The ID Hypothesis

_{Barry Arrington

August 4, 2011

Intelligent Design}

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A friend writes and asks how ID comports with the “scientific method.” I respond:

As for the scientific method, I am all for it:

Question to be Investigated: What is the origin of complex specified information (CSI) and irreducibly complex (IC) mechanisms seen in even the simplest living things?

Hypothesis: CSI and IC have never been directly observed to have arisen though chance or mechanical necessity or a combination of the two. Conversely, CSI and IC are routinely observed to have been produced by intelligent agents. Moreover, intelligent agents leave behind indicia of their acts that can be objectively discerned. Therefore, using abductive reasoning, the best explanation for CSI and IC is “act of intelligent agent.”

The intelligent design project is, essentially, the scientific investigation of this hypothesis.

Interestingly, Darwinists make mutually exclusive attacks on the hypothesis. Some claim the hypothesis is not scientific because it cannot be, even in principle, falsified. Others claim the hypothesis fails because it has been falsified. Surely you will agree that it cannot be both.

The answer is that the hypothesis is, in principle, falsifiable.

All it would take is even one instance of CSI or IC being observed to arise through chance or mechanical necessity or a combination of the two. Such an observation would blow the ID project out of the water.

I have to add that typical Darwinist circular reasoning and “just so stories” will not do the trick. That is to say, reasoning of the following sort fails to impress: CSI arose though the combination of chance and mechanical necessity. How do you know this? Well, we inferred it from the data. And on what was your inference based? It was based on our a priori commitment to explanations based solely on chance and mechanical necessity through which all interpretations of the data must be filtered.

Comments

Joseph, see Dmullenix's post 102.1. Clearly, he doesn't even know the difference between a prokaryote and eukaryote and so confuses the two repeatedly. Then says we're the ones who are ignorant! You've got to laugh. Don't expect him to even understand that "Euks are more than proks with mito or chloro".Chris Doyle_{September 8, 2011
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dmullenix, I have some bad news for you- your gullibility and ignorance do not equal scientific evidence-
1: You may be right that there’s no direct evidence that prokaryotes branched off new types of animal. There aren’t many fossils from 1.7 billion years ago and they ones that do exist don’t show us the chemistry. However, eukaryotic cells have quite a few things in common with prokaryotes: a) They are cells. c) They share a lot of basic chemistry, physiology and metabolism. c) They both manufacture proteins by copying DNA to RNA and then use the RNA to construct the protein.
Common design accounts for the similarities.
2: They doubted Lynn Margulis when she suggested that mitochondria are captured bacteria. Then they found bacterial DNA in mitochondria and the doubts pretty much stopped.
Again it boils down to "it looks like endosymbiosis", which is not a scientific test. And all ensosymbiosis provided were mitochondria and chloroplasts. Euks are more than proks with mito or chloro. There STILL isn't any way to scientifically test the premise.
3: The theory of evolution doesn’t have to account for Horizontal Gene Transfer. We can see it in action when bacteria exchange plasmids and we have DNA evidence of viral transfer. It exists and there’s no doubt that evolution uses it.
