What exactly is ID?

Just to help clarify this point, the reason that genes close to each other tend to be linked is that the chances of a recombination event occuring over a short span of DNA is low. The less DNA there is between two genes the less likely a recombination event will occur between the two genes. As the distance between two genes increases so too does the chance of recombination occuring in the gap between the two genes.

Maybe I'm just in a post lunch funk, but those last two sentences read like the opposite of what I thought you were trying to say. If I've gotten this backwards then please ignore and apologies, etc...--Percy

I reread it several times and it appears to be correct, but my mind could be playing tricks with me. I find that often happens when you read your own stuff, you project your intended meaning and can sometimes miss obvious mistakes. So here is a different explanation.Just to make the math easy, let's say the probability of a recombination event (i.e. a cross over in meiosis) occuring at any single base is 1 in a million (1 in 1E6 shorthand). If two genes (or more accurately, two alleles) are separated by 100 bases then the chances of a recombination event occuring between the genes is 1E2 in 1E6, or 1 in 1E4. If there are 1E6 bases between two genes then the chances of a recombination event between the two genes is 1 in 1. The more bases there are between the two genes the more likely they are to be separated during meiosis.

SO writes: Pretty much the same thing that is stopping all of the air molecules in your room from suddenly all being in one half of the room. Well, lest I get into a True Scotsman retreat, I'll just say I was wrong.Perhaps I would point out that in these cases, it was by Intelligent Design via Homo Sapiens.SO brings up inside we find: I would strenuously object to the words "recruited for its role", but rather something closer to "given the role".My reading of the site leads me to believe that they dont have the "Tree of Life" properly defined in their heads, especially since their own words regarding Pax 6 would seem to imply common ancestry.Continuing from the site: No - this just means that that particular sort of result is heavily favored when it randomly comes up. No, no, no. You cant have your cake and not have your cake. All the research shows is that there are ZILLIONS of ways biology evolves. Fascinating.Just because they haven't gone back far enough in the "Bush" of life doesn't mean they've falsified it.BTW Bush Of Life is probably a better way to describe it rather than insisting on only 2 branchings at a time. Yeah - it's way more complex than the untrained peanut gallery observers can imagine. There lots of systems that have "except when it doesn't" clauses that - upon careful educated scrutiny - turn out to be reasonable conclusions based the data to date.No surprises here.What I see in this site is an unbelievable amount of smugness on the authors. You can almost see them rubbing their hands and nodding to each other with grins "Oh - we got them now!" LOLThey haven't made a point at all.

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- xongsmith, 5.7d

Hi Smooth Operator. I can, whether you will consider understanding it, or not, is the bigger question.Simply put, they died.As your great great ancestors are no longer able to reproduce because they are dead, so too are all organisms that have died.In this case, millions of years ago, including all the other dead ancestors of the living populations of bears and alligators.It's a simple concept. Each generation reproduces while that generation lives, not before nor after.Evolution is the change in proportion of hereditary traits in breeding populations from generation to generation in response to ecological opportunity. ps - it's phenotype ...For another very simple reason: there is no (natural) mechanism that would cause this to happen. You don't need to worry about stopping something that will never start.There is no way for natural selection to operate, or any other mechanism known to biology and the real world, to draw the genes closer to similarity.DNA doesn't change because you want it to, the change is mostly random, and the results are then filtered by selection processes to adapt the organism to the ecology it inhabits.Both organisms are adapted to their ecology and don't need to turn into the other to be adapted to their ecology. Good, I'll mark this down as a step forward. Because they found (and continue to find) skulls with this opening and arch belonging to therapsids and therapsid descendants, but not in ancestral species or in other hereditary lineages. In later descendants the opening closes, leaving the arch as a derived new feature in all descendant species. You have this arch, as do bears.For clarity, the arch "giving a superior bite" is present in the therapsids and descendants. Descendants can take advantage of opportunities to improve the jaw further, but they don't have to: not all descendants of therapsids evolved into cyconodonts. By following the evidence of derived and inherited ancestral traits. The whole pattern of the fossils show many aspects that are not altered from ancestral forms (ancestral traits), and some that are undergoing transitions that become more derived over time (derived traits). The synapsid arch is a case in point: it appears in one species (derived), and then you see it inherited (ancestral) in descendant species with continued development (further derived) as the arch becomes more developed and the skull closes back together under the arch. This occurs through the evolution in many species, that each inherit their pattern/s of derived and ancestral traits as they evolve generation by generation.See Derive - Wikipedia
for what is meant by "derived": "In phylogenetics, a trait is derived if it is present in an organism, but was absent in the last common ancestor of the group being considered. "An ancestral trait is a trait that is shared between the species and an ancestral species (common ancestor).When a fossil is >90% similar to an ancestral species with <10% derived (evolved) from the remaining ancestral features, as we see with the synapsid arch, then hereditary lineage is the most logical explanation. This is no different than looking at species that are all similar fossils and concluding that they are all the same species. When it is between an ancestral species and a descendant species in the development of the derived traits.See Transitional fossil - Wikipedia
or Transitional features - Understanding Evolution

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Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms. There are numerous examples of transitional forms in the fossil record, providing an abundance of evidence for change over time.

