutation of genes. However most genes are instructions for building parts so a mutation in a gene results in a change of a part not the overall architecture. The information for the form is not in the parts-genes. It is in the control architecture, the regulatory networks of control units, most likely contained in the vast non parts coding regions of the genome.

Let’s call these control networks cenes for control genes. Cenes can be very basic units of control, such as protein activators, or cell directives. They can combine to form networks of cooperative, conditional control. These can be linked to form yet larger cenes. The overall control network that guides the development of an organism will be called its cenome.

Many biologists have consistently confused the genes used to build the parts with the map used to build the organism. This mistake is behind the confusion about what makes us different from mice, chimps, flies or worms when our genes are similar and the gene number is very close.

The number of genes has little to do with the complexity of the organism or the constitutive information required to form the organism. The true measure of complexity of an organism is the length of the minimal genome that is necessary to construct the organism.

The genome contains the program of development, the cenome, as well as the instructions for making the parts used to build the organism.

There are genes for parts and there are genes (or cenes) that function as commands. They regulate the use of the parts-genes and they meta-regulate other command genes.

Genetic changes are not the cause of our humanity. Genes are parts and regulators they contain no information that is relevant to our humanity.

Genetics is to a large extent irrelevant to questions of our nature and of our evolution. Genes are as essential as bricks to a building yet neither genes nor bricks have any information that would help in developing an organism or building a house.

This will not be the century of the gene. It will be the century of the genome and its regulatory architecture, the cenome.”

Very well said TM, and as for your comments above at point 2. LOLOLOL! What excellent and sarcastically humorous illustrations. tragicmishap: "If body plans are at least in part determined by physical accidents during development instead of genetic accidents, then all it would take to cause a heritable change in body plan is a bad fall during pregnancy. In fact, evolutionists could use this argument to completely circumvent the need for the correct mutations." Quite true... I had not thought of that. So now what do I do??? I suppose I must leave this issue open to research, and I must go back to my conclusion @33: "I would venture to say that the body plan information is present somewhere in the genome but on another level that may incorporate gene coding regions or parts of them as well. Go find it!" Lock
Lock , here is my blog where you can leave a note to contact me: Intelligent Design - The Anthropic Hypothesis - paper http://lettherebelight-77.blogspot.com/2009/10/intelligent-design-anthropic-hypothesis_19.html bornagain77
Thanks for that reference, Lock. I went back and reread it. 1. This argument would only really be needed by ID if its primary argument that Darwinian evolution cannot produce the required mutations within "realistic probability limits" fails. I don't see ID ever having to retreat from that argument. 2. Every time this subject comes up it seems to me such an obvious truth as to be totally uninteresting. It just seems to me a bit like saying my butt is flat instead of rounded because it's receiving higher order information from the seat of my chair. Or Luke Skywalker's right hand is missing because his body plan received higher order information from a lightsaber. 3. I don't think that this is some kind of silver bullet argument against Darwinian evolution anyway. All they will say is that well the giraffe's neck is longer because it got stretched out in the birth canal causing a heritable change. Obviously that particular example is a bad one, but you get my drift. If body plans are at least in part determined by physical accidents during development instead of genetic accidents, then all it would take to cause a heritable change in body plan is a bad fall during pregnancy. In fact, evolutionists could use this argument to completely circumvent the need for the correct mutations. At least ID's probability arguments can be quantified. I think it far better we engage them on the bed they've already made, because it's increasingly uncomfortable to sleep in. tragic mishap
Thanks... Another great video! You are really plugged in; ripe with resources! I flrted with new age myself at one time. And it is a good reminder that really, the only philosphers that maintains this outdated notion of reductionism are the materialists. Its interesting that on that count, if concensus is truely hallowed as they often claim, then they are in a real pickle. Concensus is powerful, and sometimes rightly so. More will convert, and by way of evidence and reason (science). It's only a matter of time before their game collapses, but this video is a reminder to those of us who are Christians, that the new spirituality (which will concede many truths) will not be one we advocate fully. The more truth a lie has, the more powerful it is. And mankind's resistance to Christ will remain. As with the information in biology, a few right, true, and powerful chapters put in the wrong book can be devestating. As we see with the dogmatic obstinance of materialism, let us remember that there is only one God whom mankind refuses to follow consistently. Just about any other philosphy will be sought first. Christ is most often our last resort. And he was my last resort. But I am grateful He found me. Luke 19:12,14 "A man of noble birth went to a distant country to have himself appointed king and then to return. 14 "But his subjects hated him and sent a delegation after him to say, 'We don't want this man to be our king.' Recognizing what these guys talk about in your video is only a start. I have little doubt ID will overcome, but its not the end game. In science, I think it is reasonable to fear the future spritual pantheistic foundation more than the current materialistic one. Secular humanism and pantheism are already the same thing in many ways. The main difference, is this reductionism. So, sometimes I question the value of these debates, because as George Macdonald warned, "To try to explain truth to him who loves it not, is but to give him more plentiful material for misinterpretation." ( The Curate's Awakening ) (ps. ba77 is there a way to contact you? FB perhaps?) Lock
Lock, though this is a bit 'new age' in its outlook, I did find this video interesting: The Case Against Molecular Reductionism - Sheldrake & Lipton - short video http://www.metacafe.com/watch/4899469 The entire video may be viewed here: Rupert Sheldrake and Bruce Lipton - A Quest Beyond the Limits of the Ordinary (Part 1 of 10) http://www.youtube.com/watch?v=yurzNF_Z3ec bornagain77
I had to get out my copy of Signature in the Cell and refresh my aching memory. After re-reading the relevant pages concerning what I have said here, I would modify my posiiton, or at least take a less zealous stance on body plan info being present and undiscovered in the DNA. I had forgotten that there is extragenomic information in the 3 dimensional structure of pre-existing generations that affects (or directs) body plan developement. It takes some pages to put into perspective, so... Rather than opine about matters I am still grappling with myself, I will just refer everyone to the Epilogue / pages 467-477, starting at 2. Hierarchical Arrangement, Optimized for Access and Retrieval Lock
I couldn't agree more, I was only pointing out that either answer is beneficial and interesting. And I was being sarcastic because no amount of evidence, inference or explanatory power seems to satisfy some on the Evo side of the issues. One nice thing about where we stand... we want to know the truth. Lock
In at least one way, a no answer is far more interesting to an ID advocate like myself. But a yes answer leads to great predictive power and the hallowed ‘usefulness’ that so many ‘scientists’ worship.
