Discussion of everything related to the Theory of Evolution.
Creationists hate the Lenski experiments because it blows holes in some of their most beloved paradigms:
1. Natural selection cannot lead to an increase in "information."
2. Evolution cannot produce new functions.
Interesting that you refer to "relentless pressure," as if nature is not capable of producing such pressures. It is.
Evolution works with what is already there. An entirely new metabolic pathway is unlikely to evolve from scratch. Therefore your critiscism that E.coli can normally "almost" make use of citrate anyway makes little sense. The point is a new metabolic function evolved in a relatively short period of time. And no, 30,000 generations is not a long time evolutionarily speaking. How long would it take to evolve a digestive system? Obviously longer than 30,000 generations. No one has ever suggested differently.
While extinction is important for evolution, since it frees up ecological niches that were previosuly occupied, it is not necessary for macro-evolution. In fact, the fossil record shows that many different related species can co-exist at the same time and even in the same location. Examples include the ancestors of both man and the modern horse. Now lets look at the Lenski experiment again. What would happen if the supply of glucose was cut off? It would quickly lead to the extinction of the non-citrate capable population.
You claimed that nothing else happened in 50,000 generations. This is completely false. The paper you cited mentions other examples of evolution in the introduction, including: higher growth rates on glucose, shorter lag phases, reduced peak population densities, larger average size, increased DNA supercoiling, defects in DNA repair, and changes in many gene-expression profiles. In fact, there are more than a dozen papers previously published on this project that were cited in this paper. What did you think there were about? Nothing happening in 50,000 generations?
Last edited by robsabba on Mon Jun 21, 2010 4:28 pm, edited 2 times in total.
How does the fact that historical contingency DOES work in an actual evolutionary scenario provide evidence that "Darwinian theory does not provide the answers to cell development?"
Thanks for your comments.
My response is as follows
As I am neither a creationist nor any other “ist” I’m afraid this comment of yours escapes me.
That E.coli can normally "almost" make use of citrate is not a critiscism.
It was simply stated as a fact and I am at a loss to understand how you could regard that as a critisism. I was only stating what Lenski was himself was reporting albeit I did paraphase it somewhat. However as you will note I clarified that “almost” bit in my second posting.
Actually no new metabolic function evolved. Please read the paper carefully.
The ability to digest citrate was already there. What was lacking was the ability to transport the citrate from the outside environment through the cell membrane into the interior.
This is how Lenski himself reports it in the paper
“The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions” (para 5)
How did that capability come about? Well Lenski has been unable to identify the cause.
He refers to a few possible causes in para 5 & 6.
“Indeed, atypical E. coli that grow aerobically on citrate (Cit_) have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters (44, 45).
Other findings suggest that E. coli has the potential to evolve a Cit_ phenotype. Hall (41) reported the only documented case of a spontaneous Cit_ mutant in E. coli. He hypothesized that some complex mutation, or multiple mutations, activated cryptic genes that jointly expressed a citrate transporter, although the genes were not identified.
Pos et al. (43) identified an operon in E. coli K-12 that apparently allows anaerobic citrate fermentation, and which includes a gene, citT, encoding a citrate– succinate antiporter. High-level constitutive expression of this gene on a multicopy plasmid allows aerobic growth on citrate, but the native operon has a single copy that is presumably induced only under anoxic conditions.”
Please note my emphasis on the uncertainty he and others have expressed
However Lenski himself continues with this finding (para 7)
"Despite this potential, none of the 12 LTEE populations evolved the capacity to use the citrate that was present in their environment for over 30,000 generations. During that time, each population experienced billions of mutations (22), far more than the number of possible point mutations in the _4.6-million-bp genome. This ratio implies, to a first approximation, that each population tried every typical one-step mutation many times. It must be difficult, therefore, to evolve the Cit_ phenotype, despite the ecological opportunity"
According to standard evolutionary theory, every adaptation, even the most sophisticated, is the product of a series of simple adaptive steps. Adaptive steps are thought typically to involve a single mutation, though steps requiring two independent mutations may also be feasible under some circumstances. Whether by single mutations or double mutations, though, as long as each step of an adaptive path is both feasible and beneficial, it is commonly assumed that the path will be followed
The point that Lenski is making in part of the quote I have emphasised and underlined above, is that this experiment suggests that the common assumption of the standard (Darwinian) theory of successive one step mutations providing function isn’t being borne out in his experiment.
This is the reason why he is suggesting that this experiment favours Gould’s Historical Contingency proposal rather than the standard Darwinian explanation.
If you research the history of Gould’s and Eldridge’s theory of Punctuated Equilibrium you will appreciate why they are so controversial among some prominent evolutionary scientists.
