Was E. Coli Bacteria Evolving In the Lab?

In 1988, with one single microbe started an experiment conducted by Richard Lenski, who is an evolutionary biologist.  In 2008, evolutionists were tooting their horns claiming a new ability to subsist on citrate was proof that new traits can evolve! But there was a cost along the way  as a result of activating this so-called new trait through mutations.

Michael Behe, in his paper points out…

“By examining the DNA sequence of the E. coli in the neighborhood surrounding the IS [insertion sequence] elements, the investigators saw that several genes involved in central metabolism were knocked out, as well as some cell wall synthesis genes and several others.”

“In subsequent work, Cooper et al. (2001) discovered that twelve of twelve cell lines showed adaptive IS-mediated deletions of their rbs operon, which is involved in making the sugar ribose. Thus, the adaptive mutations that were initially tracked down all involved loss-of-FCT.”

“Several years later, when the cultures had surpassed their 20,000th generation, Lenski’s group at Michigan State brought more advanced techniques to bear on the problem of identifying the molecular changes underlying the adaptation of the E. coli cultures. Using DNA expression profiles, they were able to reliably track down changes in the expression of 1300 genes of the bacterium, and determined that 59 genes had changed their expression levels from the ancestor, 47 of which were expressed at lower levels (Cooper et al. 2003).”

“The authors stated that “The expression levels of many of these 59 genes are known to be regulated by specific effectors including guanosine tetraphosphate (ppGpp) and cAMP-cAMP receptor protein (CRP)” (Cooper et al. 2003:1074). They also noted that the cellular concentration of ppGpp is controlled by several genes including spoT. After sequencing, they discovered a nonsynonymous point mutation in the spoT gene. When the researchers examined ten other populations that had evolved under the same conditions for 20,000 generations, they found that seven others also had fixed nonsynonymous point mutations in spoT, but with different substitutions than the first one that had been identified, thus suggesting that the mutations were decreasing the protein’s activity.”

After 20,000 generations, not much happened. But after a while, the types of changes taking place in the E. coli tended to decrease or eliminate protein function! Now we get to the ability of E. coli to metabolize citrate. This is where evolutionists love to toot their horn, “after a series of mutations “bacteria that use citrate dominate the population,” they say.

What they didn’t tell you is that E. coli already have the machinery to uptake and metabolize citrate (like a number of enzymes that normally use citrate and can digest it) but doesn’t do it under oxic conditions! The experiment wasn’t showing any evidence for a  biochemical pathway invented by the mutations which was entirely new! Instead, it was only activating its machinery with a cost under different conditions.

In other words, normal E. Coli lacks the ability to transport citrate through the cell membrane into the cell under oxic conditions. But Lenski’s E. Coli, the regulation mechanism of a citrate-transport gene lost its function thereby causing an over expression (turning the switch on) which then enables the bacteria to uptake the citrate under oxic conditions!

Last month, another story breaks, just like last time, evolutionists are tooting their horns once again. After 56,000 generations under some predetermined conditions such as plenty of oxygen but very limited food supply. Testing the bacteria with a small amount of glucose, to see how they would react. We see a revisit of the hype as shown below…

Science News

“Learning to eat citrate, also called citric acid, is as big an innovation for E. coli as developing eyes or wings would be for multicellular creatures, says evolutionary geneticist Paul Rainey of Massey University in Auckland, New Zealand, and the Max Planck Institute for Evolutionary Biology in Plön, Germany.”

It’s hardly an innovation! But what they are observing is nothing more than duplication and rearrangement of pre-exsiting information while loosing the regulation mechanism which then allowed the uptake of citrate by the E. Coli bacteria. Does this mean the bacteria was evolving in the lab? The answer is a resounding, no! The bacteria wasn’t evolving for the last 25 years along with its 56,000 generations!

Evolution Observed Using Intelligent Design?

Breaking news, various media outlets report that what was expected to occur within billions of years, happened in a lab in just 60 days without “mystical complexity or a lot of the things that people have hypothesized — special genes, a huge genome, very unnatural conditions,” said evolutionary biologist Michael Travisano of the University of Minnesota, co-author of a study that was published on Jan. 17, 2012.

