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Dr. Richard Lenski’s “Unicorns”
Dr. Richard Lenski’s “Unicorns”
Dr. Richard Lenski’s “Unicorns”
Posted: 27 Nov 2013 09:08 AM PST
by Sean Pitman . Richard E. Lenski is an American evolutionary biologist, best known for his 25-year long-term E.
coli evolution experiment, and his work with digital organisms, using Avida. What is impressive about Dr. Lenski is
that he is trying to show how random mutations and natural selection...
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Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
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Dr. Richard Lenski’s “Unicorns”
NOVEMBER 27, 2013
11 COMMENTS
by
Sean Pitman
.
Richard E. Lenski is an American evolutionary biologist,
best known for his 25-year long-term E. coli evolution
experiment and his work with digital organisms using
Avida.
What is impressive about Dr. Lenski is that he is trying
to show how random mutations and natural selection
(the Darwinian mechanism for evolution) can create
functionally complex systems within living things. He
argues that very small gradual changes can add up over
time to produce very dramatic functional changes,
exactly as Darwin predicted.
Of course, those who favor the concept of intelligent
design or the Biblical concept of Creation have long
argued that “micro-evolution” is possible, but “macro-
evolution” is not. In other words, small changes cannot
add up over time to produce highly complex biological
systems. In fact, the demonstration of macro-evolution is claimed to be equivalent to finding
the mythical unicorn.
So, who is right? Has Dr. Lenski really found the elusive “unicorn”?
Has he actually shown how macro-evolution via the Darwinian
mechanism is really a plausible theory?
Well, in 2012 Dr. Lenski and a few others published a very interesting
paper claiming to have demonstrated this very thing (
Link
,
Link
). He
produced E. coli bacteria that, after ~31,000 generations, evolved the
ability to use citrate for energy under oxygenated conditions –
something they weren’t able to do before. And, they achieved this
novel function via random mutations and natural selection – right in
line with predictions for the Darwinian mechanism.
Of course, many people got very excited over the
implications of this experiment. In September of 2012
the well-known science journal Nature published an
article about Lenski’s experiment entitled, “Evolution:
How the unicorn got its horn“, by
Hendrickson
and
Rainey
. Here’s part of what they wrote about the
implications of this experiment:
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Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
The discovery of the Cit + mutants in Lenski’s
experiment has been a mote in the eye for those suggesting that major phenotypic
innovations cannot be explained by micro-evolutionary (gradual) processes. Indeed,
for anti-evolutionists, lack of mechanistic detail has even allowed room for divine
intervention. After several attempts to politely address the concerns of one critic,
Lenski responded publicly in what has proven to be one of the most competent and
direct defenses of science versus dogma for some time. It includes the memorable
phrase, “In other words, it’s not that we claim to have glimpsed ‘a unicorn in the
garden’ — we have a whole population of them living in my lab!”. (
Link
)
Game over!
Finally, those pesky creationists and IDist have been put in their place once and for all!
Not so fast . . .
As is generally the case, especially for claims regarding the creative abilities of the Darwinian
mechanism, the devil is in the details. And, when one looks a bit more closely at the details
of the Lenski experiment, it loses quite a bit of its luster.
What Dr. Lenski did was to grow E. coli under oxic
(oxygenated) conditions in citrate-rich media. E. coli
bacteria are generally unable to use citrate under oxic
conditions as a source of energy. However, they can use it
under anoxic conditions. In other words, they already have
the gene for citrase in their genome. It is just that it is
normally turned off under oxic conditions. How is it turned
off? Well, the promoter for the gene that transports citrate
into the bacterium (citT) is not active under oxic conditions.
So, all that needs to happen is to move the citrate
transport gene close to a promoter that is actually active
under oxic conditions. Once this is done, citrate will enter
the bacterium and be used for energy.