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Again, it is a simple concept: species evolve, there is no species alive today that is not going through changes in the proportions of hereditary traits in breeding populations from generation to generation in response to ecological opportunities. Thus population A evolves into population B as the old members die and new members are born, and population B evolves into population C as the new members age, older ones die, and new ones are born: the members of population B are intermediate between population A and population C. Now introduce increasing numbers of generations between A and B and between B and C and you still have intermediate forms in population B that have ancestral traits in common with the ancestral traits in population A and derived traits in common with some of the derived traits in population C. Oh dear, you've made the unfounded assumption that you are a reasonable person. The vast evidence of this thread and the one about the earth being fixed with the sun orbiting around it, speak volumes to your not being a reasonable person, but an unreasonable and obstinate person. I expect you will now demonstrate how unreasonable and obstinate you are. The evidence is available in the information already presented, evidence that any reasonable person can take as a starting point and investigate further if they want to. Denying that this evidence exists is not being reasonable, and I'm not about to spend a lot more time on someone that I don't consider willing to confront the evidence realistically. Because there are no fossils of existing species in the fossil record at the time of the reptilomorphs, while there are fossils that show their evolution from the ancestral forms from reptilomorphs to todayBecause there is evidence that shows the evolution pattern given and there is no evidence that shows your pattern. I said that observing a bear and an alligator reproduce viable offspring would tend to invalidate common descent, not that any hybrid between closely related species would invalidate it.American bison - Wikipedia

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Order: Artiodactyla
Family: Bovidae
Subfamily: Bovinae
Genus: Bison
Species: B. bison

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Cattle - Wikipedia

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Order: Artiodactyla
Family: Bovidae
Subfamily: Bovinae
Genus: Bos
Species: B. primigenius

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So they are interbreeding between members of the same subfamily, not between organisms from different class levels of ancestry.Alligatoridae - Wikipedia

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Kingdom: Animalia
Phylum: Chordata
Class: Reptilia
Order: Crocodilia
Family: Alligatoridae

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Bear - Wikipedia

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Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Carnivora
Suborder: Caniformia
Family: Ursidae

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There is much much more genetic difference between bears and alligators than there is between cows and bison. They are not much more different that the hybrids of horse and donkey and zebra, some of which are fertile.Horse - Wikipedia

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Order: Perissodactyla
Family: Equidae
Genus: Equus
Species: E. ferus

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Donkey - Wikipedia

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Order: Perissodactyla
Family: Equidae
Genus: Equus
Species: E. africanus

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Zebra - Wikipedia

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Order: Perissodactyla
Family: Equidae
Genus: Equus
Species: Equus zebra, Equus quagga, Equus grevyi

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Interfertility does not necessarily cease between sibling species if there is no opportunity to interbreed and no selection pressure to change.The cow and bison did naturally interbreed, once they were introduced to the same area, but not all of the offspring were fertile, and it took a while for humans to develop a complete separate breed.There is also the "cama" - part camel part llama (only 3 so far, don't know if they are fertile).http://taylorllamas.com/Camel-LamaCrossPhotos.htmlCamel - Wikipedia

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Order: Artiodactyla
Family: Camelidae
Genus: Camelus

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Llama - Wikipedia

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Order: Artiodactyla
Family: Camelidae
Genus: Lama

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Members of the same family, but cannot breed naturally.Cama (animal) - Wikipedia

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A Cama is a hybrid between a camel and a llama, produced via artificial insemination at Camel Reproduction Centre in Dubai.[1] The aim was to create an animal with the size and strength of the camel, but the more cooperative temperament of the llama.[2]

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The Dromedary camel is six times the weight of a Llama, hence artificial insemination was required to impregnate the Llama female (matings of llama male to Dromedary female have proven unsuccessful). Though born even smaller than a Llama calf, the Cama had the short ears and long tail of a camel, no hump and llama-like two toed pads rather than the dromedary-like pads. All six camelids are pedopods, having two padded toes instead of hooves.

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At four years old, the Cama became sexually mature and interested in llama and guanaco females. This first Cama has been a disappointment behaviorally, displaying an extremely poor temperament. Four Camas have since (April 2008) been produced using artificial insemination [4] .

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Despite approximately 2—3 million years of evolutionary separation, both Old World and New World camelids have by chance maintained the same number of chromosomes, seventy-four, making this extraordinary cross-breeding between not only distinct species, but distinct genera, much easier and more likely to produce fertile offspring.