Evolutionists believe multicellular life forms evolved from single-celled ones but are unable to explain how single cells could unlearn the selfishness that is required for survival and learn to work as a team.  Also a very important aspect that is used quite often to measure evolution is called fitness.  This is also  important to use in determining the value of this particular experiment.

The subject of the experiment was yeast. In Wired, the experiment went like this…

“Once per day they shook the flasks, removed yeast that most rapidly settled to the bottom, and used it to start new cultures. Free-floating yeast were left behind, while yeast that gathered in heavy, fast-falling clumps survived to reproduce.”

“Within just a few weeks, individual yeast cells still retained their singular identities, but clumped together easily. At the end of two months, the clumps were a permanent arrangement. Each strain had evolved to be truly multicellular, displaying all the tendencies associated with “higher” forms of life: a division of labor between specialized cells, juvenile and adult life stages, and multicellular offspring.”

The authors admitted that this was not “natural selection” at work,  “by selecting for yeast cells or clusters that settled most quickly.”  Their reasoning for the lab experiment was this was give them knowledge on how this could have worked in the distant past. They have the idea if they can perform it in the lab, nature could surely do it also. A problem with that is, this is how they would accomplished it in the lab but how do that know that this is how nature would accomplish the same task in the real world?

So during the experiment the scientists would select to keep only the large clusters that sank to the bottom, then select the best snowflake-formers to survive and reproduce.

Remember evolution is measured in terms of “fitness” so how fit were the artificially produced ones from the originals? Michael Behe comments on the research with this…

“… Examination showed that the fast-sedimenting cells formed clusters due to incomplete separation of replicating mother-daughter cells.

“The cell clusters also were 10% less fit (that’s quite an amount) than the beginning cells in the absence of the sedimentation selection. After further selection it was seen that some cells in clusters would “commit suicide” (apoptosis), which apparently made the clusters more brittle and allowed chunks to break off and form new clusters. (The beginning cells already had the ability to undergo apoptosis.)”

The experiment fails the fitness factor, the yeast became less fit than the originals. Also how could it be called evolution in general when the yeast could form snowflake clusters before any selected pressure was applied to them? In other words, no new ability, they were the same snowflake clusters producers throughout the process. No new information had evolved in the lab and when you take into account the failed measure of fitness, the breaking news was just all hype.

Intelligent Design Papers Are Making Noise

The theory of intelligent design science considers itself to be a detector of patterns arranged in such a way, that it reveals something intelligent was beyond its cause.  There are similarities but also differences with creationism. Despite the differences, this blog does support the ID movement’s efforts to question Darwinism but do not encourage Christians to embrace all aspects of it.

Recently, it has been making some noise in peer-review papers. One was on “Plant Biology” Wolf-Ekkehard Lönnig, the author of this particular paper who is a biologist at the Planck Institute for Plant Breeding Research, he writes…

“Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment (as predicted) instead of regularly producing a range of new systematic species…”

The research collected data from 240,000 plants. Lönnig then refutes the idea that a step by step process with an enormous amount of slight variations then sides with Michael Behe who is known for advocating concept of “irreducible complexity” and Dembski’s arguments which has to do with universal probability bound.

Dembski and Robert Marks who are major players in the intelligent design movement. Their paper was published in Journal of Advanced Computational Intelligence and Intelligent Informatics where they argue fitness fails (which is how evolution is measured) without specified information about its target.

“We prove two results: (1) The Horizontal No Free Lunch Theorem, which shows that average relative performance of searches never exceeds unassisted or blind searches, and (2) The Vertical No Free Lunch Theorem, which shows that the difficulty of searching for a successful search increases exponentially with respect to the minimum allowable active information being sought.”