And, this is exactly what happened. Nothing structurally new needed to be evolved. After
about 31,000 generations, in a large population of bacteria, there was a single genetic
mutation in a bacterium that ended up moving the citT gene and placing it under the control
of a promoter (rnk) that is active under oxic conditions. The fact that just this single
translocation mutation took so long to achieve should clue everyone in to how difficult it is to
achieve even such low-level changes in function via random mutations. The protein product,
however, remained the same – i.e., <500aa with no required amino acid changes to achieve
a selectable effect. All that was required was to move a pre-existing gene close to a promoter
to turn it on during oxic conditions. That’s it. The protein itself didn’t need to be changed for a
useful advantage.
Now, at this point, multiple copies of the gene were rapidly produced in some colonies.
However, having just one copy was enough to produce a selectable growth/survival
advantage in the citrate-rich environment. It doesn’t matter if there are 1 – 9 copies of the
gene – the same function is realized to different levels – i.e., the cit+ function can exist, to a
selectable degree, with just one copy of the gene producing the the very same protein.
Additional “refinements” are easy once at least a minimum useful level of a particular type of
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Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
Beneficial Sequences in Sequence Space Ocean
function is realized – not a problem at all.
Again, Dr. Lenski’s pet “unicorn” is a very low-level example of evolution in action where
nothing structurally new was produced to achieve the function in question. The only thing that
happened was a mutational move of a pre-existing gene from one location to another within
the genome so that it could be turned on in a particular environment. That’s not a problem at
all for the Darwinian mechanism. Statistically, such a mutation is very likely to happen, within
a few tens of thousands of generations, given a fairly large colony of bacteria.
Now, compare this with the challenge of
explaining how random mutations can
search through the vastness of protein
sequence space (a space comprised of
all possible sequences of a particular
length) to find the extremely rare islands
of novel beneficial sequences that could
produce something qualitatively new –
an entirely new type of function that
requires an new protein-based system –
a new physical structure. Such unicorns
are much harder to find because
random mutations have to search
through vast oceans of non-beneficial
sequences before they can find the very rare isolated islands of beneficial sequences. The
question is, are there any examples of this sort of evolution actually happening?
Well, yes, there are many examples were truly novel protein sequences with selectably
beneficial functionality are discovered by random mutations. Most of these examples are
single-protein enzymes and the like that require a minimum of no more than a few hundred
specifically arranged amino acid residues (amino acids are the building blocks of proteins,
with a total of 20 different amino acid “characters” within the “alphabet” of proteins).
However, there are no examples of evolution in action producing any protein-based system
that requires a minimum of more than 1000 specifically arranged amino acid residues – not
even close. The reason for this is because sequence space at this level is unimaginably
enormous (i.e., 20^1000 = 1e1301 sequences). To get an idea as to how large this number
is, consider that the total number of atoms in the visible universe is about 1e80 atoms. What
is more important, however, is that the ratio of potentially beneficial vs. non-beneficial
sequences in the 1e1301 sequence space is incredibly tiny – so miniscule that any cluster of
beneficial sequences in the enormity of sequence space is surrounded, on all sides, by an
enormous ocean of non-beneficial sequences that is so vast that, if the beneficial islands of
sequences were like stars in the sky, no other stars would be visible in the universe from the
perspective of one of these islands. That means that getting from one of these islands to the
next closest beneficial island, by random mutations, would take trillions upon trillions of years
of time.
As a real life example, consider that the
famous rotary flagellar motility system
that exists within various types
of bacteria requires a minimum of over
5000 specifically arranged amino acid
residues. No such system has ever
been shown to evolve nor has anyone
presented any statistically tenable
argument for how random mutations and
natural selection could gradually build
such a system.
The problem is that the proposed
beneficial steppingstones in a pathway
of a complex multi-protein system, like a
flagellar motility system, are themselves
Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
Featured, Media, Opinion
Cit+, Citrate, Creationist Resources, E. coli, evolution, featured, intelligent design, macroevolution,
Richard Lenski, sean pitman, sequence space, Unicorn
The Basis of Biblical Credibility
far far too widely separated in protein sequence space, by distances that would cover many
universes, for random mutations to get across any of the non-beneficial gaps this side of
trillions of years of time. That is why evolutionary progress stalls out, in an exponential
manner, with each step up the ladder of functional complexity (i.e., minimum size and/or
specificity requirements for a system to work to a selectable level of usefulness).