Thanks for admitting the theory cannot account for it.Joseph_{September 8, 2011
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Chris, I like to argue with people, but you’re just ignoring what I write and saying it aint so with nothing to back your word up. Unfortunately, there’s no way to convince a hyper-skeptic. The record indicates that this only applies to you, Dmullenix. And I'm more than happy to leave it at that.Chris Doyle_{September 8, 2011
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Joseph, Chris, I have some bad news for you. It turns out that your ignorance is vincible and thus provides no excuse. Sorry. Joseph: 1: You may be right that there’s no direct evidence that prokaryotes branched off new types of animal. There aren’t many fossils from 1.7 billion years ago and they ones that do exist don’t show us the chemistry. However, eukaryotic cells have quite a few things in common with prokaryotes: a) They are cells. c) They share a lot of basic chemistry, physiology and metabolism. c) They both manufacture proteins by copying DNA to RNA and then use the RNA to construct the protein. 2: They doubted Lynn Margulis when she suggested that mitochondria are captured bacteria. Then they found bacterial DNA in mitochondria and the doubts pretty much stopped. 3: The theory of evolution doesn’t have to account for Horizontal Gene Transfer. We can see it in action when bacteria exchange plasmids and we have DNA evidence of viral transfer. It exists and there’s no doubt that evolution uses it. Chris, I like to argue with people, but you’re just ignoring what I write and saying it aint so with nothing to back your word up. Unfortunately, there’s no way to convince a hyper-skeptic.dmullenix_{September 8, 2011
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Dmullenix, if you just don't get it, then just be honest and admit that (and then, privately, work out why you don't get it, in your own time, on your own terms) rather than pretend otherwise. You haven't even attempted to respond to my post which clearly demonstrates that the last great hope for evolutionists - bacteria - is actually just another nail in the coffin of evolutionist beliefs. I've put the truth on a plate for you and you just can't handle it. So, let's go back to the beginning. In light of everything you would've learned from my posts on this thread if the cognitive dissonance hadn't kicked it, what exactly do you imagine we’ll see if you run Lenski's LTEE for a million years?Chris Doyle_{September 7, 2011
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1- There isn't any evidence that prokaryotes can evolve into something other than prokaryotes- the theory of evolution is dead at bacteria. 2- Endosymbiosis for the origin of mitochondria and chloroplasts boils down to "it looks like it to me"- ie it is untestable and therefor unscientific 3- The theory of evolution cannot account for HGT, it can only try to explain it.Joseph_{September 7, 2011
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What I'm having trouble comprehending is your astonishing confusion on so many different fronts. To begin with, HGT is not the same as mating. HGT takes a single, small chunk of DNA and transfers it from one organism to another. There's no need to carefully match thousand of genes for compatibility, as in mating. Thanks to viruses, it's entirely possible that there's been some HGT between dogs and cats. Without googling for it, I believe that you and I have some bacterial DNA in our own genomes. I've already covered bacterial diversity and it seems to have shot right past you so I won't waste my time on that again. My explanation of why we don't see new prokaryotes emerging from modern bacteria also seems to have hung fire. I can only lead you to water, I can't make you drink.dmullenix_{September 7, 2011
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Good Afternoon Dmullenix, Thanks for taking the effort to “fully comprehend” what I’m saying and engaging with it: most evolutionists don’t come this far! You put it to me that: You also seriously underestimate the diversity in the bacterial kingdom. I do appreciate “the diversity in the bacterial kingdom” but they are all close enough to each other to exchange genetic material through Horizontal Gene Transfer, plasmids, bacteriophages, etc. Try combining the genetic material of two relatively closely-related mammals like a dog and a cat and see where it gets you... never mind a hedgehog and a cactus! Frankly all strains of bacteria are still just bacteria: single-celled prokaryotes that share many fundamental components (see my previous post, 102). Can we say, all animals are still just animals? No, because within the animal kingdom you have a dramatic variety of body plans, body parts and organs, physical abilities, biological functions, biochemistry, etc, etc. Consider all the differences between a human being and an amoeba: both are eukaryotes. Can you really identify two prokaryotes that are just as different to each other as humans are to amoebas? Throw the plant kingdom into the mix and the varieties and distances between species becomes even more vast and unbridgeable: just consider the difference between a Giant Redwood tree (some of which are over 2000 years old) and the tiny Red Bugs known as Chiggers (if we were the