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So we see that evolution doesn't necessarily change the ability to breed between species that do not normally come into contact.There have also been no successful attempts to mate cows and camels even though they have coexisted for thousands of years and belong to the same order level above family (but which excludes horses and bears). There have been no successful attempts to mate species at higher\older levels of ancestry, and the common ancestor level of alligator and bear is significantly higher\older than these examples.Enjoy.Edited by RAZD, : splng

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This may be a bit OT but i feel it is an important question to ask.Recently to my great embarassment, I learned of Norman Borlaug's demise. Of course I did not learn that through my usual sources - Google News, the NYT, or BBC News. I found out from Cracked.com.Now for those few here, but evidently many elsewhere, Norman Borlaug is famous because through his hybridization of various food crops during the 60's he saved between one and two billion lives.That number, even at the lowest estimate, is far larger than all the people Hitler, Stalin, Mao, Pol Pot, Timur, Genghis Khan, Attila the Hun, and Torquemada along with many others managed to kill.As it is clear, there is no great amount of publicity for saving lives, only for shortening them.Well, it is easy to understand that bad news crowds out good, so despite such mainstream media bias, I offer the ID and YEC supporters their chance, right here, right now.Given that truth I was wondering - How many lives has the concept of Intelligent Design or Young Earth Creationism saved or even financially improved? After all, ID has been around since the 80's and hardcore YECism since 1961. Isn't it time we should be seeing some results?I mean, crap, just on Google right now I'm reading about some ceramic box that can produce electricity at less cost and environmental impact than previous technologies.So what is the deal with ID and YEC? Can you give the world something positive or is it just like Juche, the official religion of North Korea, which incidentally and evidently has something against generating electricity.Isn't it time to put up or shut up, after all us supporters of science seem to come up with something better every day while you........Please chime in should you have something to crow about.Edited by anglagard, : add n to give for the sake of the mighty, yet fallible, English languageEdited by anglagard, : add 'great amount of' before 'publicity' for honest accuracyEdited by anglagard, : Add connecting paragraph to make more sense.Edited by anglagard, : that aforementioned paragraph needed some more tweaking

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The idea of the sacred is quite simply one of the most conservative notions in any culture, because it seeks to turn other ideas - uncertainty, progress, change - into crimes.
Salman RushdieThis rudderless world is not shaped by vague metaphysical forces. It is not God who kills the children. Not fate that butchers them or destiny that feeds them to the dogs. It’s us. Only us. - the character Rorschach in Watchmen

They've given you hours of free entertainment.

I'm a supporter of science too. What have you done for me lately ?

Do you have a cell phone? When was the last time you went to a Doctor? In another thread you were talking about the work of the ENCODE project. These a just small samples of what Science has done for you.Can anyone show us anything ID has given us? Other than headaches, laughs and a barometer with which to gauge how stupid some people can be?Edited by AZPaul3, : the usual culprits.

You see that machine you are using to type that idiotic message? SCIENCE did that.

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"Some people think God is an outsized, light-skinned male with a long white beard, sitting on a throne somewhere up there in the sky, busily tallying the fall of every sparrow. Othersfor example Baruch Spinoza and Albert Einsteinconsidered God to be essentially the sum total of the physical laws which describe the universe. I do not know of any compelling evidence for anthropomorphic patriarchs controlling human destiny from some hidden celestial vantage point, but it would be madness to deny the existence of physical laws."-Carl Sagan

If you believe in some global flood from 4350 BCE, then you do not support any normal understanding of the sciences of physics, chemistry, geology, biology, or anthropology. Well, just last week I helped a few nursing students find reliable sources of information so they don't accidentally kill someone through ignorance of, what us academics call a normal understanding of chemistry and biology.Someday, one of those nurses may be involved in healing your illness. Edited by anglagard, : clarity

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The idea of the sacred is quite simply one of the most conservative notions in any culture, because it seeks to turn other ideas - uncertainty, progress, change - into crimes.
Salman RushdieThis rudderless world is not shaped by vague metaphysical forces. It is not God who kills the children. Not fate that butchers them or destiny that feeds them to the dogs. It’s us. Only us. - the character Rorschach in Watchmen

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I am quite happy to leave it at the known function was lost, but we don't know if there were any other functions which remained or other functions gained. You, on the other hand will only leave it there if we hide the fact that you originally argued that ALL functions were lost.

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Why would I argue for that when I said before, and now, that that is NOT my main argument? My main argument is to find out how much mutations can a certain function take before it becomes useless.

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Because your reason was incorrect, but the closest you will get to admitting it is trying to conceal the fact that you said it.

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So you are again accusing me of lying...