ID "advocates" are scientists. If we lay claim to be the heirs of the scientific revolution, to men like Newton, then we have to start acting like it. We have to take responsibility for the future of science and stop acting like whiny subversive losers acting out our own insecure faith. tragic mishap
InVivoVeritas @9... THAT's what I'm talkin about! maybe I should have just read the whole thread :) Lock
@gpuccio #49 First of all, thanks for taking the time to review the paper. I found another paper paper published in Cell on February 5, 2010 related to prions and long term memory. This time, they studied, slugs (of all things) and how they "twist" the protein to lock in a memory. I don't know how one can study slugs and make a jump to human's, but the paper suggests that this mechanism could possibly be used by humans as well. Presumably, since this particular protein (CPEB - cytoplasmic polyadenylation element binding protein) behaves similar to a prion but aren't "infectious" with their folding. Perhaps these folds are replicated to other prion like structures elsewhere to form a sort of redundant storage of memories. It's a thought, but not too fanciful I should think; considering what we do know about prions and prion-like behavior and how injuries to the brain don't necessarily delete memories. Another source, a Howard Hughes Medical Institute Blog (I know...not scholarly, but informative none-the-less) ruminates as I have on the involvement of prions in forming long term memories. Just for grins and entertainment, let's assume protein folding was responsible for long-term memory storage. Wouldn't it be reasonable to estimate the storage capacity of the brain based upon the number of proteins available for folding? ciphertext
What does everyone think about "mental effort?" I mean, think about when you are trying to remember something. It feels like you are lifting mental weights, especially when you are going on too-little sleep, to recall something. Does the brain actually start working harder to locate the memory? Or do you just get frustrated and interpret that as effort? Collin
kairosfocus @37 F/N: Lock, 500 4-state elements and 1,000 2-state ones have the same configuration space size, 1.07 *10^301. G I think I understand that well enough and perhaps I am out of my depth here, but I am looking at the possibilities in terms of hierarchical complexity. I believe Meyer touched on it in 'Signature in the Cell'. He spoke of the hierarchical complexity of the English langauge. The digits can make words, and the words sentances, and the sentances paragraphs, and the paragraphs chapters, and the chapters a book. I took this to be at least part of the point of the OP article though in the smaller context of differences in species. And that certainly is an excellent application of the concept. Certainly I am not the only one who thought of it or is making this point. The point being that just because we see no sign of bodyplan in the genome (or cnome etc), we may find and should look for an even deeper layer of complexity that stores it. Perhaps it is merely there intrinsically with each genome. That would leave the question of the initial origin and design at least in my mind being far more reasonable a scientific conclusion. I am not making the case that a quaternary code is more efficient than binary even in terms of space or volume, but rather that it allows for deeper hierarchcical complexity than binary. But I am not by any means an expert on information, so perhaps this is a counterintuitive mistake on my part? Its just a thought. And it seems to me an obvious one. Whether there is body plan information in the genome somewhere I do not know. But as Gonsalez said regarding the question of life elswhere in the galaxy, the answer, whether yes or no, is interesting. In at least one way, a no answer is far more interesting to an ID advocate like myself. But a yes answer leads to great predictive power and the hallowed 'usefulness' that so many 'scientists' worship. And the more levels of complexity the better for a design inference (as if there are not enough already). Has the question of whether body plan information exists in the genome really been determined sufficiently? Lock
The ability to prevent or simply influence memory recall has no bearing on the actual storage of memories. The memories can be there, but somehow it becomes impossible or difficult to retrieve certain memories. Does anyone know what the experimental approach would be to conclude successful prevention of information storage? Why I ask this is because it is clear that claiming that a specific memory has been prevented from being stored, are always subject to the possibility that what actually happened was a prevention of recall and not storage per se. mullerpr
P.S. I consider indeterministic quantum phenomenon as "not-so-physical" by nature. mullerpr
gpuccio, I think that an accurate study into the information storage requirement to account for human long term memory (conscious and unconscious) will be very enlightening. Regardless of the physical nature or not-so-physical nature of such a storage mechanism, my intuition tells me that it could contribute greatly to science. Wasting time on non-starter hypotheses about human long term memory should be avoided, by embracing the fact that there IS something beyond the daftly confounded dogma of materialism. mullerpr
ciphertext: I have looked at the abstract of that paper. First of all we have to be cautious with that kind of information, but let's assume that what the paper says is correct and significant. Anyway, it just means that that protein is implied in the formation or in the working of those parts of the brain which are necessary for long term memory. That does not mean that the protein stores memory data. When I say that we don't know how the brain stores data, I don't mean that we don't know anything about the areas in the brain which are necessary for memory to work correctly. I just mean that we don't know how the data themselves are stored, and where. So, it is perfectly possible that a localized ledion will cause the loss of a function, such as short or long term memory. But what we do not observe is that a localized damage cuases the loss of some specific data, and not of others, as though those data were phisically stored in those neurons. That's why I say that we don't see a true mass memory, but rather a dynamic, olistic memory. As for proteins to be memory storage, it's not impossible, but it does not seem as an easy solution. Personally, I don't think that both DNA and proteins can store memory in their gross primary structure (the sequence of nucleotides or aminoacids). But they could do that at other levels (quantum levele remaining an extreme possibility). gpuccio
mullerpr: You are very right. And that makes me consider that probably the amount of long term memory stored in our subconscious mind (whatever it is) is much greater than what we usually are able to retrieve. Many experiences, like for instance the state of hypnosis, demonstrate that in particular conditions we can access memories which seem usually lost, but that must be there, somewhere, somehow. gpuccio
Since the genes of chimps and humans are 98.8% identical, the differences between chimps and humans cannot be the result of the information in those few different genes.