same size as them, we’d have to run at 173mph just to keep up). So, not only are you overestimating the diversity in the bacterial kingdom, but you’re massively underestimating the diversity in the animal and plant kingdoms. To put it another way, bacteria are like stamps: their numbers are countless, there is a huge variety of them, all over the world, but fascinating and diverse as stamps are, they are still just stamps. The variety we find in them, does not compare to the variety we find in planes, trains and automobiles (or phones, or computers or books). Nor do stamps shed any light whatsoever on any other design series... which brings me onto the next thing that you said: They’re all highly evolved waste free stripped down containers for sophisticated chemical factories that make anything man has designed look pathetic. Now, replace the word ‘evolved’ with ‘designed’ and I’m in complete agreement with you! And that’s only the tiniest tip of the iceberg. Prokaryotes are much, much simpler organisms than eukaryotes. Sometimes, I’m flabbergasted that anybody has convinced themselves that any living organism effectively made itself purely from random mutations in its DNA... Now, let’s go back in time to the ‘appearance’ of the first living organisms (which, only for the sake of argument, I will grant are indeed prokaryotes). Without knowing about the future, what would Darwin’s theory of evolution predict? That, in 3 billion years, prokaryotes would still just be single-celled organisms: no body plans, no body parts or organs even and certainly no prokaryotic men? Of course not! The theory was designed to explain the origin of species: and yet there are no species in prokaryotes: only strains that all exchange genetic information with each other. But now, let me withdraw my generosity for a moment: how do we know that prokaryotes came before eukaryotes? Furthermore, how do we know that eukaryotes came from prokaryotes? Don’t forget, Lenski’s LTEE demonstrated that when a splinter group of organisms turn to a new food supply, then BOTH the original group and the splinter group thrive. So there is no reason why the eukaryotes would thrive any more than the prokaryotes in your thought experiment. Nor any reason why the prokaryotes wouldn’t eat the newly evolved,vastly outnumbered, eukaryotes! And which eukaryotes today would prevent newly evolved “half-eukaryotes” from establishing a foothold anyway? Look, we can all invent just-so stories, but none of them are any good without evidence to support them. Furthermore, a just-so story that contradicts the account of another just-so story merely creates a stalemate that can only be resolved by the evidence. So, let’s stick to the indisputable facts: If evolution, specifically macro-evolution occurred, it only happened to eukaryotes. And yet, from the moment that eukaryotes ceased to reproduce asexually, they were at an immediate reproductive disadvantage to prokaryotes. And remember, bacteria is the most advantaged living organism we know of in terms of evolution: they’ve been around longer than anything else, there is more of them in existence than anything else, they reproduce quicker than anything else, they can survive more hostile environments than anything else and they can even obtain new and often useful genetic information - lamarck-like - in the course of their lifetimes which is then passed on to their offspring. You couldn’t ask for a better organism to express the full potential and creative power of evolution. Three billion years ago, if the theory of evolution made a single highly-risky, reputation-staking prediction it would be that the prokaryotes we call ‘bacteria’ would evolve into all of the mind-bogglingly sophisticated and perfectly-designed plants and animals we see today. But, we know they didn’t. Bacteria today is virtually identical to the oldest bacteria we know of. And it’s no good getting excited about nylon: at the molecular level, nylon is still composed of organic compounds, the likes of which bacteria has utilised for billions of years. The ability of a bacterium to manufacture nylonase probably just involved a single point mutation of pre-existing genetic code. Even if nylon was truly alien to bacteria, getting excited about that is a bit like getting excited about a Penny Black stamp with Charles Darwin’s face on it: great if you’re a stamp collector, entirely non-illuminating if you’re trying to manufacture cars or smartphones. So, my question still stands: why, despite all of the unique evolutionary advantages available to bacteria, hasn’t it evolved into prokaryotic animals or prokaryotic plants? If evolution was true, then the theory not only predicts but demands that such lifeforms should now fill our planet. On the other hand, if the theory of evolution wasn’t true and life on Earth didn’t evolve, then, even though bacteria has all of these amazing evolutionary advantages, it would still just be bacteria... and 3 billion years later, would be showing no signs of becoming anything else. Now do you see, Dmullenix, why bacteria does not provide evidence for evolution after all? In fact, bacteria conclusively demonstrates that life on Earth didn’t evolve: because if bacteria couldn’t evolve into humans, then nothing could.Chris Doyle_{September 4, 2011