Punctuated Equilibrium is a theory that does not agree with Darwinian explanation
I hope this also answers your last question in your second post quoted below
I’m a little bit tied for time to respond to your other comments but will do so very shortly
Here is the problem. Evolution, as we now see it includes point mutation, but it is far from the only source of novelty in genomes. Horizontal gene transfer (multiple mechanism involved) and gene duplication are also essential to the ability to evolve new genes. From this point of view, the Lenski experiment is overly simplistic as there are very limited possibility of exchange of genes in his populations :
-They are maintained in exponential growth: no dead cells to scavenge
-Absence of phages
-Absence of other bacteria that can act both as donor for new genes and also as a way to accelerate intraspecific gene exchange
-Limited environmental stress that could affect the genome (ie: UV)
So yeah it is far from being a true reflection of all that could drive evolution, but hey, you have to start somewhere, and this is a darn good one. And that demonstrate that creation of a gene de novo is probably not a very frequent event.
And as far as I understand it, the historical contingency is definitely a huge part of the evolution as it is now accepted, and was already part of Darwin's understanding, even if he did not emphasize it in the the origin of species. Granted, my lecture of it was probably contaminated by my knowledge of recent biology, but it does not seem that Gould was revolutionary on this respect.
Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
I included the ability to transport a molecule across a cell membrane as a "metabolic function." You can split hairs about that if you like, but the point is that these bacteria were now able to make use of a new carbon source that the ancestral population could not. As far as the rest is concerned, I may have misunderstood your use of the term "Darwinian." Many people use it interchangably with "evolutionary." It is hard nowadays to understand what people mean by the term. If you are specifically refering to classical evolution according to Darwin, then all I can say is that the science of evolutionary biology has advanced well past Darwin. In fact, Darwin knew nothing about where the variability that evolution works with actually comes from. He knew nothing about DNA or genes or mutations. You seem to be citing this parer in agreement with this conclusion. If so, I agree. Is that really your only point?
I don’t accept I was splitting hairs, - bringing meat to the table and digesting that meat are two different functions, the function that evolved in the Lenski experiment is the “bringing” bit. However we can agree to differ I’m sure,
When I use the expression Darwinian I am of course referring to the Modern synthesis or neo Darwinism as it is often known.
To avoid any further misunderstandings Let me firstly explain my current understanding.
Evolution is a fact. I don’t think anyone seriously argues that point.
The question that needs to be properly answered though is
“what are the limits, if any to what evolution can achieve”?
The fundamental tenets of the modern standard theory are random mutations of genetic material followed by natural selection operating on populations, the process is gradual and this drives towards speciation.(new species)
A central tenet being in the words of Simon Conway Morris “that evolution is for all intents and purposes open-ended and indeterminate in terms of predictable outcomes.”
A tenet incidentally that he actually disagrees with.
http://rstb.royalsocietypublishing.org/ ... 3.full.pdf
Eldridge and Gould argued that gradualism is not manifest in the fossil record as that shows rapid periods of evolution followed by long periods of stastis., hence Punctuated Equilibrium.
As canalon has noted, Darwin was aware of this privately but did not try to explain in his “Origin of Species” .His theory was based on gradualism and this gradualism has been retained in the modern synthesis.
Historical Contingency is a main driving mechanism according to Eldridge and Gould
As such it renders evolution fundamentally quirky and unpredictable and not repeatable.
According to Simon Conway Morriss however, evolution is broadly repeatable ( nearly non random) with contingency mostly confined to minor details.
This experiment is what good science is all about.
It is not relying on historical science but experimental science and therefore the data is dependable. What conclusions can be drawn from the results?
Lenski interprets the results in support of the Gould hypothesis, i.e. historical contingency
However Simon Conway Morris interprets these same results to support his understanding of
Michael Behe the articulator of the ID community interprets the results as supporting his view.
There are of course other opinions from eminent scientists
So who is right - is there a definitive answer?
In arguing his case Conway Morris puts it this way.
“That evolution is not utterly random is evident from the ubiquity of homoplasy, ( convergent evolution) at least within clades that encompass lower parts of the taxonomic hierarchy. The question, however, is does this principle extend to the major divisions of life? No definitive answer can yet be given, not least because the origins of the great majority of major groups are shrouded in obscurity, although jointly molecular data and the fossil record continue to make major assaults on this citadel of ignorance.”
In English – science doesn’t have an answer.
So why so much heat when someone dares to question standard theory?
I do find Morriss’s take on this really amusing.
“Yet, if evolution is glaringly obvious, why is it not only greeted with growing hostility, but the siren-call of anti-evolutionary dogma, notably ‘intelligent design’, remains a rallying point to individuals that in any other respect fail to manifest any obvious sign of mental instability?
The reasons, of course, are complex and so far as the explication (and defence) of the science of evolution is concerned, it can hardly be assisted by those who ironically treat it as a religion (Midgley 1985).”
The fact is science does not have an answer to the origin of speciation
So as I see matters the original question of this thread “whether there have been any experiments conducted that provide empirical support for macroevolution.”
As yet no
Lenksi’s experiment is probably the most extensive yet and after over 20years of selective pressure over some 360,000 generations ( 12 x 30,000) has produced a minor novel trait.
