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E coli hybrid copes with 700 mya engineered gene

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From Quanta Magazine:

Several years ago, Eric Gaucher, a biologist at the Georgia Institute of Technology in Atlanta, even resurrected a 700-million-year-old protein from E. coli.

Now, in a new twist on paleogenomics, Kacar has engineered that ancient protein into modern E. coli and tracked how the microbe adapted to it. The new approach, which Kacar presented yesterday at NASA’s Astrobiology Science Conference in Chicago, provides a more integrated view of the mechanisms of evolution — for example, how a protein’s position in a broader network influences its rate of change or how protein networks evolve as a whole.

They seem to have a mind of their own.

Kacar then synthesized that gene and inserted it into E. coli in place of the existing version. (She dubbed the hybrid the Rip strain, after Rip Van Winkle, because the gene has awoken from a 700-million-year sleep.)

The hybrid E. coli clearly suffered from the archaic component. The hybrids grew much more slowly than their normal counterparts, producing 25 percent fewer offspring. Just as a modern laptop would run poorly if its processor were replaced with an 1980s-era computer chip, the microbes’ modern molecular machinery simply wasn’t well suited to the ancient version of the protein. That’s because EF-Tu is a hub protein, interacting with 50 or more other proteins as it carries out its function in the cell. “When we put in the ancient form, we are undoubtedly disrupting some of those interactions,” Gaucher said. The partner proteins have undergone their own evolutionary changes over the last 700 million years — they’re designed to work with the laptop’s modern components, not the outdated chip.

Unlike a computer, however, the bacteria quickly bounced back. Kacar grew the hybrids in the lab, checking their growth rates and other factors every few hundred generations. Within a couple of months — about 500 generations — the hybrid E. coli were growing as well as their modern counterparts. These survivor strains must have evolved ways to overcome the problems caused by the outdated protein. But how? More.

Maybe they never got the memo that after 700 million years, they were just supposed to some how fail?