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It's taking me a while to fully comprehend you Chris, but if I understand you right, you're wondering why we don't see any modern bacteria evolving into prokaryotes and then into roses, redwood trees, humans and dung beetles. Is that close? Assuming it is, then let's think about it for a while. Let's assume for the sake of argument that several billion years ago there were nothing but bacteria in the world, then some of them evolved into prokaryotes. Think of their situation: kilo-mega-gazillions of bacteria in the world, all of them fighting for the limited supply of bacteria food and struggling for possession of every cubic micron of bacteria friendly environment. Now let some of those bacteria evolve into prokaryotes. Shazam! Prokaryotes can eat different food than bacteria and live in different environments - and there's no competition for the new food and the new environments are empty because there aren't any prokaryotes! The prokaryotes can stuff themselves on the new food and multiply like crazy! And, being single-celled organisms, they do just that and in a very short time by geologic standards, the world is crawling with prokaryotes fighting for every piece of prokaryote food and and every cubic micron of prokaryote livng spaces. Now let a modern bacteria evolve into a half bacteria - half prokaryote. Whoops! There are kilo-mega-gazillions of prokaryotes already out there, they've already eating all the prokaryote food, they're already living in all the prokaryote friendly environments and they've been evolving and perfecting themselves to compete for that food and those environments for billions of years. The brand new half bacteria-half prokaryotes don't have a chance. Does that clear up why we don't see bacteria evolving into prokaryotes any more? It's because we already have prokaryotes and there's no way a half-prokaryote is going to compete with them. You also seriously underestimate the diversity in the bacterial kingdom. They're all highly evolved waste free stripped down containers for sophisticated chemical factories that make anything man has designed look pathetic. There's tremendous diversity between different species of bacteria, probably more than between different species of procaryotes. This is actually an ID talking point. Remember how Darwin is supposed to have thought of bacteria as being simply "protoplasm" and didn't understand how incredibly complex they are? Remember the molecular machinery in bacteria that would supposedly have discouraged Darwin from his theories if he'd only known of them? And how do we know that the strains of bacteria today aren't identical to bacteria billions of years ago? Well, I'm betting that no bacteria was manufacturing nylonase so it could break down nylon and eat it billions of years before nylon was invented, for one thing.dmullenix_{September 4, 2011
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Dmullenix, answer me this question: what exactly do you think Darwin was attempting to explain in “the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life”? Was it to explain which creatures dominate the Earth or why it is that there are so many different, yet perfectly ‘adapted’ creatures (with a variety of body parts, body plans, organs, etc)? Also, do you accept that the variety we see between say, a Giant Redwood tree and a blue whale and a human and an ant demands a much greater explanation than the variety we see in every single strain of bacteria put together? After all, bacteria are all still nothing more than single-celled organisms with a nucleoid, cytoplasm and ribosomes with-in a membrane, with-in a cell wall with-in an enclosing capsule. Pili protrude from the membrane and a flagellum usually provides motility. There is some trivial variation. Bacteria come in some different shapes and sizes. Different bacteria eat different things. Different bacteria are destroyed by different things. But that’s it. There are no bacterial flowers, fish, trees, whales, fungi, mice, canaries, dinosaurs, humans, etc. I strongly suspect that you are going to overplay the variety we see in bacteria as something that is equivalent to the variety we see between a rose and a dung beetle. If you genuinely believe that the two most different strains of bacteria you can identify are equivalent to the two most different plants or animals you can identify, then you are deluding yourself in the name of your evolutionist beliefs. And this conversation is over. But hopefully, you do recognise the fundamental difference between two different bacteria and an animal and a plant. It is very simple, Dmullenix. Tell me why is it that (even in ‘just’ the last billion or two years) no single-celled prokaryote has evolved into anything other than a single-celled prokaryote? You asked us to be impressed with Lenski’s LTEE and to “imagine what you’ll see if you run that experiment for a million years!” yet we know for a fact, that for at least the last billion years, nothing of any macro-evolutionary significance has occurred. Bacteria has only given rise to more bacteria (with, at best, some trivial variation in size, shape and feeding habits). Sub-specific variety in dogs is far more significant than the variety you describe in all of the strains of bacteria. Also, how do you know that virtually all of the strains of bacteria alive today did not actually exist a billion years ago (with all the same shapes and colonising, almost all the same feeding habits and environmental resistance)?Chris Doyle_{September 1, 2011