Some similar genes may be 98.5% identical, but no one knows the over-all similarities between the two genomes. Joseph
Also, his phrase "no reason" is obviously based on a theological not scientific argument. Collin
Bornagain, Thanks for those references. My friend a biology student and atheist was telling me that there's "no reason" for whales to have lungs. They are obviously just mammals who have evolved. A designer would have just taken a design for gills (which he says are more efficient) and plugged them into whales. But we don't see that, we see a nested hierarchy. I thought about that and came up with 2 objections. The first is that one that you said John Sanford came up with, polyconstrained complexity (?) or whatever. Gills cannot just easily be shoved into an animal built around lungs. And 2, lungs may be less efficient but maybe they still draw more oxygen at one time, which would support the whales large brain. Collin
One of the most convincing arguments of evolutionists, in my mind, is the nested hierarchy argument.
Evolution does not predict a nested hierarchy. Eric Knox "The use of hierarchies as organizational models in systematics", Biological Journal of the Linnean Society (1998), 63: 1–49.
Regardless of what is eventually learned about the evolution of Clarkia/Heterogaura, the complex nature of evolutionary processes yields patterns that are more complex than can be represented by the simple hierarchical models of either monophyletic systematization or Linnaean classification.
Nested hierarchies are completely an artificial construct- OUR way of catergorizing things. Joseph
So, the brain would seem like a PC with RAM only, and no mass memory. TRhat’s why the concept of lomg term memory becomes specially difficult to explain. -- gpuccio
I wonder if the storage medium is folded proteins? I'm not a biologist, and google can be a dangerous thing, I found a paper from the journal Human Molecular Genetics indicating a prion gene was associated with human long-term memory. I've always understood prions to be "bad" things in that they are vectors for invariably fatal neuro-degenerative disorders. Prions would be an example of data corruption, I should think. But, assuming the paper points in the correct direction, perhaps protein folding is the implementor of memory functions such as "read" and "write"? ciphertext
We have to consider the success of information theory when we consider any information storage. It will be naive to claim that we do not know how much information can be stored in a physical storage system like the DNA. The amount of pattern forming possibilities in the DNA can be inferred, which means we can calculate how much memory can possibly be stored in the DNA. When we look for long term memory in the brain it becomes clear that the pattern forming capabilities of synapses are highly unstable leaving us with a great problem. No wonder that some honest scientists would like to consider the far more stable DNA structures to possibly account for long term memory. However this "DNA long term memory" proposal cause a lot of problems. Just try to think of a possible mechanism to store and retrieve long term memory from a DNA storage system... I am not saying long term memory is not physical, what I am saying is that the brain does not look like the type of mechanism that store "mass memory", like gpuccio rightly points out. If we consider an analysis of how our long term memory present itself in our conscious acts then it is clear that we do have some kind of "mass storage" capability ...at least to account for the uniform nature of our consciousness. A personal experience of long term memory came into play when we (my family) recently were robbed of all our digital family photos and videos. It is a great loss and I was very upset since our daughter is only 15 moths old and we lost all the pictures of her birth. In this upset state I started to push my memory of the events to the extent that I can almost start drawing pictures of how she looked when she was born, when she first opened her eyes, when her mom held her for the first time... The clarity of these memory were almost scary, but it just underpin the awesome reality of human long term memory. mullerpr
ciphertext: As far as I know, nobody has really any idea of how memory is encoded. That's exactly the problem. What we know would suggest that there is no traditional "mass memory" in the brain: that is, we cannot identify any specific part of the brain, or any specific neurons, which carry the memory of some specific data. That's why all the models for memory (and believe me, they are really vague) tend to refere to some dynamic system. So, the brain would seem like a PC with RAM only, and no mass memory. TRhat's why the concept of lomg term memory becomes specially difficult to explain. gpuccio
You can't of course believe that long term memory requires a spirit. Otherwise I should probably be sharing the gospel with my desktop right now. tragic mishap
Interesting question cipher.
Has this “little problem” with materialistic long term memory disappeared? If it did what is the solution?
I have no idea. However since computers have "long-term memory" it seems quite safe to suggest that brains could have that capability as well, both being intelligently designed, physical machines. tragic mishap
Has anybody determined if human memory storage is standardized between instances of human beings? In other words, if I were to take a CD ROM for example, I could duplicate the CD-ROM contents quite easily (leaving aside the various copy protection schemes employed by the creator of the data) to another CD-ROM or other storage medium.This is due in large part because the technology was designed so that the data could be easily transferred and consumed by the masses of electronic components that need access to the data. Things such as storage geometry on the storage medium (number of sectors, pits, lands, etc...), data storage format (DVD+, DVD-, Blue Ray, Red Book (audio), etc...), etc... were all standardized.While I see that the technology such as the reading and writing components are standardized (yet you cannot easily replace them due to tissue rejection), I don't know that the same can be said for the geometry of the memories. Certainly the memory storage has been determined to be an etched pathway in our brain material (similar to how optical media is etched by a laser), but do we know if the etching is transferable? Assuming the etching is transferable, do we know that the encodings are the same between humans or are the encodings as unique to each set of brains as each human is unique to their environment? ciphertext
F/N: Lock, 500 4-state elements and 1,000 2-state ones have the same configuration space size, 1.07 *10^301. G kairosfocus
Another quote from the New Scientist article I discussed above: You must remember this
But a handful of researchers has recently suggested a new and radical idea. Perhaps long-lasting memories are inscribed not into synapse patterns but into our brain's DNA. Perhaps, say the researchers, we create gene-like codes in which we permanently record the blueprints of our memories. It's not that hard to hang onto a memory for a short time—where you last saw your keys, say, or where you parked your car. To strengthen the network temporarily, all you apparently need is a more plentiful supply of messenger chemicals poised at key synapses, ready to transmit the prepared signal. Trouble is, this effect doesn't last long. For a more permanent memory, your brain needs something substantially more stable.