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THe reason why it is more likely for dice is that the result of the throw is random. The production of proteins is not random - the structure is controlled by the gene. So getting multiple copies of the same protein is not at all like throwing dice.

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But genes are the ones that are under teh question of being designed. It's notl like they are a product of some natural law. There is no natural law that directs a DNA sequence to code for a flagellum. It was either produced by chance, or it was designed.

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Of course what you say is quite silly. If we simply consider Dembski's idiosyncratic usage of complexity getting 500 heads in a row is a "complex" sequence. But in normal usage it would be seen as simple.

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I see you basicly have no more arguments. You are not arguing with me anymore, nor with Dembski, nor with the whole mathematical community. You are now in an argument with the logic itself. As far as I'm concerned, our discussion is over. I'll continue it simply because I will do so, but in reality there is no real reason to do so.If you deny something as simple as the inversly proportional relation between complexity and probability than we have nothign to talk about anymore.If you want to get 6 on all dies you have the relationship between probability and complexity will be something like this.More dice, less probability.
Less dice, more probability.5 dice, a certain probability.
3 dice, more probable than 5 dice.
7 dice, less probable than 5 and 3 dice.This is what you are denying. You are denying pure logic. This is not something I or Dembski made up. This is something you learn in the first year of college.

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I wouldn't like to speculate on Dembski's motives here.

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Neitehr am I asking you about the motives.

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I didn't say that it was.

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Well you can't have it both ways! Either its used or it's not. Either you accept the principle of insufficient reason or you don't. Do you or do you not. If you do, than fine. If you don't, explan why.

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That's also wrong. Statistics are useful in dealing with approximations (e.g. calculation of error bars) but approximations are no better in statistics than in any other branch of maths.

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What!? What did I say that was wrong?

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And you will notice that your wikipedia quote says nothing about uniform probability or the reasons for assuming it... In fact all it does is give the reasons for treating dice in terms of probabilities instead of exact predictions. Maybe you should have quoted the previous paragraph, but then that contains a reason FOR assuming that each number is equally likely.

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Yes it does. It says that it's because we do not know the exact mechanics behind the dice roll.

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Dembski claims that his method produces a mathematical proof of design - so no, approximations aren't good enough,

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LOL! He never, ever said that. NEVER, as in NEVER. He actually said that the design inference is NEVER perfect. And that is why he compared the Explanatory filter with a net. He said that it catches some design, and leaves out other instances of design. He also said that some things are still possible without being probable. And his method would falsify such a hypothesis that is possible, but not probable. That's approximation.You have no arguments left. You are just making things up now as you go...

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I don;t see why they should be expected to come here to back up your claims. And if they were supposed to show it in the paper all you have to do is to find the section where they did it.

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What exactly is it that you want to see? They modeled that reproductive fitness with size of the population, reproduction, selective pressure and recombination as variables is this not a representative of a living population?

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Well that's a confused mess. Nevertheless it seems clear that even an inviable cheetah embryo will have more genetic information than a perfectly viable RNA self-reproducing RNA strand - so obviously the absolute measure is not what we need.

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No, you are the one who is confused. Please explain the following logic to me."inviable cheetah embryo has more genetic information than a perfectly viable RNA self-reproducing RNA strand THEREFORE there is no such a thing as an absolute information measure"Please do explain this logic. It's totally meaningless.

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The same thing that you asked me to do. That is what "you are refusing to do the same thing" means.

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You are making absolutely no sense anymore...

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Just two problems with that. On is that inventing the gene gun doesn't require a knowledge of population genetics. The second is that it is quite possible that Sanford doesn;t agree with you.

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1.) The gene gun is used to genetically modify genes. Genes are studied in population genetics, he studied about it, he knows it.2.) He agrees with me, because I agree with him. I actually quoted him here, but you obviously don't care much about that.

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In other words "reality itself" does not say that the full genome is passed on by sexually reproducing species. Only half the genes are, and those are mixed by recombination. This is why we can't use the genome as the unit of selection - it doesn't persist long enough for the statistical effects to build up and dominate over noise. We need something that lasts, something that can spread through a population - and the full genome obviously isn't it.

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You are missing teh point.BEFORE!!!Do you hear me!?BEFORE!!!!!Before that HALF of genome can be passed on, the FULL, do you hear me again, the FULL GENOME will be evaluated by natural seelction! Not HALF of the gene, but the full gene. Based on all genetic and non-genetic traits. The most "fit" based on all of those traits will be selected. Not based on how good individual gene is, but how good the whole genome is!And by saying soemthing so stupid as the genome is not lasting, you are just digging an even deeper hole here. Are genes longer lasting!? You said yourself that only half of the genes get passed on. So guess what? Some genes do not go to the next generation. Obviously they are even less lasting. So how in the world could they be a unit of selection!? Some are even destroyed by mutations in one generation! LOL! Who are you kidding?