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Chris, eukaryotes first appeared more like a billion or two years ago. Why do you think that “absolutely nothing” has happened to bacteria since? Do you have any samples from back then? There are none that I know of. Fossils? There are a few, but they don’t show any internal detail and certainly no chemical detail. So why do you say they haven’t changed? Do you have any data or are you just saying that? Try looking up “bacteria” in wikipedia: http://en.wikipedia.org/wiki/Bacteria The following is mostly paraphrased from that article: Bacteria have evolved many basic shapes: wiki lists round, rod-shaped, curved, comma-shaped, spiral-shaped, tightly coiled, and long rods with star-shaped cross sections. Here’s a drawing of some of the shapes: http://en.wikipedia.org/wiki/File:Bacterial_morphology_diagram.svg Many bacteria characteristically join in pairs, chains, or grape-like clusters. Lots of them form filaments which help many cells join together in a colony. They also form biofilms ranging up to a half meter in thickness and containing multiple species of bacteria. The films also make it hard to kill them which you may someday discover to your displeasure if they’ve infected you. Some bacteria join together with their clonal sisters by the hundreds of thousands, differentiate various biological functions amongst themselves and then produce spores! Bacterial cell walls have become very complex, letting some materials in and chucking waste out. Some walls are very thin, some are multi-layered and very thick. Some bacteria have developed flagella, which I’m sure everybody on UD knows about (there’s a nifty animation in the article) and some have developed fine hairs called fimbriae. Some surround themselves with slime layers. Some bacteria (anthrax and tetanus for example) form spores called endospores that can be frozen, baked, irradiated with UV light and even gamma rays and survive. Some have been found that are forty million years old and survived. Some bacteria evolved the ability to use sunlight to break down water into hydrogen and oxygen and we literally owe our lives to them. They also feed on organic and inorganic compounds. More than anything else, however, bacteria have become the premier chemical factories of earth and have evolved the ability to feed on just about anything, including that brand new molecule, nylon. I’m sure that as new compounds come into existence, bacteria will evolve to eat them. In short, quite a bit has happened to bacteria and it’s still happening. If you're wondering why they haven't formed bodies - one likely reason is that animals with bodies need oxygen and by the time the bacteria had manufactured enough oxygen for animals to form, they already dominated the earth.dmullenix_{September 1, 2011
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dmullenix you're missing the point. I already granted you the possibility that eukaryotes were created by a one-off miraculous never-seen-since synthesis of prokaryotes. But think about it: since that event hundreds of millions of years ago, EVERY prokaryote remained almost indistinguishable from every other prokaryote. They did not evolve body plans. They did not even evolve into body parts. On the basis of Lenski's LTEE, you ask what would happen to bacteria in a million years. The answer is: we already know what happened to bacteria after hundreds of millions of years: absolutely nothing. Bacterial evolution shines no light whatsoever on how it is that a single-celled eukaryotic common ancestor evolved into trees, ants, dinosaurs, whales and humans. Which is exactly what evolution was supposed to explain in the first place!Chris Doyle_{August 22, 2011
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Prokaryotic cells didn't evolve into anything at all? Is that an observation? Got a citation? Where did eukaryotic cells come from then? Poof? Are you aware that prokaryotic cells, especially bacteria, are, overwhelmingly, the dominant form of life on this planet? Their variety is unparalleled, they live in every niche and environment from the top of Mt. Everest to kilometers underground, their total weight exceeds that of ALL other living organisms combined, they contain chemical factories that can eat anything from iron to you and me, and for that matter, your body contains more bacterial cells than human. ALL eukaryotic cells, including the cells that make up you and me, are afterthoughts, filling the very few environmental niches that bacteria disdane. If every eukaryotic organism on earth was to drop dead today, life would go on. If all the bacteria died today, all the eukaryotics would join them in weeks or a few months at the most. This is the Planet of the Bacteria. Lenski's E. coli are evolving into another species of bacteria because that's where the action is, not in dead ends like eukaryotes that survive when and where bacteria allow them to. And as his tiny little experiment shows, they are evolving FAST!dmullenix_{August 16, 2011