For further information on the statistical limits to the Darwinian mechanism see the
“
Steppingstone Problem
“.
Share
Richard Gates
Reply
November 28, 2013 at 7:22 am
Holly Pham
Reply
November 28, 2013 at 8:43 am
James V. Kohl
Reply
November 29, 2013 at 3:19 am
11 Responses to “Dr. Richard Lenski’s “Unicorns””
This is precisely the kind of information that one needs to evaluate
scientific lab experiments.
It is impressive to read reports, even in reputable science journals, that
describe and often interpret experiments in a way which almost invariably
reflects the bias of the reporter. However someone knowledgeable in the
discipline is always needed to take a closer look at the issues, as has
happened in this case.
This is the kind of “peer review” that serves truth.
Thank you for respecting the reader’s intelligence!
(Quote)
Well-liked:
15
Thanks Sean for telling us the “rest of the story!” Very interesting!
(Quote)
Like Comment:
5
They eliminated natural selection for nutrients via the medium used to
Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
Bob Helm
Reply
November 29, 2013 at 8:16 am
Sean Pitman
Reply
November 30, 2013 at 6:43 pm
James V. Kohl
Reply
November 30, 2013 at 6:34 pm
grow the organisms. This limits the metabolism of nutrients to species-
specific secreted byproducts called pheromones that control the
physiology of reproduction. Thus, all biophysical constraints on conserved
molecular mechanisms of nutrient-dependent pheromone-controlled
adaptive evolution are eliminated and results are reported in terms of
mutations.
This experiment was designed before researchers knew anything about
molecular epigenetics. Nothing is illuminated by first eliminating variables
that include the epigenetic ‘landscape,’ which becomes the physical
landscape of DNA in the organized genomes of species from microbes to
man that adapt to their environment.
I am surprised at attempts to explain the evolution of organismal
complexity in the context of mutation-driven evolution, when no
experimental evidence from model organisms in their natural or typical
environments supports that idea. Instead, all experimental evidence
supports nutrient-dependent pheromone-controlled adaptive evolution.
Lenski and many others ignore an important fact; Darwin clearly stated
that ‘conditions of life’ precede any consideration of natural selection.
Conditions of life are nutrient-dependent and pheromone-controlled.
There’s nothing random about that, and obviously there never has been.
(Quote)
Like Comment:
1
Sean, you really ought to try to publish this material in a mainstream
scientific journal or at least in a creationist journal like “Origins.” Simply
posting it on an obscure site like “Educate Truth” that few people read is
not enough. Just a friendly suggestion!
(Quote)
Like Comment:
5
@
Bob Helm
:
Most of this information, in this particular article, has already been
published by others in various journals. The only thing I contributed
here of any uniqueness is the concept of changes in the ratio of
beneficial vs. non-beneficial sequences in sequence space at various
levels of functional complexity.
When I submitted the technical argument for sequence space to
Origins (a few years ago), they told me that it was too technical for
their readership to understand. I should probably try again to submit a
toned down version for more general readership.
(Quote)
Like Comment:
8
Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
Sean Pitman
Reply
November 30, 2013 at 7:04 pm
James V. Kohl
Reply
November 30, 2013 at 7:17 pm
Sean and Bob,
I’ve published in Hormones and Behavior, Neuroendocrinology Letters,
Journal of Psychology and Human Sexuality, and twice in Socioaffective
Neuroscience & Psychology. No matter how clear it becomes that
mutation-driven adaptive evolution is not possible due to biophysical
constraints, each time random mutations are introduced into any
explanation helps the nonsense about mutation-driven evolution to
spread.
As a Creationist, Dobzhansky supported mutation-driven evolution in
1973 and attributed single amino acid substitutions to mutations. They
are obviously nutrient-dependent and facilitate rapid changes in
organismal complexity in 5-10,000 years, not millions of years, as
evidenced in the current literature.