In the International Journal of Design & Nature and Ecodynamics by Dominic Halsmer came out pretty strong in favor of intelligent design.  He writes

“Human-engineered systems are characterized by stability, predictability, reliability, transparency, controllability, efficiency, and (ideally) optimality. These features are also prevalent throughout the natural systems that make up the cosmos. However, the level of engineering appears to be far above and beyond, or transcendent of, current human capabilities. Even so, there is a curious match between the comprehensibility of the universe and the ability of mankind to comprehend it.”

“This unexplained matching is a prerequisite for any kind of reverse engineering activity to be even remotely successful. And yet, mankind seems to be drawn onward toward a potential wisdom, almost in tutorial fashion, by the puzzles of nature that are continually available for us to unravel. Indeed, the universe is so readily and profitably reverse engineered as to make a compelling argument that it was engineered in the first place, apparently with humanity in mind.”

While the modern intelligent movement avoids identifying what an intelligent agent is which is part of the problem, it lacks history, engineering has observed to be performed with intelligence. Engineering is not a natural phenomena that just happens on it’s own. Rather it’s a phenomena concerning a finely tuned universe which was produced by a highly advanced intelligence namely, God!

How Much Explanatory Power Does Accidents Have?

If scientists were trying to explain certain phenomenon as a freak of nature or a freak of natural law, how sufficient is this particular explanation? In TalkOrigins it tries to refute the idea in response to intelligent design proponents in particular (Michael Behe’s Black Box) who refer to evolution that way…

“…the recurring attacks on evolution comes from those who find the notion of random change distasteful…Genetic changes do not anticipate a species’ needs, and those changes may be unrelated to selection pressures on the species. Nevertheless, evolution is not fundamentally a random process.”

One wonders if talkorigns thinks it’s “distasteful” for proponents of evolution to do the same thing? New Scientist has been running a series called, “Cosmic Accidents” which says

“The countless simple cells living in many different environments on Earth have had over 3 billion years to evolve complexity.  It could have happened repeatedly – and yet it appears to have happened just once, perhaps 2 billion years ago.  All complex life is descended from a single common ancestor.”

“Why is that so?  Because, says Nick Lane of University College London, natural selection normally favours fast replication, keeping simple cells simple.  Then a freak event occurred: an archaeon engulfed a bacterium and the two cells formed a symbiotic relationship. That transformed the dynamics of evolution, leading to a period of rapid change that produced innovations such as sex.  The incorporated bacterium eventually evolved into mitochondria, the energy generators of complex cells.”

Le Page then added, “it seems there was nothing inevitable about the rise of the complex cells from which we evolved.” At the very core of Le Page’s explanation is pure chance because in his opinion, prokaryotes were trying to evolve complexity for a billion years, but were unable to do so. TalkOrigins statement was meant to minimize intelligent design which means a “freak accident” is ruled out. Which also means, the big bang is ruled out, the origin of consciousness is ruled out, the origin of language is ruled out. For example, if an environment itself was able to create language, every organism in the environment would end up talking!

TalkOrigins seems to suggest exploratory power in accidents lacks greatly, rather it’s core argument has to do with experience rather than accidents or anticipation of needed mutations to enhance life as some intelligent design proponents would suggest. In other words, an experience of a animal trying to catch fast prey is transmitted to create mutations that natural selection can then choose which would eventually make future generations fast enough to catch that particular prey in order to survive.

But as such things as the fruit fly experiment demonstrates by showing after so many generations the fruit flies start to degrade instead of showing promise of improving through mutations. So this explanation also lacks explanatory power as well as “freak” accidents.

Carl Zimmer vs Michael Behe On Thornton’s Work

Like many of these types of debates about evolution with few exceptions, proponents on one side or the other conduct themselves within the confines on where they feel most comfortable  in order to avoid a face to face meeting, this particular one is without exception.

Carl Zimmer, a highly regarded so-called science writer who promotes evolution while trying to attack intelligent design. He recently posted this to Michael Behe about the work Thornton had conducted, it reads as follows…

“Thornton’s new work turned up last week on a web site run by the Discovery Institute, a clearinghouse for all things intelligent design (a k a the progeny of creationism). Michael Behe, a fellow at the Institute, wrote three posts (here, here, and here) about the new research, which he pronounced “great.” Why the change of heart? Because Behe thinks that the new research shows that evolution cannot produce anything more than tiny changes. And if evolution can’t do it, intelligent design can. (Don’t ask how.)”