Has this "little problem" with materialistic long term memory disappeared? If it did what is the solution? mullerpr
Thank you for talking sense Lock. I am a Christian and I believe that human beings have spirits. The one thing that a physical system cannot ever explain is free will. That is the one thing that must be spiritual. And when you think about it, the ability to make a choice is the one thing that matters eternally. Choosing between following God or not is the one thing that matters if you are a Christian. There is no need to believe that memory, short or longterm, must be a spiritual phenomena. In fact I think it highly probable it's a physical thing. tragic mishap
Beyond my lazy mispellings, I forgot a question mark above... "Is it not obvious that a quaternary digital code can have multiple levels of coding (and function or meaning) compared to a binary code constrained by the same digital size constraints?" Lock
GREAT article, and confirmation for me. This idea of 'regulatory architecture' hit me immediately upon coming into contact with the design arguments concerning the presence of information in biology. I did not have a term myself, but the concept was plainly intuitive enough. The illustration I used to explain this to friends was the movie 'Contact'. To unravel the code meaningfully and fully they had to look at it from several dimensions simultaneously. Perhaps there is a beter way to say that, but the point is clear. Is it not obvious that a quaternary digital code can have multiple levels of coding (and function or meaning) compared to a binary code constrained by the same digital size constraints. And that is why I was suprised to hear ID advocates, in certain published works, referring to the body plan information as not being present in DNA. I see know reason why it cannot be. Though it may remain to be proven, a set of digits in the DNA could participate in many overlapping functions or specifications when placed in the context of surrounding regions and the genome as a whole. Lots of room here for predicitions and research. I would venture to say that the body plan information is present somewhere in the genome but on another level that may incorporate gene coding regions or parts of them as well. Go find it! Lock
a few more for you Collin: 'The theory makes a prediction (for amino acid and nucleotide sequence studies); we've tested it, and the prediction is falsified precisely.' Dr. Colin Patterson Senior Principal Scientific Officer in the Paleontology Department at the British Museum https://uncommondesc.wpengine.com/intelligent-design/stephen-meyer-on-ids-scientific-bona-fides/comment-page-8/#comment-359598 Walter T. Brown, In the Beginning (1989), p. 7 Excerpt: "There is not a trace of evidence on the molecular level for the traditional evolutionary series: simple sea life > fish> amphibians > reptiles> mammals. In general, each of the many categories of organisms appear to be equally isolated." http://evolution-facts.org/Appendix/a21.htm Bones, molecules...or both? Excerpt: Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology. Can the two ever be reconciled?,,, When biologists talk of the 'evolution wars', they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging (between Darwinists) within systematics. http://www.nature.com/nature/journal/v406/n6793/full/406230a0.html The universal ancestor - Carl Woese Excerpt: What then was this universal ancestor? A discrete picture of the ancestor began to emerge only when many more sequences representing all three phylogenetic domains became available. These sequences could be seen as putting phenotypic flesh on an ancestral phylogenetic skeleton. Yet that task has turned out to be anything but straightforward. Indeed, it would seem to require disarticulating the skeleton. No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. http://www.pnas.org/content/95/12/6854.full Shilling for Darwin — The wildly irresponsible evolutionist - William Dembski - Oct. 2009 Excerpt: The incongruence of gene and species trees is a standing obstacle, or research problem, in molecular phylogenetics. https://uncommondesc.wpengine.com/evolution/shilling-for-darwin-the-wildly-irresponsible-evolutionist/#comments Do orthologous gene phylogenies really support tree-thinking? Excerpt: We conclude that we simply cannot determine if a large portion of the genes have a common history.,,, CONCLUSION: Our phylogenetic analyses do not support tree-thinking. http://www.ncbi.nlm.nih.gov/pubmed/15913459 Uprooting The Tree Of Life - W. Ford Doolittle Excerpt: as DNA sequences of complete genomes have become increasingly available, my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs. http://people.ibest.uidaho.edu/~bree/courses/2_Doolittle_2000.pdf bornagain77
Collin, I'm not sure what neo-Darwinists have sold you on for genetic evidence,,, but as more genomes become sequenced, as well as more functionality being discovered for what evolutionists predicted to be Junk DNA, yet IDists predicted to be functional DNA, I find many articles that state the sequences are all over the map; Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html Since evolutionists continually misrepresent the true state of the evidence for molecular sequences, here are several more comments and articles, by leading experts, on the incongruence of molecular sequences to Darwin's theory: Testing the Orchard Model and the NCSE’s Claims of “Nested Patterns” Supporting a “Tree of Life” Excerpt: Perhaps the reason why different genes are telling “different evolutionary stories” and “one group suggests one biogeographic pattern, and another group suggests another” is because the genes and organisms have wholly different stories to tell, namely stories that indicate that not all living organisms are ancestrally related, thereby fulfilling a testable prediction of the orchard model. http://www.evolutionnews.org/2010/03/testing_the_orchard_model_and.html Botching Evolutionary Science - Casey Luskin - April 2009 Excerpt: The textbook touts the cytochrome C tree, but it ignores the cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article in Trends in Ecology and Evolution stated: “[T]he mitochondrial cytochrome b gene implied,, an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.” (See Michael S. Y. Lee, “Molecular Phylogenies Become Functional,” Trends in Ecology and Evolution, Vol. 14: 177 (1999).) http://www.evolutionnews.org/2010/04/the_biggest_problem_in_asking.html#more Congruence Between Molecular and Morphological Phylogenies - Colin Patterson Excerpt: "As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology." http://www.arn.org/docs/odesign/od171/sampler171.htm bornagain77
So where exactly is the "cenome" that Eric Werner talks about? Bornagain, One of the most convincing arguments of evolutionists, in my mind, is the nested hierarchy argument. But I wonder if the similarity of kangaroo genes is a refutation of that argument. Collin
And while we don’t know the procedures behind the workings of the brain, we do know the form of the data stored in human memory.