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Hat tip: Pos-Darwinista

Comments
wd400:
In a (countably) infinite population we could know the frequency of an allele in the next generation precisely if we knew the selection coefficient.
There is usually more than one, they can and usually do change. Hence the impotency of natural selection. Whatever is good enough gets through.Virgil Cain
June 22, 2015
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Mung, Ok, let's try to be fair. Imagine a drop of water bouncing around randomly in a hot skillet. Now tip the skillet very slightly, noting the angle precisely. -QQuerius
June 22, 2015
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Indeed, Dr JDD. What immediately occurs to me is that they "strain at a gnat and swallow a camel." It's a sort of selective skepticism with some mighty big camels and mighty small gnats! -QQuerius
June 22, 2015
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Querius : Ever read the phrase "they suppress the truth in unrighteousness" anywhere? JDr JDD
June 21, 2015
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In a (countably) infinite population we could know the frequency of an allele in the next generation precisely if we knew the selection coefficient. Drift is the non-directional "noise" added to that infinite prediction. That being the case, it should be obvious that drift is not very important when selection is strong.wd400
June 21, 2015
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wd400, I'm not sure that even makes sense. :) There's a non-random bit of random sampling?Mung
June 21, 2015
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OK, so it's perhaps more precise to say drift is the random bit of random sampling (i.e. drift is non-directional).wd400
June 20, 2015
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Mung: All evolution is due to drift. Some alleles drift faster than others. wd400: Nope. Genetic drift is specifically about random sampling. Indeed. And random sampling from a probability distribution is still random sampling. Or so I've been told. So my statement is correct. All evolution is due to drift. Some alleles drift faster than others. Drift doesn't only occur when the probability distribution is uniform. Zachriel: Both drift and selection can be directly observed. No, they can't.Mung
June 20, 2015
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Evolutionists seem to be able to explain everything and nothing at the same time. Yes, evolutionists have come up with many synonyms over the years to make their "theory" seem more credible and sophisticated, but when it comes down to it, logically, it's simply about accumulating genetics mistakes/accidents, what I like to call a biological "garbage collection" mechanism. In the end, whatever "function" happens to rear its ugly head, is up for "selection". Whatever survives, survives, whatever doesn't, doesn't. When I hear talks about "drift", "neutral theory", etc...,it's all just white noise to me. How can one be a "professor" of evolutionary theory? It's an impossible title to have, IMHO.computerist
June 20, 2015
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You still don't seem to know what the neutral theory is.wd400
June 20, 2015
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Zachriel:
Both drift and selection can be directly observed.
And that is why we know they are incapable of covering the claims of evolutionism.Virgil Cain
June 20, 2015
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bornagain77, You keep coming up with these gems:
The isolation of microorganisms from ancient materials and the verification that they are as old as the materials from which they were isolated continue to be areas of controversy. Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. http://mbe.oxfordjournals.org/content/19/9/1637.full
So the results of 250 million years of random sampling and supposed genetic drift among some of the fastest reproducing organisms on the planet, using the most rigorous protocols with regard to possible contamination demonstrates conclusively that . . . . . . there are academics who stubbornly cling to archaic speculations and rationalizations about the neutral theory of evolution despite rigorous proof to the contrary. Thus, one must conclude that their science is actually a pseudo-scientific religion. Now religion isn't necessarily a bad thing, wd400, as long as you're not in denial about it. You have a lot faith in the neutral theory of evolution. So admit it. It's nothing to be ashamed about. Just realize that scientific progress has passed you by. -QQuerius
June 20, 2015
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Querius: From what I understand, the neutral theory of evolution suggests random drift as demonstrated by carefully thought-out speculation, and the “tape recording” theory of evolution suggests a deterministic path as demonstrated by (ugh) actual genetic experiments. Both drift and selection can be directly observed. The question is the relative importance of each over life's history.Zachriel
June 20, 2015
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Virgil Cain @ 18, But as wd400 will assure you, they do count as Actual Experiments even if they don't completely confirm their entire position at this precise moment in time, and they do correlate with observed data to well within an order of magnitude . . . :-) -QQuerius
June 20, 2015
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wd400- every experiment those evolutionary biologists have conducted demonstrate that evolution is very limited. That science demonstrates the claims of evolutionism cannot be covered by natural selection and drift.Virgil Cain
June 20, 2015
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I think you are missing the bit where evolutionary biologists got out and actually do experiments/analyse populations and determine when and to what extent selection and drift apply. You know, the science.wd400
June 20, 2015
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bornagain77 concluded,
Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.
Very interesting, thank you. Seems like genomes are slowly collapsing. Seems like this matches the fossil record. -QQuerius
June 20, 2015
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. . . as though evolution were a tape recording that could be rerun over and over again to produce the same outcome.
So, this would be the "tape recording" theory of evolution? From what I understand, the neutral theory of evolution suggests random drift as demonstrated by carefully thought-out speculation, and the "tape recording" theory of evolution suggests a deterministic path as demonstrated by (ugh) actual genetic experiments. The sum total is that sometimes evolution is random while other times it's deterministic. And all of the time it's whatever mighta happened. I see. ;-) -QQuerius
June 20, 2015