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And that is simply an assumption.

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No, it's not an assumption. It's a fact. About 175 new mutations enter the human population with every new individual, how can natural selection remove that? It can't.

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Oddly enough the "noise" didn't stop the alleles producing the melanic form of the peppered moth from spreading, once pollution turned the trees black.

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You miss the whole point. No wonder you don't unedrstand the topic. You are totally clueless about what is being talked about. I never, ever argued that natural selection can't change the frequencies of alleles withn a population. Yes it can. But what it can't do, is keep the population on the same level of genetic information, or increase it.Genetic entropy is decreasing the informational content. And while this is happening, there is absolutely no problem whatsoever for shifting frequencies within a population.

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Natural selection can overcome noise.

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And do what? Shift frequencies from light do dark moths? Yes.Maintain or increase the original genetic information? No.

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And it also fails to happen every day. Recombination mixes things up.

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How is recombination going to overcome the effects of epigenetics? How is recombination going to overcome the effect of both parent's gene being mutated beyond repair? You can recombine it, but it still doesn't work.For an example, human GULO gene. ALL humans have this gene mutated so it doesn't work. How teh hell is recombination going to repair it? Guess what? IT'S NOT! It's stays dead! And it's passed on to every single offspring!

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It's a simple question. Being CSI is having more bits of information than the bound. How is that measured in bits ? Why would you ever need more than one ?

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Oh, I don't know. Maybe because we want to know how much CSI is there in a human genome and in some other genome. If they are different size, than there are different amounts of information. So we have to measure them in different amount of bits.

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If it's not in the specification his calculation of the probability can't use it.

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Than where is it?

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And do you really think that log2-P(D*) is 50 proteins ?

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It's actually P(T|H) in the new paper which would correspond to P(D*|H) in TDI.
Which, let me remind you, you agreed that these two are the same few posts ago!

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And that is what is wrong. There is no such thing as a genetic block which is immune from recombination. It sounds like you don't know what genetic linkage really is, it is no universal law producing indivisible genetic blocks, it is a statistical reflection of the distance between discrete genetic loci.

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These discrete loci could even occur within one gene. To state baldly that genes cannot undergo recombination Intragenically is simply to ignore the molecular biology in favour of your own fantasy.

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The fact that you wilfully ignore the reality of crossing-over naturally lead you to continue being wrong when you talk about natural selection.

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Once more. I never said that genes do not undergo recombination. Only you keep saying that I claimed so. Yes they do undergo recombination. But take a look at this.

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We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations.

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Just a moment...In other words, what this article claims is that there are recombinatorial hotspots, and cold spots. Some parts of the genome get constantly recombined, others do not. So you can't just invoke recombination on every single gene, to be recombined with every other single gene. Because there is no evidence that such a thing ever happened.

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Yes, of course it is organisms that survive and pass on their genetic material, but they don't pass it all on and the allelic complements get rearranged by meiosis.

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Again, you miss the point. We are talking about natural selection, and what natural selection evaluates befre it let's it get passed on. Does it evaluate every single gene, or genome? Obviously it does so with the genome, not the gene.And the second point you missed is, that there is evidence that soem regions neevr got recombined. So you can't simply invoke recombination as a mechanism that would get rid of all mutations.

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It is this rearrangement which allows the breaking of linkage between alleles not genes and can allow us to consider the gene an appropriate level of selection.

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If all genes got rearranged than that would still not be true. Because individual genes are not what gets evaluated by antural selection.

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Obviously the genome isn't since the whole genome is never passed on,

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Again, please stop missing the point. It doesn't matter what gets passed on. What matters is what gets evaluated.

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your contention that a beneficial mutation must carry with it every deleterious mutation in its originating genome just flies in the face of so many basic principles of genetics it is hard to know where to begin.

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Like what? Name one.

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Um, for someone who likes to whine about being misrepresentied you seem to be doing a bang up job here yourself. The point is that selection is a statistical phenomenon, by breaking linkages between discrete allele loci mechanisms such as recombination allow for the alleles to be selected more independently.

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Fine I agree with that.

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No one other than you is positing any mechanism in the cell picking out the best genes. What I am describing is that within a population the various rounds of recombination will lead to a dissociation of particular genetic allelic combinations, which will be proportional to their linkage but still provides the possibility of even the most closely linked loci being seperated. Over time this means that selection will tend to lead a favourable allele to increase in proportion.

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I more or less agree. But the question is, what do you get out of it? What do you get over time by such a mechanism. Let's say you have a single cell 3.6 billion years ago. And that mechanism went on from that time 'till today. What do you suppose we are going to get with it?