Really? You have a theory that accounts for false memories, fading memories, sensory memories. I wasn't kidding about things getting fuzzy. From my point of view, long term memory does exactly what Crick predicted. It gets increasingly grainy with time. Large features remain, and features associated with strong emotional events, but detais become increasingly hard to recall. Regarding emotional fixing of memory, I can recall the names of five out of six elementary school teachers, but not a one of my middle school teachers, and only half a dozen names from high school. Petrushka
RE: gpuccio #17 --Again, I'm purely speculating. At best this is an entertaining thought experiment, at worst I've wasted all of a day considering the possibilities.Perhaps what is installed in our brain structures during this "quantum network installation" is really an OS, rather than a specific, human, application. Certainly, the OS would allow for the introduction, operation, and subsequent removal of "human applications". Much like we do with classical computing resources. Maybe, during our growth and indoctrination, what we are doing can be thought of in terms of installing applications and training for their use.I'm not sure that sort of scenario couldn't play out in strictly classical terms, (i.e. DNA and RNA being sufficient to carry the necessary information to perform an OS install) but utilizing a method of exchanging information via quantum entangled pairs would, theoretically, enable the OS repository to exist a far distance from Earth. Perhaps the quantum entangled pairs are passed along during conception? I could only guess. Theoretically, all matter here could be entangled with other particles elsewhere could it not?I wonder what the cost of communicating (energy wise) would be in using quantum entangled pairs. Presumably it would increase the larger the organism became.That may have killed my daydreaming right there. The shear cost, in energy, to effect meaningful communication via quantum entangled pairs.Oh well, it was fun while it lasted. :) ciphertext
By the way, the difficulty in finding a "mass memory for memory" us really astonishing. Indeed, it is contrary to all we do in programming, where sorage of data is the first problem to be solved. What is really surprising is that data storage, both in analogical and in digital form, must necessarily have some connection with the form of the data themselves. And while we don't know the procedures behind the workings of the brain, we do know the form of the data stored in human memory. So, it is specially surprising that we cannot find any trace of them gpuccio
BA: I appreciate your focus on NDEs. They are a fascinating topic. gpuccio
I don't know how much relevance this will have to the topic, seeing as the more we learn about the complexity of the higher levels of information in a cell, and for body-plans, the more we learn that there is vast amounts that we don't know about where that information actually resides, but, none-the-less, the following observation from mind/brain research may be of interest to the topic: A Reply to Shermer Medical Evidence for NDEs - Pim van Lommel Excerpt: For decades, extensive research has been done to localize memories (information) inside the brain, so far without success.,,,,Nobel prize winner W. Penfield could sometimes induce flashes of recollection of the past (never a complete life review), experiences of light, sound or music, and rarely a kind of out-of-body experience. These experiences did not produce any transformation.(15-16) After many years of research he finally reached the conclusion that it is not possible to localize memories inside the brain. http://www.nderf.org/vonlommel_skeptic_response.htm bornagain77
Petrushka: Mine were fuzzy at ten... gpuccio
mullerpr: It's pretty simple: all "materialistic proposals for human long term memory storage" sound "a bit desperate" :) gpuccio
#16 Gpuccio I did not mean to get into the specifics of CSI/FSCI/dFSCI or whatever acronym comes next. I just wanted to point out that complexity in a more general sense can be the result of simple processes. However, I notice you refer to the work of Dembski and Marks in this area - which presumably means their work on the LCI. This has, of course, been attacked, and in my view refuted, by many people. I even wrote one short item on it myself - really just to pull together my thoughts. markf
Thank you gpuccio and InVivoVeritas for some very information-rich comments.
Information has an inverse relationship with increasing uncertainty. Therefore those comments, and most of the comments on this thread, are not information rich. tragic mishap
Nearing 65, my molecules are becoming hopelessly fuzzy. Petrushka
Slightly off topic, but maybe in the ball park, I would like to ask a question about the materialistic proposals for human long term memory storage. What is the current consensus about the physical storage of long term memories? I have come across this interesting approach that actually sounds a bit desperate. From:
You must remember this 15 September 2001 From New Scientist Print Edition. Bryant Furlow ""It sounds plausible enough. But building permanent, stable connections is no simple process. Nearly all of the brain's molecules, including those that form the neural connections, are replaced every week or two. How long-lasting memories can be stored with such distinctly impermanent media has confounded theorists for years. The problem, says neurobiologist Sandra Peña de Ortiz of the University of Puerto Rico in San Juan, is that molecular turnover would eventually degrade these structural proteins. They'd become hopelessly fuzzy, like photocopies of photocopies. No less a luminary than Francis Crick—co-discoverer of the chemical structure of DNA—first pointed this out, back in 1984."