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dmullenix, all animals and plants are made out of eukaryotic cells. Bacteria are prokaryotic cells. Even if we assume (and that is a big, unsupported assumption by the way) that a prokaryotic cell somehow turned into a eukaryotic cell, the all-important point is this: only the descendants of the first eukaryotic cell turned into animals and plants. Prokaryotic cells did not evolve into anything at all: they have remained as prokaryotic cells for their entire history: no body plans, no body parts even. Did you not realise that?Chris Doyle_{August 15, 2011
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And where do you think all the non-bacterial organisms came from? They didn't poof into existence. They came from other organisms, very possibly bacteria, which found themselves in an environment where becoming more than bacteria paid off. When a new organism evolves into being, the old organisms don't automatically die. "If men evolved from apes, why are there still apes?" is a classicly unwise question.dmullenix_{August 15, 2011
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dmullenix, here's another way of looking at it: E. coli has several pre-existing enzymes – coded from its gene pool – that use and digest citrate, especially in the absence of oxygen. The only problem E. coli normally has is bringing citrate through its membrane in the presence of oxygen. Nonetheless, E. coli (outside of Lenski’s experiment) has been identified which can do just this thanks to an over-expressed protein. There are also plasmids which perform the same function on its behalf. We don't need to imagine what we'll see if we run the experiment for a million years, dmullenix. We already know what happened in the real world over a vastly longer period of time. Bacteria is believed to have been in existence for 3,000,000,000 years. It has the ability to asexually reproduce so quickly that populations can double in size every 10 minutes. It thrives in all environments, extreme or otherwise. It obtains genetic information from plasmids, bacteriophages, mutations and even other bacteria (no matter how distantly related they may be). There are about 5,000,000,000,000,000,000,000,000,000,000 of them on the planet today. With so many features to facilitate evolution, bacteria should have given rise to a multitude of species: things like flowers, fish, trees, whales, fungi, mice, canaries, dinosaurs, humans, etc. All those random mutations, all that time and all those opportunities for natural selection… yet not a single body plan or even body part to show for it! In light of these indisputable facts, dmullenix, don't you think we should look at bacteria, especially in the light of evolution, and ask "so what?"Chris Doyle_{August 15, 2011
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I don’t understand you. Are you saying that nothing was broken in Lenski’s experiments or that functional complexity was not achieved. Hey, here’s an idea. Instead of “breaking”, why don’t you say the DNA was “re-written”? Since the DNA was changed and the change seemed to produce a very definite improvement (as in alive instead of dead), I think “re-written” makes more sense than “broken”. And remember, this re-writing only took 20 years. Imagine what you’ll see if you run that experiment for a million years!dmullenix_{August 15, 2011
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dmullenix, and your depending on breaking things to explain the origination of functional complexity??? You live in sheer denial dm!!!bornagain77_{August 11, 2011
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BA77 at 94 “But was any functional complexity/information gained over and above what was already present dm ???” Do you consider staying alive instead of starving to death “functional”? If so, then YES!!! “It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen.” Thus enabling the E. coli to stay alive instead of starving. And it only took a minuscule sample of E. coli 20 years to evolve that ability. Now let’s be VERY conservative and say that E. coli has only been around for a million years. 1,000,000 / 20 = 50,000 mutations * 2 = 100,000 new base pairs. And this in a tiny sample of a bacteria that is already fully functioning and highly fit. “If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.” Oops. Try again. “The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function.” Which is about what you’d expect – it’s a lot easier to break something than to build something new. But apparently new things are built, even in highly evolved, highly fit organisms. Oops. “The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases.” Did you actually read that paper? I suspect not. I found the abstract at http://www.mendeley.com/research/deletional-bias-and-the-evolution-of-bacterial-genomes/ Here’s an excerpt: “Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality.” Gee, you’d almost think that Dr. Abel misread the paper and everybody else has just been copying his reference without actually reading the paper themselves.dmullenix_{August 11, 2011
