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.