UB: First of all, thank you for your always appropriate contrinbutions. I appreciate them very much. You say: In the past three/five years there has been some reporting within the primary literature (which raised the eyebrows of many ID proponents) which characterized the sequencing of DNA in terms of overlapping codes. Of course, some of this has become more clearly understood, but I am wondering about your thoughts on how this might effect the issue of storage space and additional information. The problem of storage space in the genome is complex. As I see it, 3 Gbases of space is not much (and the protein coding space is obviously extremely limited). Moreover, their is the problem that most non coding DNA has apparently a partially repetitive structure, which has certainly some function (IMO), but does not seem immediately appropriate to store vast dFSCI. The possibility of multi-leveled codes is intriguing, and there are many proposals about that, none of which, as far as I know, has gained for the moment ample consensus. We know still too little about the DNA molecule to understand all possible levels where information could be stored, and anyway the quantum level certainly opens immense potentials. So, I think that at present we can only recognize that a problem exists, and that it is a big problem, and recognize our ignorance of a satisfying solution. gpuccio
ciphertext: It's an interesting possibility. As far as I am aware, such a model has never been proposed for individual cells, but something like that has been proposed for the human brain: a model where the brain would act as a terminal, receiving most of its information from a diffuse informational network (I think it is a model by some russian scientist, but I don't remember the reference). But in theory it is obviously possible, especially at quantum level. It would be interesting to thinkl in those terms to try to explain complex coordinating behaviours in the animal world, starting from bacteria (see the recent thread about bacterial communication). We certainly see forms of general high level control in multicellular beings by biochemical and neural networks (hormones, cytochines, immune system, CNS). gpuccio
markf: But whatever does control that development can be orders of magnitude simpler than the organism itself. Quite simple instructions can lead to very complicated and heterogeneous outcomes – think of fractals or the game of life. As Richard Dawkins put it – the genome is more like a recipe than a blueprint. No, I don't think so. As UB has already remarked, the example of fractals is completely inappropriate: that kind of output is simply unable to bear CSI. Let's make an example: id a B lymphocite need a specific transcriptome to achieve its phenothype, the sequence of information will be a pseudo random string, because the appropriate genes to be expressed have to be chosen for specific functional reasons, and only an understanding of those reasons can guide the writing of the appropriate information. Mandelbrots are fascinating and complex, but they are not dFSCI: first of all, their Kolmogorov complexity cannot be higher than the calculation system and the input formula, and secondly vthey have no function. Try to obtain a functional software by mere iteration of a fractal. The truth is that the only "simple" reality which can generate complex functional outputs is a conscious being (if you consider consciousness essentially simple, as I do). But even in that case, at least in the case of human consciousness, it seems to need the very complex interface of the human brain. Out of that, we have no examples of simple non conscious entities which can output dFSCI. Computers can output dFSCI only if they are complex (that is, if they have already received dFSCI: see the work of Dembski and Marks). A mapping of human transcriptomes, or of human CNS, or of any other complex functional information in biological beings, certainly needs adequate mass memory to be stored. (By the way, can I ask if you are Mark Frank with a new nickname?) gpuccio
mf, Aren't fractals a product of recursive or repeating order, describable by mathematics? This is in direct opposition to the non-ordered aperiodic nature of, say, nucleic sequencing for instance. Upright BiPed
GP, InVivo, et al, May I ask a question? In the past three/five years there has been some reporting within the primary literature (which raised the eyebrows of many ID proponents) which characterized the sequencing of DNA in terms of overlapping codes. Of course, some of this has become more clearly understood, but I am wondering about your thoughts on how this might effect the issue of storage space and additional information. Upright BiPed
It would be interesting to determine if there are structures in the human cellular replication process (maybe only active during the growth phase of a human's life) that are able to obtain information from an external source. Sort of like installing a computer's OS from a network location. You don't need all of the information to put an OS on the system, just enough to manage the hardware and get the network up and running. Then you use the small amount of necessary data to access the repository to download the data and initiate installation.It is pure speculation on my part, but it would seem that to avoid detection this long, such a structure would need to communicate using a mechanism we don't have knowledge of, or one in which we don't have a good enough understanding to fully comprehend. Something akin to communicating through quantum entangled pairs maybe. Though, I'm not sure how one could argue that a communication structure (for lack of better term) could obtain one of the entangled atoms with which to communicate.Maybe I've been reading too much science fiction these days! ciphertext
I am not a biologist so I will not argue the specific question of whether DNA is complicated enough to control the development of an organisation. But whatever does control that development can be orders of magnitude simpler than the organism itself. Quite simple instructions can lead to very complicated and heterogeneous outcomes - think of fractals or the game of life. As Richard Dawkins put it - the genome is more like a recipe than a blueprint. markf
Thank you gpuccio and InVivoVeritas for some very information-rich comments.
One thing is for sure: they are in some form in the cell at the beginning, in the zygote. That should be obvious from what we know.
gpuccio, you are right, this should be obvious. And yet, I just don't see how the information could all be there, certainly not all in the genome, for reasons that InVivoVeritas outlined (much more clearly than I could have, as a non-biologist). Your comment is really good, InVivoVeritas. You ask some fascinating questions. Granville Sewell
InVivoVeritas: wonderful post indeed.As you can see form my post #8, we seem to share the same ideas. I have just a couple of comments/suggestions. First, you can certainly include in your "map" of the missing information the specific information about individual transcriptomes in the cells, as I have mentioned in my post. If you consider that each cell type (or even each cell state) has to "choose" the right set of genes to express from a repertoire of at least 20000, you can see the complexity of the problem. Let's say we have 100 different cell types (indeed, they are probably many more). Let's say that eaxh cell type expresses a transcriptome of n genes (I really have no idea how big an average typical transcriptome may be, probably a few thousand genes). Some simple combinatorial calculation will show that the search for the right transcriptome is really demanding. And the information must be there, somewhere. Moreover, it's not only a questions of which genes are transcribed: it's crucial also hwo much each gene is transcribed, and in what order, and for how much time. And so on. Not to speak of post transcriptional and post-translational regulations. So, I do believe that our perplexity is justified, even if we only consider CSN organization and transcriptome regulation. Regarding where the information could be, I agree that non coding DNA, while certainly implortant, cannot be the only answer. You say: "What if the information (or part of it) for some (or most) such processes DOES NOT HAVE a material support, .i.e., resides outside of the Physical world." Your suggestion will have you immediately labeled as a neo-vitalist (don't worry, I have been labeled as such once here, and I have survived :) ). But I could agree, at least as a possiblility. Only I would prefer not to rely on the old dichotomy betwe3en physical and non physical, which is always frustrating. Let's say that there are things we can know about our external reality, and other that we probably don't know. The traditional DNA code is well understood at the biochemical level as a supporter information in its nucleotide sequence. I think that we could potentially keep in the loop quantum mechanics for possible deeper levels of information, given that it is usually a candidate for the physical basis of mental activity (see Eccles). And maybe the real support of deeper biological information really eludes us becasue we have not yet understood some of the properties of living beings, of systems far from equilibrium, and so on. Does that make us neo-vitalists? I don't know, but in case I can live with that. gpuccio