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dm you state: ‘A wall? Lenski takes 12 flasks of E. coli, which fit into a single laboratory shaker, and lets them evolve for only 20 years and they evolve a way to eat a new food? And he saves enough samples so they can go back and find out exactly which TWO mutations made this possible? And you call this a wall?’ But was any functional complexity/information gained over and above what was already present dm ??? Multiple Mutations Needed for E. Coli – Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.' In fact dm, despite the severe obfuscation that neo-Darwinists obscure this issue with, there has never been an observered violation of what is termed Genetic Entropy by natural processes; Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010 Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)' ================= “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.' The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009.....6/3426.pdf http://www.us.net/life/index.htm The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_L.....iency.html Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video http://www.metacafe.com/watch/3995248 Evolution Vs Genetic Entropy – Andy McIntosh – video http://www.metacafe.com/watch/4028086 Dr. David Berlinski: Random Mutations – video http://www.youtube.com/watch?v=DGaUEAkqhMY ================== Jessa Anderson- Fireflies (Lyric Video)? – Music Videos http://www.godtube.com/watch/?v=K7WPDLNXbornagain77_{August 10, 2011
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dm you state: 'A wall? Lenski takes 12 flasks of E. coli, which fit into a single laboratory shaker, and lets them evolve for only 20 years and they evolve a way to eat a new food? And he saves enough samples so they can go back and find out exactly which TWO mutations made this possible? And you call this a wall?' But was any functional complexity/information gained over and above what was already present dm ??? Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ In fact dm, despite the severe obfuscation that neo-Darwinists obscure this issue with, there has never been an observered violation of what is termed Genetic Entropy by natural processes; Michael Behe's Quarterly Review of Biology Paper Critiques Richard Lenski's E. Coli Evolution Experiments - December 2010 Excerpt: After reviewing the results of Lenski's research, Behe concludes that the observed adaptive mutations all entail either loss or modification--but not gain--of Functional Coding ElemenTs (FCTs) http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html ================= “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009/v14/af/3426/3426.pdf http://www.us.net/life/index.htm The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 Dr. David Berlinski: Random Mutations – video http://www.youtube.com/watch?v=DGaUEAkqhMY ================== Jessa Anderson- Fireflies (Lyric Video)? - Music Videos http://www.godtube.com/watch/?v=K7WPDLNXbornagain77_{August 10, 2011
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Only if E coli. reproduces once every 20 years.dmullenix_{August 10, 2011
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dm, 50,000+ e-coli generations is equivalent to 1,000,000+ years, not 2500.junkdnaforlife_{August 9, 2011
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Junkdnaforlife at 80: “The lenski studies + mathematics will eventually erode Darwinism. 10-20 beneficial mutations over 50,000+ generations. 12 independent populations, after millions of mutations (lenski claims every single point mutation has mutated), and we end up with is the same distribution of 10-20 beneficial mutations in each of the 12 independent populations after 50000+ generations. It looks like a wall.” A wall? Lenski takes 12 flasks of E. coli, which fit into a single laboratory shaker, and lets them evolve for only 20 years and they evolve a way to eat a new food? And he saves enough samples so they can go back and find out exactly which TWO mutations made this possible? And you call this a wall? SOME WALL! Say, if it took those 12 flasks of E. coli 20 years to find two beneficial mutations, how long do you think the E. coli in billions of human guts to find 50,000 beneficial mutations? I’d guess about 50,000/20 = 2,500 years. Why don’t you try this tactic: DEMAND to know why we don’t see cows evolving into whales every 2,500 years! Go talk to Andrew Schlafly about Lenski and his experiment. See if Schlafly’s wounds have healed yet. I’ll bet he advises you to just leave that experiment alone. Don’t even talk about it because it really bites hard when you do.dmullenix_{August 9, 2011
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KR at 78: What theistic evolutionists think of ID is unimportant. What is important is that “CSI or IC being observed to arise through chance or mechanical necessity or a combination of the two” does not invalidate ID. The deeper problem is that Dr. Dembski decided that CSI can’t be produced by material means and then built his entire CSI/Explanatory Filter apparatus around that mistaken belief. This leaves ID based on a falsehood. Since Behe built his irreducible complexity apparatus on the mistaken belief that evolution can only proceed step by step and neglected to factor in co-option and scaffolding, ID finds itself high and dry philosophically and scientifically.dmullenix_{August 9, 2011
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Elizabeth Liddle:
There are indeed some walls in bacterial evolution (breached by HGT however).