The changes are clearly constrained by thermodynamically futile cycles
that enable de novo creation of olfactory receptor genes, which allow
nutrient uptake (as in the case of citrate in E.coli) and nutrients are
metabolized to pheromones that help to achieve the organism-level
thermoregulation that is required for species-wide epistasis.
If the epigenetic landscape changes, however, a novel nutrient can initiate
the same process of nutrient-dependent pheromone-controlled
adaptations (e.g., in species from microbes to man). Lenski has simply
showed that nutrient stress and thermal stress have the same effects on
seemingly futile cycles of protein biogenesis and degradation.
(Quote)
Like Comment:
2
It doesn’t matter what stressors may or may not contribute to protein
biogenesis. The fact remains that whatever else might contribute to
mutagenesis, novel proteins are dependent upon novel genetic
mutations. In this particular Lenski experiment, no novel protein was
produced. However, there was a novel genetic mutation that gave
rise to the new functional abilities of the E. coli bacteria. This genetic
mutation simply allowed a protein-coding gene to be turned on in a
different type of environment by moving a gene to a different location
within the genome. Statistically, this isn’t a problem given the number
of bacteria in the steady-state population over the course of a few
tens of thousands of generations. It’s very predictable in fact –
statistically. What is not statistically tenable, however, is the evolution
of a qualitatively novel protein-based system of function that requires
more than 1000 specifically arranged residues. Such a feat is not
statistically feasible – and Lenski should know better than to suggest
otherwise.
(Quote)
Like Comment:
7
Sean Pitman
:
novel proteins are dependent upon novel genetic mutations.
Dr. Richard Lenski’s “Unicorns” | Educate Truth
http://www.educatetruth.com/featured/dr-richard-lenskis-unicorns/[12/16/2013 5:18:39 PM]
Sean Pitman
Reply
November 30, 2013 at 7:21 pm
James V. Kohl
Reply
November 30, 2013 at 7:52 pm
Sean Pitman
Reply
November 30, 2013 at 8:13 pm
The ability of mutations to cause production of functional novel proteins is
biophysically constrained. Mutations perturb the required thermodynamics
and organism-level thermoregulation. Nutrient uptake enables seemingly
futile cycles of protein biogenesis to result in production of proteins that
contribute to increasing organismal complexity via controlled reproduction.
I am surprised that you immediately turned back to mutations theory,
when the de novo creation of olfactory receptor genes excludes
mutations theory from any further consideration whatsoever.
(Quote)
Like Comment:
0
I’ve read your blog about the Lenski experiment “Microbes: living in
the past”. However, I think you’re mistaken. You wrote:
The adaptations arose [in the Lenski experiment] due to the de novo
creation of olfactory receptor genes under conditions that would
otherswise lead to death by starvation.
This simply isn’t true. No new receptor genes evolved at all –
olfactory or otherwise. The very same genes stayed exactly the
same. The only thing that changed is the location of the very same
genes within the genome. Also, the bacteria were not starving. They
simply started using citrate as an additional source of energy to the
nutrients that they were already being provided with – over the
course of the decades that Lenski has been running this particular
experiment. I see no evidence for epigenetic factors in play here or
thermodynamic instability before or after the changes in function.
Sean Pitman
http://www.DetectingDesign.com
(Quote)
Like Comment:
8
“No new receptor genes evolved at all – olfactory or otherwise. The very
same genes stayed exactly the same.”
Perhaps I’m mistaken, but I don’t know of any other way for citrate uptake
to occur if it is not receptor-mediated. Should I refer to the de novo
creation of the olfactory receptor gene, as de novo creation of a chemical
receptor gene?
(Quote)
Hot debate.
3
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There was no change in the citrate receptor or transport protein, or
any other protein. No structural change took place at all. You simply
don’t understand the Lenski experiment. All that happened was that
the gene that codes for the citrate transport protein, which already
existed and was active under anoxic conditions, was turned on in an
oxygenated environment by being placed next to an active promotor.
That’s it. There’s simply no new receptor being made here. No new
gene or protein – olfactory or otherwise.
(Quote)
Hot debate.
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