One of the issues that is coming clearer and clearer with every passing day and with the advancements in cell biology is that there is enormous amount of information that is needed to guide the development of an adult (human, dog, fish) from a single cell as well as controlling the day-to-day life of a child or adult at all biological levels. And so far, this information that must reside SOMEWHERE is far from being identified. Let me illustrate what I mean with the scenario of the development of the adult nervous system from a single cell. Current accepted figures are that an adult human has on average 100 billion neurons (nervous system cells). See "Brain Facts and Figures" at: http://faculty.washington.edu/chudler/facts.html This is 10 power 11 denoted here as 10 ** 11. On average, each neuron has 1,000 to 10,000 connections (synapses) with other neurons - through axons and dendrites. This is 10 power 3 (to take the smaller estimate) or 10 ** 3 with our notation. This leads to a total estimated number of synapses in a human brain as: 10 ** 11 times 10 ** 3 = 10 ** 14 or one hundred miliion millions of such synapses. No one knows for sure, but it mkes more sense that when the human development reaches the certain stage these 10 ** 11 neurons are not connected RANDOMLY between them, but rather following a "wiring plan" that is the foundation of the functioning of the whole nervous system and the brain. To try to give you a concrete idea how large is this number of 10 ** 14 synapses in the brain let's do the following exercise. Our planet population is estimated to be 6-7 billions. Let's round that up to 10 billion, i.e. 10 power 10 (or 10 ** 10). We know that humans are well connected through networks (local area, wide are, wired, wireless, in IT server farms, hubs, switches, routers, etc.). Let's try to assume that for every human there are presently 100 (10 ** 2) network connections. This leads to a total estimated number of network connections in the world to 10 ** 10 times 10 ** 2 = 10 ** 12 which is a milllion of million connections. The number of neural synapses in an adult human brain is 100 times greater than that. And this fits (mostly) in a volume of 1400 ml of the human brain. Coming back to the idea that the neurons are not connected randomly but most probable they connect to each other (in this extremly complex web-like wiring) according to some - God only knows- plan. Now the question - formulated from a pure materialist position - is the following: where in the original cell that grew into the adult human resided the following CATEGORIES of information: A. Information about how many cells to develop as nervous system cells and, in particular, to develp as different kind of neurons (various parts of the nervous system have different kind of neurons) B. Information about how to connect each neuron to other (on average 1000-10,000) neurons? This is precise geometrical (body GPS) information having permanently associated with it a timing/ synchronization component (to happen at the proper relative time in regard to the development of the other parts of the nervous system and, in general, of the body plan). C. Information about the "body plan" of the "under construction" nervous system: some of the cells will become neurons in the brain, some will become neorons in the spinal cord, some will become cells in the optic nerve, or in the eye and its parts. D. Time-based planning information. At what particular time (hour, day, week, month) in the develoment of the embryo, certain number of cells (not more, nore less) will specialize as nervous system cells, but this will happen no sooner nor later than a particular timing, dependent on the apparition and growth of the other parts (tissues, organs) of the body plan. The list above is far from being exhaustive. At the first sight the 3 billion base pairs in the human genome (or as G Sewell mentioned: the 0.75 gigabytes of information of the genome) appears to be MUCH, MUCH less that is needed to supply the information in the categories A, B, C, D above (there are many other categories not listed above). In brief, I would predict that the future development of the cellular biology, genetics and in general bio sciences will be underlined by a contimuous effort to identify the sources of this enormous quantity of information that drive with amazing geometrical, timg and functional precision the bilogical processes enumerated above. I hypothesize that, at the highest level, the sources (the "fountains") of biological information may be identified among one or more of the following lines: A. The genome is a multi-dimensional source of super-positioned information - complexly encoded and read by various cellular processes (protein construction) and control mechanisms. The revelations on this "path" already started years ago. B. What about discovering that there are more subtle sources of the information in the genome, in the base pairs? On a speculative basis, what about the idea that there might be subtle geometrical spatial varieties of the base pairs in the genome - that convey additional, significant information - so far not seen. C. There are alternative and parallel sources of information in the cell - rhybosomes, and other cell structures - this again is not a new idea. Maybe new existing and new cell structures or possible biological components "traversing" multiple cells, tissues and organs may be identified as the "depots" or sources of such biological information. D. It might become more and more difficult to examine the workings of the cell, tissues, organs and full body processes and the sources of information for these processes as well as the mecahanisms for distribution and coordination of the information driving these processes. The growing difficulties may be based on: - the finess and the microscale of the elements of the cellular world - the lack of power, resolution and the small footprint of coverage of such investugative tools when faced with the number of elements (celular components, individual microscopic proteins and cell structures that need to be accurately monitored in vivo and in real time in order to be able to decipher the essence of the cellular control mechanisms. E. The control through a software program (structured information) of much simpler problems (like a hospital information system, a database, etc.) requires still huge amounts of information. For a software engineer it is easy to undeerstand that behind all biological processes resides INCOMENSURABLE amounts of information, MANY ORDER OF MAGNITUDE larger than todays most sophisticated software systems. Thiis observation may lead to a non-conventional but christian-defensible hypothesis: what if our starting assumption WAS WRONG ? And the starting assumption was that we can identify and explain all biological processes - to an "unlimited" level of details - using a pure materialist perspective. More precisely, in this case that: a. There is unlimited progress of the level of detail we can understand the most intimate structures of life and its most delicate and complex mechanisms. What if we will find out that there are limits (theoretical or practical) beyond which our level of knowledge cannot increase, or the progress in knowledge will slow considerably? b. There is material support (in the cellular molecules, cellular components, genes, etc) for all information driving cellular processes, and more so the whole set of biological processes at the molecular and - up the scale - cellular, tissue, organ, and whole organism level. What if the information (or part of it) for some (or most) such processes DOES NOT HAVE a material support, .i.e., resides outside of the Physical world. This sounds like a metaphysical speculation. But what if someone may quantify (estimate) one day the amount of information needed to DRIVE all bioogical processes (child development from a unicellular embryo as well as day-to-day control biological processes) and find out that the number of bits of such information is higher than the estimated number of molecules in an organism? (actually should be greater than the number of distinct arrangements of these moleclules). No matter what, as a Christian, how should I understand the John 14:6 verse: "Jesus answered: 'I am the way and the truth and the life'...." Isn't Jesus Himself a sine-qua-non ingredient in every form of life ? ... Also, I see a potential justification of this thinkging in the closing verse from John 21.25: "Jesus did many other things as well. If every one of them were written down, I suppose that even the whole world would not have room for the books that would be written" One of the possible interpretation of this verse is that John makes reference not only to Jesus' miracles and His acts on Earth but also to His whole creation, including the whole material Universe and its crowning jewel the Life and material life - in its miriad of manifestations. In essence, this verse may say that if the CREATIVE information would be materialized down - through serializing in writing - it would not fit (would be much more VOLUMINOUS than) in the whole universe. By one excusable extension we may say that the biological inforamtion is so vast that it does not fit (cannot be from a point of view of capacity contained) within a cell or within the beneficiary (of such information) organism.In other words, the creative information for biological life extends (cannot be contained by) beyond the the subject organism. InVivoVeritas