Carl Zimmer takes a jab at Michael Behe, falsely accusing him of being a creationist like it’s some sort of dirty word and how dare he (Behe) conclude that intelligence is the source of organized information which produces and maintains life. Zimmer also wrongly believes science and Christianity are at odds with one another which they are not.  Behe responds

“I must say, it never ceases to amaze me how otherwise-very-smart folks like Zimmer and Thornton fail to grasp pretty simple points when it comes to problems for Darwinian mechanisms. Let me start slowly with a petty complaint in Carl Zimmer’s intro to the post. Zimmer is annoyed that I think Thornton’s latest work is “great”, yet I thought his previous work published a few years ago was “piddling”. “Why the change of heart?”, wonders Zimmer.”

What Michael Behe fails to grasp, they really do get the simple points that he likes to write about, but because he disagrees with evolution it changes full range of dynamics on how they treat him. Who would really argue over a generalization about disagreeing with one study and then later on agree with another? Behe further explains by comparing it to a crane and it’s massive promise of what it could do, Behe calls this “piddling” but later on a more detailed study comes out that demonstrated a realistic evaluation on what the crane could actually do. Thus, Behe praises the work!

I believe Zimmer understands this position, that is not to say he agrees with it, but like I pointed out earlier, it’s the conclusions of science that dictates the dynamics of how he treats him! It’s a sad commentary for those who are so well educated but act so immature.

Biochemists Study Focuses On Attacking Intelligent Design

What appears to be a growing concern, “intelligent design” we now have scientists conducting studies in order to try and disprove a principle known as “irreducible complexity” which became more mainstream for detecting thought behind a creation rather than a mindless process. It’s not the only thing used for such detection, but one aspect of it.

Evolutionists have used a formula for explaining specialized complexities in nature. This is known as the “preadaptation” explanation. In this particular study lead by a team of researchers from Australia’s Monash University, they used a transporter system in mitochondria and argued that components were available elsewhere, thus it was a mindless process which supposedly created the complex structure. The paper mentioned intelligent design in a negative sense and claim this research proved that nature can go from “irreducibly” to “reducibly” complex.

Keep in mind, Michael Behe of Lehigh University did not use this transporter system as an example for “irreducible complexity.” Did intelligent design proponents respond to this research directed at them? Yes, they did, but PNAS refused to print Michael Behe letter to them and others. So not only PNAS refuses to include evidence against evolution but letters as well.

Here is what Michael Behe stated in response to the research…

Recently a paper appeared online in the journal Proceedings of the National Academy of Sciences, entitled “The reducible complexity of a mitochondrial molecular machine” (http://tinyurl.com/mhoh7w). As you might expect, I was very interested in reading what the authors had to say. Unfortunately, as is all too common on this topic, the claims made in the paper far surpassed the data, and distinctions between such basic ideas as “reducible” versus “irreducible” and “Darwinian” versus “non-Darwinian” were pretty much ignored.

To the Editor

Reducible versus irreducible systems and Darwinian versus non-Darwinian processes

The recent paper by Clements et al (1) illustrates the need for more care to avoid non sequiturs in evolutionary narratives. The authors intend to show that Darwinian processes can account for a reducibly complex molecular machine. Yet, even if successful, that would not show that such processes could account for irreducibly complex machines, which Clements et al (1) cite as the chief difficulty for Darwinism raised by intelligent design proponents like myself. Irreducibly complex molecular systems, such as the bacterial flagellum or intracellular transport system, plainly cannot sustain their primary function if a critical mechanical part is removed. (2-4) Like a mousetrap without a spring, they would be broken.

Here the authors first postulate (they do not demonstrate) an amino acid transporter that fortuitously also transports proteins inefficiently. (1) They subsequently attempt to show how the efficiency might be improved. A scenario for increasing the efficiency of a pre-existing, reducible function, however, says little about developing a novel, irreducible function.