Breached by HGT? Do you know what conjugation is?Mung_{August 9, 2011
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Elizabeth Liddle:
Given a highly structured search space, I submit that Darwinian search works extremely well...
Yet more improbables pile on improbables. How does adding to the improbability of it all help your case? Oh luck, we just happened to stumble on a highly structured search space. Oh look, we just happened to stumble upon an effective search algorithm fitted to the nature of the search space. Whee! Looks like design to me.Mung_{August 8, 2011
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Elizabeth Liddle:
CSI, by Dembski’s definition, is a pattern is vanishingly unlikely to have arisen through chance and necessity, and given that the only other inference allowable is design, then it assumes its conclusion.
A lie.
Not in the same sense as in a non-cloning population.
But you aren't equivocating, are you. You just got caught with your hand in the cookie jar, and you're excuse is there's no cookies in it because you already ate them all?Mung_{August 8, 2011
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kf:
Dr Liddle: Sorry, you have proposed precisely what is not available, a handy ladder to whatever configs can work, and stepping-stones from one island of function to the next.
Yes indeed, kairosfocus! And what I dispute is that such "handy ladders" are not available! That is the crux of the issue (or an important one, anyway!). Or, to put it another way - your "islands of function" are not islands at all but connected by bridges and tunnels and isthmuses (isthmi?)
Such a near arranement coems about by design.
Well, it seems quite natural from here. If a slightly longer neck gives a slight advantage, and a slightly longer neck still gives a lightly greater advantage, then those two "solutions" are next door to each other along a single dimension of search space. There may be some "irreducible" areas even those are often not as cut-off as they seem, and can be reached by way of, for example, greater complexity downwards, or indeed with the help of drift.
In the case we do have to deal with, deeply isolated needles, even if present in great number, as long as tghey do not dominate the 1 light monthsh onthe side haystack, are overwhelmingly not going to come up if you do the equivalent of pulling just one straw [or if you are lucky, needle] by chance.
Only if you are correct about the needles being deeply isolated. I don't think you are :) But that's worth discussing, I think.
the overwhelming pattern is gibberish or non functional configs.
Sure. And if each functional solution was a lonely island in a "sea of gibberish or non functional configs" then Darwinian evolution would indeed be useless. But I think this is a false premise.
You have to get to the shores of an island of function first — a function that is highly complex and specific — the challenge in hand — before the hill climbing on differential function can happen.
Sure, if the function is really a lone island in a vast sea of functionlessness. This is what I dispute (and what Darwinists dispute).
That is why GAs and the like all fail to be material, they start within islands of function and follow gradients on defined fitness functions that are not dominated by non-function.
This isn't true. They do all start with the basic function of self-replication, but that's a prerequisite for Darwinian evolution anyway. But in many cases that is all. In that clock evolution example, the vast majority of "clocks" started with no clock function at all, but a couple of percent found minimal function by random search. Once on the shores of one of those islands, the journey to clocks was pretty well guaranteed. Now, I know that your argument is based on the premise that a minimal self-replicator is itself on an island, which is a fair enough point (though not an impregnable one, in my opinion) but do you agree that once you have that minimal self-replicator, the rest of the solution space is joined up?Elizabeth Liddle_{August 8, 2011
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