Granville et al. : The concepts in this post are very interesting, but they are obviously issue with which we in ID have been familiar for years. Good to see that others are joining. Granville, you ask: At the risk of sounding like a crackpot…is it possible that the information needed is not all there, ANYWHERE in the cells? (If quoted, I will deny having asked that question.) Well, you can start do deny... :) Just kidding. Indeed, the question is appropriate and interesting. I will add a couple of comments. 1) First, it is obvious that at least part of the regulatory code is in non coding DNA, hoewer much darwinists try to deny the evidences which are already abundant. We have discussed those issues here many times. But still we must remember that the genome is the same in all the cells of a multicellular individual. So, not only the genes, but also the regulatory part of the genome needs procedures, probably very complex, to implement the different transcriptomes of the different cell types, and to buil macroscopic and microscopic order, and to connect and supervise the different parts, and to guide adaptation to external conditions, and so on. I don't know where and how those procedures are written. I have said many times that the problem of the "missing procedures" is one of the biggest in our current understanding of biological beings. But I am sure that those procedures are there in some way, that they are complex and big, and that some form of mass memory is needed to store and transmit them. 2) So, the question is: where are they? and how do they work? One thing is for sure: they are in some form in the cell at the beginning, in the zygote. That should be obvious from what we know. But are they in the genome? Or are they in the cytoplasm? Or both? And how are they written? Should we look for them in the traditional sequences of information (nucleotides), even if in non coding DNA, or should we look for some other level of organization, more complex and subtler? The fact is that at present we really don't know. But making the right questions is the necessary step to start finding answers. gpuccio
I would also like to point out that evolutionists were very biased in this following study for determining gene similarity: This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 'ORFan' genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science! Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true. This following site has a brief discussion on the biased methodology of the preceding study: https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358505 If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins: A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358868 In fact it turns out that the authors of the 'kick the ORFans out in the street' paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias: https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358547 Thanks to gpuccio for walking me through their biased methodology. bornagain77
Love the paper except for the 98.8% remark. Some Darwinian myths refuse to die: Chimp chromosome creates puzzles - 2004 Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in 'Nature' that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed "significant structural changes". In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, "we have seen a much higher percentage of change than people speculated." The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity. http://www.nature.com/news/1998/040524/full/news040524-8.html Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005: http://www.ncbi.nlm.nih.gov/pubmed/15716009 To put it mildly this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists? The Unbearable Lightness of Chimp-Human Genome Similarity Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors. http://www.evolutionnews.org/2009/05/guy_walks_into_a_bar_and_think.html#more Chimpanzee? 10-10-2008 - Dr Richard Buggs - research geneticist at the University of Florida ...Therefore the total similarity of the genomes could be below 70%. http://www.idnet.com.au/files/pdf/Chimpanzee.pdf Moreover, when scientists did a actual Nucleotide by Nucleotide sequence comparison, to find the 'real world' difference between the genomes of chimps and Humans, they found the difference was even more profound than what Dr. Richard Buggs had estimated: Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] http://www.apologeticspress.org/articles/2070 Even this more recent evolution friendly article found the differences in the protein coding genes of the Y chromosome between chimps and Humans to be 'striking': Recent Genetic Research Shows Chimps More Distant From Humans,,, - Jan. 2010 Excerpt: “many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human” since “the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans.”,,,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,," http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html Chimp and human Y chromosomes evolving faster than expected - Jan. 2010 Excerpt: "The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes. http://www.physorg.com/news182605704.html The evolutionary scientists of the preceding paper offered some evolutionary 'just so' stories of 'dramatically sped up evolution' for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes the evolutionists are required to explain. CHROMOSOME STUDY STUNS EVOLUTIONISTS Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry. http://www.reasons.org/interpreting-genesis/adam-and-eve/chromosome-study-stuns-evolutionists Evolutionists were recently completely surprised by this genetic study of kangaroos: Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 bornagain77
As we continue to discover the functionality of the non-coding genetic information, the myth of 1% difference between the human and chimp genome will continue to fade away. When you believe that 98% of the genome is meaningless junk, then why compare junk with junk? But as we begin to understand the functionality, comparisons will have to be made for the 98% of the genome that is non-coding. It is highly likely that this portion of the genome is where the real differences lie. That's what the author is saying. tragic mishap
There are 3 billioin base pairs in the genome, however a very low percentage of that number actually codes for genes. The author of this article is talking about the non-coding areas of the genome. He is not saying that this "higher order information" as Meyer called it is not in the genome. He's saying precisely what I have said on this blog every time the subject comes up. This "higher order information" is in the genome just like genes are, but it is not contained in the genes themselves. The information is in the DNA, just not in the genes. So yes, it is most likely "there". I think there has been a lot of confusion about this, so it's important to get this point clear. The term "genome" refers to all the DNA in an organism. The term "genes" does not. Genes are protein-coding areas of the genome, and they also contain certain types of non-coding DNA. However most of the "genome" is not "genes". As for the size issue, I would think an expert coder would take pride in stuffing so much information into so small a size. Not just a small size in terms of bits, but also a small physical size as well. tragic mishap
Meyer touched on this kind of idea in his original paper that caused the firestorm. avocationist
And how could anyone have believed that it only takes about 10 Mb of information to convert a chimp to a human! Granville Sewell
This is really fascinating and important. The human genome contains about 3 billion base-pairs, thus 6 billion bits, or 0.75 gigabytes of information. It always seemed obvious to me that the information needed to reconstruct a human being would have to be FAR more than that! At the risk of sounding like a crackpot...is it possible that the information needed is not all there, ANYWHERE in the cells? (If quoted, I will deny having asked that question.) Granville Sewell

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