Even as evidence for the applicability of Darwinian processes just to reducibly complex molecular machines, the data are greatly overinterpreted. A Darwinian pathway is not merely one that proceeds by “numerous, successive, slight modifications” (1) but, crucially, one where mutations are random with respect to any goal, including the future development of the organism. If some mutations arise non-randomly, the process is simply not Darwinian. Yet the authors say nothing about random mutation. Their chief data are sequence similarities between bacterial and mitochondrial proteins.

However, the presumably homologous proteins have different functions, and bind non-homologous proteins. What is the likelihood that, say, a Tim44-like precursor would forsake its complex of bacterial proteins to join a complex of other proteins? Is such an event reasonably likely or prohibitively improbable? Clements et al (1) do not provide even crude estimates, let alone rigorous calculations or experiments, and thus provide no support for a formally Darwinian process. Their only relevant data in this regard is their demonstration that a singly-mutated bacterial TimB can substitute for Tim14 in mitochondrial transport. While that is certainly an interesting result, rescuing a pre-existing, functioning system in the laboratory is not at all the same thing as building a novel system step-by-random-step in nature.

Biologists have long been wary of attempts to fill in our lack of knowledge of the history of life with imaginative reconstructions that go far beyond the evidence. As I have discussed (5), extensive laboratory evolution studies over decades offer little support for the plausibility of such felicitous scenarios as Clements et al (1) propose. The authors may well be overlooking formidable difficulties that nature itself would encounter.

How they could come up with calculations on something they never observed is beyond me. For example, nothing was shown in this study a component,  the Tim44-like precursor would move out of one complex protein then go into another complex protein. They just assumed it would, because it’s there and similar. This is hardly evidence!

Some have said, this was a misunderstanding of  the nature of “irreducible complexity” used by evolutionists. I think not, it’s more trying to fit the data into their one and only framework, evolution while trying to make an emotional connection  rather than a practical connection to those whom they are trying to reassure or sway.

John McWhorter’s Controversial Webcast Causes Confusion

Dr. John McWhorter who is a linguist by practice and who also doesn’t believe in the existence of God conducted an interview with biochemist Dr. Michael Behe on a liberal website called; bloggingheads tv.  John McWhorter surprises Michael Behe with his profound enthusiasm for his book “Edge of Evolution” which was published back in 2007.

According to Dr McWhorter, though he had a keen interest in evolution, but didn’t feel the concept was rock solid. He questions mutations for example where there is no solid evidence that produces a ton of intermediate animals which shows a loss of  functions and then the gains of other functions before it comes another animal. He finds when he tries to discuss his doubts about evolution, people in his circle accuse him of trying to bring God into it even though he actually denies His existence.

The interview continued with discussing such things as proteins, and some of the jobs they can perform in general. John McWhorter even said he has come closer to believing in the existence of God after reading Behe’s book even though he hates change. When the interview concluded, Michael Behe was very impressed and thought bloggingheads tv was a pretty nice outfit.

Here is where the confusion started, the same day the video was posted for the public to view, it was removed! Then there were accusations of censorship being implied such as “maybe we aren’t quite as free as we think” said Michael Behe. What happened was, John McWhorter received a lot of heat for not being hard on Michale Behe, caved in and requested the video to be removed. He then states, “with regret, that this interview represents neither himself, Professor Behe, nor Bloggingheads usefully.” Next, he apologized to anyone who found his interview to be objectionable.

Let me say, Dr John McWhorter welcome to the world of controversial issues on a broadcast! What you have gone through is typical of any host who brings up issues people feel strongly about. I suspect he thought he had violated some sort of rule or rules which later the site put up some clarification about. This particular site is operated by Robert Wright who is a well known liberal. The funny part of this story, Wright claims he never thought this would happen on his site! Where has he been? There are controversial issues all over the net. How could you not consider such a thing happening on a site which promotes “diversity” of views? I’m not sure why John McWhorter chose bloggingheads tv, but one thing is for sure, he could do better.