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No one is denying the existence of deleterious hitchiking residues, there is plenty of genetic evidence for them although since you don't seem to accept gentic evidence, questioning as you do the idea of sequence conservation between mammalian genomes, I guess you must just be assuming this based on common sense since you deny the actual scientific basis which has allowed those determinations to be made.

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I accept genetic evidence. What I do nto accept is assumptions presented as evidence.Please explain the logic between mammalian conservation of genes. I would really like to hear it. You do understand that you first have to assume that all mammals were once one single species to be able to do that? Yet you have ZERO evidence that that was ever the case, or that it is even possible for such a thing to be true.

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Sorry about the mixup on the 5% thing, I was talking about the ENCODE data, which is what you claimed you were talking about. It turns out that in fact you were talking about a part of the review you cite which in fact had nothing to do with ENCODE. I think this rather supports my contention that you don't know what ENCODE did.

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Yes, so just becasue they mention the word "ENCODE" every few lines doesn't mean that they are actually talking about the ENCODE Project is, or what it did. Than what were they talking about? The Flintstones?

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What you are ascribing to ENCODE is research that has been ongoing for decades, the review itself discusses how Jaques Monod in the 60's was disrupting the naive 'one gene == one trait' conception. That doesn't make the idea of a gene being the unit of selection erroneous, although myself I think the nucleotide might be a better choice since it is a truly discrete genetic unit, it just shows that the historical conception of what constitutes a gene was erroneous.

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Yes, they mentioned him also. I never argued that they didn't. What I argued is that the ENCODE Project found out that the classical view of genes is obsolete. Which is what the article claims.

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The classical view of a gene as a discrete element in the genome has been shaken by ENCODE

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The ENCODE consortium recently completed its characterization of 1% of the human genome by various high-throughput experimental and computational techniques designed to characterize functional elements (The ENCODE Project Consortium 2007). This project represents a major milestone in the characterization of the human genome, and the current findings show a striking picture of complex molecular activity. While the landmark human genome sequencing surprised many with the small number (relative to simpler organisms) of protein-coding genes that sequence annotators could identify (∼21,000, according to the latest estimate [see Ensembl genome browser 107]), ENCODE highlighted the number and complexity of the RNA transcripts that the genome produces. In this regard, ENCODE has changed our view of what is a gene considerably more than the sequencing of the Haemophilus influenza and human genomes did (Fleischmann et al. 1995; Lander et al. 2001; Venter et al. 2001). The discrepancy between our previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome prompts us to reconsider now what a gene is. Here, we review how the concept of the gene has changed over the past century, summarize the current thinking based on the latest ENCODE findings, and propose a new updated gene definition that takes these findings into account.

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This is the quote from the article. Are you still going to deny the mentioned ENCODE, and claimed that ENCODE changed our views on genes?

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You say you don't care about the distinction the ENCODE project highlight between biochemical function, a region of DNA being transcribed, and biological function/effect. But by this standard it is trivially easy to show the generation of novel biochemical function in the genome, many trx factor binding sites and transcription start sites are comparatively simple to create by chance and certainly may be moved around very easily.

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Show me some examples.

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All you are doing by talking about pervasive neutral evolution is agreeing that in fact most of the genome serves no biological function even if it is biochemically functional. I though the more common ID position was the exact opposite of that, that the majority of the genome does perform a neccessary function but that we just don't understand it yet.

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What I'm claiming is that positive evolution is almost non-existant. Majority of what exists is neutral selection. But that doesn't mean the majority of genome is non-functional. It' ssimply means that darwinism is false.

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Here you have confused weight for number, if I have 1 block of granite wieghing a tonne and you have 800 feathers weighing only a few kilogrammes then clearly my block outweighs your feathers for all that they outnumber it. It isn't the number but the effect that is important. Of course deleterious mutations are hitchhiking, and some are just being fixed by drift, it is the size of the effect of these mutations that is important.

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I totally agree, I never said otherwise. And the comparison between feathers and granite was unneccessary since I never claimed otherwise.The point is that beneficial mutations don't have such a strong effect, and are almost always drowned by the noise of non-genetic selective traits.And the other point is, that if we say that on average beneficial mutations will have the same strenght as deleterious mutations, than by simple shere numbers, they will overcome the deleterious ones.And the third point is, that they are more numerous however strong they are. Actually the less effect they have the worse it gets. Because than there is more chance they will get passed on, becasue they will be in the range of slightly neutral mutations that are invisible to natural selection.

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I think your problem is that you say whatever is expedient at the time. Here's you saying that common descent is impossible in Message 1038:

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You misunderstood me. I said that the notion of "design without a designer" is impossible, not common descent. I simply said that evolution is built on common descent and as such is tryng to be an explanation for how design comes about withoput a designer.

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So, reinterpreting the above in light of your reemphasis that you have no problem with common descent, this is apparently saying that ID states that evolution's removal of the designer from the process is impossible.