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All evolution is due to drift. Nope. Genetic drift is specifically about random sampling.
wd400
June 20, 2015
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Zachriel:
Neutral theory states that most evolution is due to drift, not that all evolution is due to drift.
All evolution is due to drift. Some alleles drift faster than others.Mung
June 20, 2015
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What are you on about querius? Do you really think someone claims that the neutral theory explains all evolution.wd400
June 20, 2015
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BA77,
In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. -- bornagain77 We know that the whole creation has been groaning in travail together until now; and not only the creation, but we ourselves, who have the first fruits of the Spirit, groan inwardly as we wait for adoption as sons, the redemption of our bodies. -- St. Paul
The initial creation is slowly winding down. the "groaning" Universe steadily approaches "maximum entropy" or "heat death." Genetic entropy increases in ourselves and in all life forms. We "groan inwardly" as we wait for the end. But the ultimate end is not death, but a new birth -- a new creation. We can enter into it now:
Therefore, if any one is in Christ, he is a new creation; the old has passed away, behold, the new has come. -- St. Paul
BA, you are some kind of human encyclopedia. Amazing!harry
June 20, 2015
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I would like to reiterate that evolutionists cannot account for the origination of even one unique gene or protein, much less millions of completely unique ORFan genes found across life in a very non-Darwinian fashion:
Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm
Of related interest to falsifying universal common descent, it is now found that, many times, different genes are involved in generating similar structures in different species:
Homology -- do common structures imply common ancestor? (14:17 minute mark) - video https://www.youtube.com/watch?v=4Ydajcf2SBw&feature=player_detailpage#t=862
As to this comment from the article:
"as though evolution were a tape recording that could be rerun over and over again to produce the same outcome."
Although referring to the compensatory mutations which are implemented via the sophisticated programming of the cell as evolution makes my skin crawl, perhaps these researchers would do well to talk to these other Darwinian researchers who just found that Darwinism was 'unpredictable', so as to at least get on the same page with their just so stories?
If evolution is unpredictable and irreversible, … - June 13, 2015 Excerpt: Using simulations of an evolving protein, they show that the genetic mutations that are accepted by evolution are typically dependent on mutations that came before, and the mutations that are accepted become increasingly difficult to reverse as time goes on. https://uncommondescent.com/evolution/if-evolution-is-unpredictable-and-irreversible/
But perhaps their worst mistake of all, these researchers have absolutely no empirical basis for assuming that bacteria have fundamentally changed over 700 million years:
Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 Scientists discover organism that hasn't evolved in more than 2 billion years - February 3, 2015 Excerpt: Using cutting-edge technology, they found that the bacteria look the same as bacteria of the same region from 2.3 billion years ago -- and that both sets of ancient bacteria are indistinguishable from modern sulfur bacteria found in mud off of the coast of Chile. http://www.sciencedaily.com/releases/2015/02/150203104131.htm The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961
In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' I had asked him about:
"We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki
Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.bornagain77
June 20, 2015
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as to this:
Scientists have long been able to insert proteins from one organism into another, a basic component of genetic engineering. That’s how researchers engineer microbes to make fuels or medicines. But the results of these experiments can be unpredictable. “Sometimes it doesn’t work at all, and we don’t really understand why,” Gaucher said. A protein called elongation factor Tu (EF-Tu) is one such troublesome example. Despite being highly conserved (it’s present in all life on Earth) and essential (without it, cells die), it lacks flexibility. Putting a yeast or fruit-fly version of the EF-Tu protein into E. coli doesn’t work. “It’s one of the most highly conserved sequences in life, but it’s not swappable among life forms,” Gaucher said. “That’s odd.”
Being able to switch genes between widely divergent species is actually an argument against neo-Darwinian evolution being true. Crev.info comments here:
Genetic Evolution Falsified - May 23, 2015 Excerpt: Hundreds of your genes work just fine in yeast and plankton, after supposedly a billion years of evolution separating us. Evolutionists say “common ancestry.” Creationists say “common design.” Who’s right? Ask Science Magazine, which just published a study from the University of Texas at Austin that should shock evolutionists. The commentary by Mitch Leslie in Science expresses the surprise right in the first sentences:
Yeast and humans have been evolving along separate paths for 1 billion years, but there’s still a strong family resemblance, a new study demonstrates. After inserting more than 400 human genes into yeast cells one at a time, researchers found that almost 50% of the genes functioned and enabled the fungi to survive. “It’s quite amazing,” says evolutionary biologist Matthew Hahn of Indiana University, Bloomington, who wasn’t connected to the study. “It means that the same genes can carry out the same functions after 1 billion years of divergence.”
,,,Yet “Despite a billion years of evolution separating humans from the baker’s yeast in their refrigerators, hundreds of genes from an ancestor that the two species have in common live on nearly unchanged in them both, say biologists at The University of Texas at Austin,” comments PhysOrg.,,,
To study this effect systematically, Kachroo et al. replaced over 400 essential yeast genes with their human orthologs. Roughly half of the human genes could functionally replace their yeast counterparts. Genes being in the same pathway was as important as sequence or expression similarity in determining replaceability. ,,,
New Scientist says that it’s not just yeast. Studies of genes in ocean plankton caused the same stunned response by an evolutionist:
We’re a step closer to understanding the microbial community that inhabits the ocean — and it has some striking similarities to the community that lives inside our guts. The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways.… In both, there was an almost identical abundance of genes involved in replication, ion transport and cell motility. “This certainly was rather a big surprise to us because we expected different ecosystems would have microbial communities with functions that would be completely different,” Sunagawa said at a press conference this week.
If prediction is a measure of scientific validity of a theory, this amounts to a falsification. This “certainly” was not what the evolutionists expected. http://crev.info/2015/05/genetic-evolution-falsified/
Dr. Sternberg comments here:
On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files.... ,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences),,, when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences (between species). http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/
Of related interest to common design vs. common descent, Dr. Hunter comments here on finding identical, unconstrained, DNA in otherwise distant species'
Evolution Professor: Orphans Not a Problem for Evolution? - Cornelius Hunter - May 2014 Excerpt: …practically every major prediction of evolution has failed. For example, one of those puzzles was the finding of long stretches of identical, unconstrained DNA in otherwise distant species. Such a finding, an evolutionist had told me years earlier, would falsify evolution, period. His point was that evolution was falsifiable. That was yet another false claim. That finding of identical, unconstrained DNA did not so much as put a dent in the evolutionist’s certainty (and yes, he is still believes in evolution). http://darwins-god.blogspot.com/2014/05/evolution-professor-orphans-not-problem.html
Moreover, directly contrary to Darwinian thought, there are now found to be a substantial percentage of unique ORFan genes which are not shared between species but that are unique to individual species:
,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.” Paul Nelson – quoted from 8:53 minute mark of the following video Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166 "Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8] Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc…" Cornelius Hunter - Darwin's (failed) predictions Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf
As alluded to above, and completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract
Dr. Giem has a new lecture video up on this devastating problem for neo-Darwinists:
New Genes Are Essential 6-13-2015 by Paul Giem - video https://www.youtube.com/watch?v=6qgGPV1AO1E It has been noted that ORFan genes (genes that are not related to genes in other organisms) are common. Research on fruit flies shows that a substantial portion of those genes are essential for development, raising the question of how so many of those genes can evolve so rapidly.
bornagain77
June 20, 2015
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What has been demonstrated here is the adaptability of life forms. We already knew that life forms have a capacity for that built into their genomes. What remains to be demonstrated is that that adaptability extends so far that one kind can, over multiple generations, adapt itself into an entirely different kind. Dog breeders have demonstrated that a lot of versions of the "dog kind" are present within the canine genome, but it appears that the information for some other "kind" just isn't in there, otherwise dog breeders would have eventually bred dogs into something else entirely. That didn't happen. They bumped into limits of different types. There appear to boundaries set by the genome even while it allows for wild variety. Artificial selection has demonstrated that a genome allows for a wide, but definitely limited range of adaptations. This adaptability is an indication of brilliant design. Let me know when E. coli evolves into something else.harry
June 20, 2015
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nightlight: What the experiment shows is that the cellular biochemical networks are highly intelligent systems capable of innovating and guiding coherent evolution, generating in the process specified information. The intelligence is intrinsic to the network, similar to how a neural net integrates new information.Zachriel
June 20, 2015
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It looks like the E coli engineered themselves to accompany the new gene. James Shapiro and Lee Spetner must be smiling.Virgil Cain
June 20, 2015
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"These survivor strains must have evolved ways to overcome the problems caused by the outdated protein. But how?" What the experiment shows is that the cellular biochemical networks are highly intelligent systems capable of innovating and guiding coherent evolution, generating in the process specified information. In other words, contrary to the Discovery Institute's ID (aka Meyerism), one doesn't need to look up to heavens for a white bearded father figure of ancient mid-eastern shepherds as the source of the intelligence behind evolution and CSI -- that intelligent system is already there, exactly where it is needed and with the capabilities required to account for the process of biological evolution. Of course, that doesn't explain how did such intelligent system arose or why are the physical laws apparently extremely finely tuned for their emergence. What that implies is that the fundamental physics needs to undergo revolutionary developments analogous to those in cell biology of 1950s when what was previously thought of as a dumb, analog and aimless system was discovered to be an ultra-sophisticated digital computer far beyond any human technology. Such ideas in physics are already being played with and seriously explored (pregeometry, digital physics, cellular automata) -- see an earlier post on the subject here (links are in the second half of that post).nightlight
June 20, 2015
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Querius: Betul Kacar was just really lucky and she had a highly stable environment, so it’s still the neutral theory of evolution somehow. Neutral theory states that most evolution is due to drift, not that all evolution is due to drift. Really not sure what you're trying to say. No one doubts the importance of natural selection to adaptation. The question in this experiment was whether the inserted protein would evolve, or whether other proteins in the network would evolve to compensate.Zachriel
June 20, 2015
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. . . as though evolution were a tape recording that could be rerun over and over again to produce the same outcome.
Let it sink in. Roll it around in your mouth like a fine wine. In the article, the sentence was intended to describe Dr. Kecar's experimental result. Does the neutral theory ever produce the same result as if it were a "tape recording"? So either Dr. Kecar is wrong, or your theory is dead, pal. -QQuerius
June 20, 2015
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