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I would say it a bit differently, that evolution is a theory that explains the evidence through a process of descent with modification and natural selection, while ID is a theory that explains the evidence through the intervention of a designer. You're in effect claiming that a theory that doesn't include a designer is impossible, so if ID has evidence of the designer then this is the time to introduce it, but what we usually hear from IDists is that we cannot know the identity of the designer or how he designed.

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ID is simply the science of design detection, and as such does not deal with the designer or it's mechanisms.Evolution on the other hand is trying to explain design without the designer. Which it fails to do.

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Yes, we know. And what happens if you project this requirement back in time? Let's say that life on Earth was created by an intelligence. Where did that intelligence come from? Maybe, following Shermer's example from the November debate, that intelligence came from Antares (a nearby star). Maybe intelligent aliens from Antares came to Earth a few billion years ago and placed the first life on this planet.

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But since there must have been an intelligence at the start, Antarean life must also have come from an intelligence, so where did the Antarean life come from? A planet orbitting a star in the Andromeda galaxy maybe? And where did that life come from? And the life before that and before that?

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After a while we're back to the plasma of the Big Bang before there were atoms, and there was no life anywhere to create the next life. So where did that first life in the universe come from?

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Your question is useless. It's totally irrelevant where the designer came from. The question is where the designed object came from, not where the designer came from.I'm not sayign that we should not ask where the designer came from. i'ms imply saying that it's irrelevant to ID. Imagine if you were walking down the street and found a pen. A guy asks you how did it come about. You say it was designed. But the guy say that it's not a good answer becaue than you would have to explain where the designer came from.That's totally wrong. Because you do not know where the designer came from, yet your answer that the pen was designed is true. It's true regardless of you knowing where the designer came from, or how. No infinite regress happened, and the pen is indeed designed.Basicly by asking the next question you would destroy science. You do not need to have an explanation for an explanation. When a first person proposed an atom, did he also have to propose the existance of the nucleous? Did he also have to propose the existance of protons, neutrons and electrons? Did he also have to propose quarks? You can go to infinity like that an never come to an end.Basicly, your criticism is invalid.

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At this point most IDists concede that they believe the designer is God, and at that point they've definitely left the realm of anything supported by scientific evidence, although they'd already done that when they posited a designer for life on Earth in the first place.

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You are wrong on both accounts here.Saying that God or anything else designed the universe is not unscientific. Simply becasue if the universe didn't create itself, and it's not eternal, it had to be caused by something outside it. So an outside cause is not an assumption but a logical necessity.Second part where you went wrong is saying that positing a designer for life is unscientific. Why would it be? Why is positing design in other branches of science scientific, but not biology?

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All four are predictions made after the fact and aren't predictions at all, plus all four are consistent with evolution. Does ID make any predictions that are different from evolution?

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1.) It was not known that molecular machines were irreducibly complex before Behe said it. The same goes for all other predictions.2.) Again, being consistent with evolution does not mean that any other theory is any less valid. General relativity and Newtonia gravity are consistent in some parts. That doesn't make any one of them wrong.3.) Evolution is a very, very broad term. You have to tell me what kind of evolution is consistent with these predictions. Please define the word "evolution" you are using here.

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To be more clear concerning point 1, evolution is consistent with specification and complexity, since evolutionary solutions must by necessity be very specific to the requirements of the environment and since competition generates increasing complexity in a way analogous to escalating arms races,

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So in other words, you are saying that evolution, again, I don't know what you mean by evolution here, generates CSI. Fine. Can you show me where has that been demonstrated?

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but evolution is not consistent with the irreducible complexity of Behe for which there is no evidence.

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The bacterial flagellum is a nice example.

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You mean evidence like orthologous ERV's, shared pseudogenes, etc.? We have that evidence in spades. The genetic evidence is conclusive.

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Well fine. Show me some examples. Listing them is not showing an example. Explain how are they evidence for CD:

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Ignoring the evidence is not helping you. We do observe a nested hierarchy. Yes, there is a little noise as would be expected from homoplasies and reverse mutations, but the overwhelming signal is a nested hierarchy.

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Let's see...

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For a long time the holy grail was to build a tree of life, says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. We have no evidence at all that the tree of life is a reality, says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

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Which part of "Many biologists now argue that the tree concept is obsolete and needs to be discarded" do you not understand? Do you have problem reading English? The tree concept is dead. It doesn't exist anymore. If you have anything to show against this conclusion, if you can show me the evidence I'm ignoring, than show them now.

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A bush is a nested hierarchy.

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No. A bush is an exact opposite. Branches is what was supposed to be seen, not a bush.

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They agree with me. The nested hierarchy is unambiguous.

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You don't get it. You are confusing interpretations and assumptions with evidence and facts.It is a fact that a tree of life is a bush, and not a branching tree. It is an observable fact. Meaning that you can't construct a unambiguous nested hierarchy. Those are facts.Assumptions and interpretations of those facts is that regardless of the facts, that chimps are our relatives. There is no evidence for that. That is an interpretation and an assumption.And no, they do not agree with you on the nested hierarchy part. They agree with you that humans and chimps are related, but in spite of there not being a nested hierarchy, but a bush.

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Why aren't airbags found in a single lineage of cars?

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Why aren't eyes found in a single lineage of animals?

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Why don't cars fall into a nested hierarhcy?

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Why don't all animals?

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Feathers are found in a single lineage of vertebrates.

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Yet they evolved independently few times. So what does that tell you?

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Powder down has evolved independently in several taxa and can be found in down as well as pennaceous feathers. They may be scattered in plumage in the pigeons and parrots or in localized patches on the breast, belly or flanks as in herons and frogmouths.

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Feather - Wikipedia

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Three middle ear bones is found in a single lineage of vertebrates.

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And it would seem they also evolved independently few times?

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Evidence that the angular (homologous with the mammalian ectotympanic) and the articular and prearticular (homologous with the mammalian malleus) bones retained attachment to the lower jaw in a basal monotreme indicates that the definitive mammalian middle ear evolved independently in living monotremes and therians (marsupials and placentals).

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Just a moment...

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So why aren't airbags found in a single lineage of cars, both morphologically and chronologically?

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Because they weren't designed that way.

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Why are there cars with jet engines? If cars can have jet engines why can't bats have feathers?

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Who said they can't? They simply don't.

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Why do human constructs consistently fail to produce a single nested hierarchy?

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Oh really? Since when?

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A nested hierarchy or inclusion hierarchy is a hierarchical ordering of nested sets.[5] The concept of nesting is exemplified in Russian matryoshka dolls. Each doll is encompassed by another doll, all the way to the outer doll. The outer doll holds all of the inner dolls, the next outer doll holds all the remaining inner dolls, and so on. Matryoshkas represent a nested hierarchy where each level contains only one object, i.e., there is only one of each size of doll; a generalized nested hierarchy allows for multiple objects within levels but with each object having only one parent at each level.

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Hierarchy - Wikipedia

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You tell me. Why can't a designer change the architecture at will? Why a nested hierarchy?

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He can. There is no nested hierarchy. Even if tehre was, what would that mean?

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Do you have any siblings? If so, the features you share are due to common descent. It really isn't that hard to figure out.

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I'm talking about universal common descent. It's very different than simple common descent. Because with universal common descent we are talking about species that were never known to interbreed, producing offspring. Is that even possible?

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At the same time, can you show how mutations that occur in one species can spread to another species? It doesn't happen in metazoans. This produces a nested hierarchy.

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What?

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You seem to be really mixed up here. A nested hierarchy can not be built for a bat with feathers. Can't be done. A nested hierarchy is clearly falsifiable.

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Why not? Explain why.

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A flagellum is just one possible solution for motility, and those odds are only for a flagellum like the one that appeared. I'm sorry, but your probabilities are built on baseless assertions.

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Listen, you don't know what you're talking about. The number 10^20 has nothing to do with the flagellum. It's the complexity of the specification. Please don't go into this, it's out ov your league.

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I already spelled it out for you with the hemoglobin S example. It is plain as day. You say it is stupid, and yet that is exactly what the data indicates. The single nucleotide change in hemoglobin S has been selected through positive malarial resistance selection (positive) and sickle cell anemia selection (negative selection).

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You miss the point. The whole organism was selected that contained that mutation. Not the mutation itself. The whole organism was evaluated. Do you think that mutation would be passed on if the organism was sterile?

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So ID is not trying to determine why bacteria have flagella? Really? So I guess we can say that ID explains nothing about biology?

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It simply explains the source of design.

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Evolution deals with CHANGE in life, not the origin thereof. Abiogenesis deals with the origin of life.

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No kidding Einstein, so if evolution doesn't deal with the origin of life and just deals with the development of life, why should ID deal with anything besides detection of design?

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My example demonstrated that the specificity of an enzyme changed due to random mutations.

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No. What your paper showed is that it changed due to random mutations and intelligent selection. Which is not equal to random mutations being operated on by natural selection.

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The authors simply created an environment where such mutants would be detectable using their methodologies. That's it.

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And they directed and selected which individuals get to reproduce.

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This is no different than penicillin intelligently selecting for resistance mutations in bacteria. Is penicillin an intelligent agent?

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Penicilin is not intelligent, and it's not selecting anything. It's simply binding becasue it's chemical properties.

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If you could be so kind, could you give the link for that paper again.

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http://hal.archives-ouvertes.fr/...53/PDF/ajp-jp1v5p1501.pdf