However canalon has quite reasonably pointed out that the growth environment is somewhat simplistic, as it does not compare in wild nature. But this is a good start.
Here is some more food for thought
http://www.bioone.org/doi/abs/10.1095/b ... 104.031302
some more information here
http://findarticles.com/p/articles/mi_m ... n13595924/
Attention, I did not say that. What I said is that historical contingency was tacit in the Origin of Species, at least when I read it, but certainly not punctuated equilibrium. Which is a definitely new evolution (pun intended) of the theory brought by Gould and Eldridge. I do not think that Darwin was anything but gradualist.
As for the convergence argument, I will need more time to read Simon Conway Morris argument in full, however, what it seems to go to, i.e. that convergence disprove contingency, seems to me quite wrong. Once again, my limited understanding of evolutionary theory being stated, I would say that those arguing historical contingency are not arguing that, in a very broad sense, the way life will develop cannot be predicted, but that how it will get there is constrained by history. hence that sometimes less than optimal solution will be adopted because a better one, that might have evolved from an ancestor has been lost and cannot be regained to improve the descent. But yes one can predict that life will try and exploit as many niches as possible in the environment. Mammals, insects and reptile (as birds) all have members that can fly. But the way flight evolved took very different path.
In that sense historical contingency is strong. And every time a new structure/pathway evolve, it will create both new possibilities and new constraints for the future generations of organisms. And those cannot neither be predicted, nor, and I think this is were I diverged with Conway-Morris, be dubbed as insignificant. For example the fact that insects have exoskeleton rather than endoskeleton will forever bring massive constraints as to the size/shape that they will be able to reach because of simple mechanical problems.
As far as I know, once again, the split between macro and micro-evolution is mostly used by ID/creationist rather than biologists who all assume that there is only a continuum (although probably not completely smooth, but certainly not a massive divide). That said, no, there are no controlled experiments that led to massive changes but:
- Think about time scale, doing this kind of experiment is not easy, for one thing funding to run an experiment that long is not exactly easy to secure (why is there only one Lenski? money is an important reason). And bacteria are quite fast at replicating.
- Look at dogs, certainly not a controlled experiment, but over a much reduced (compared to Lenski's bacteria) massive changes in body shapes, abilities and diversity have been selected in many domesticated animals.
- Controlled environment and nature are very different, how do you introduce phages, UV, other bacteria and other very important factors in your experiment? Those are challenges that have for the moment no answers, but they would be valuable.
In conclusion, the simple fact that Lenski has been able to do what he is doing, is wonderful and you should remember that if his bacteria have not evolved one specific trait, on the other hand they have changed a lot as compared to the ancestors, and maybe there are other important changes that have not been noticed in this experiment just because noone has looked at them yet...
Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
My apologies, I understood from your comment that you were aware of the private note of Darwin that Eldridge drew attention to in an interview as curator Darwin at the American Museum of Natural History.
http://www.amnh.org/exhibitions/darwin/ ... dredge.php
You are quite correct, Darwin was a gradualist however he did note that the fossil record did not support his theory of gradualism and so put it down to a faulty/incomplete fossil record.
The problem as I see it is that paleontology is an historical science and therefore the data is subject to interpretation depending on the model used. It was in this background that Darwin formulated his theory.
However now we can rely on the science of genetics which of course presents actual data from experimentation. It is here that Darwinian theory is proving unfounded.
I would like to take up your other points shortly.
A further response to canolan’s last post
Actually all biologists do not all assume this continuum as you suggest. In fact for every biologist (Phd) who holds to the view of this micro/macro continuum another can be named who challenges that view
I would encourage you to examine the works of Jim Shapiro and others. Here is a start.
http://shapiro.bsd.uchicago.edu/21st_Ce ... _Evol.html
Your example is one of artificial selection not natural selection. A better example would perhaps be wolves and dogs, however in both cases the examples are varieties within the same species. I would argue your example supports the divide between species rather than a continuum.
I agree with you in the matter of controlled and natural environment being different, however I do not agree that the introduction of phages or UV would impact on the experiment to the degree that one might expect.
May I quote from part of the Shapiro paper cited above.
“The conventional view is that genetic change comes from stochastic (random), accidental sources: radiation, chemical, or oxidative damage, chemical instabilities in the DNA, or from inevitable errors in the replication process. However, the fact is that DNA proofreading and repair systems are remarkably effective at removing these non-biological sources of mutation.
For example, consider that the E. coli cell replicates its 4.6 megabase genome every 40 minutes. That is a replication frequency of almost 2 kHz. Yet, due to the action of error-recognition and correction systems in the replication machine and in the cell to catch mistakes in already-replicated DNA, the error rate is reduced below one mistake in every 1010(10 to power 10) base-pairs duplicated, and a similar low value is observed in mammalian cells (32). That is less than one base change in every 2000 cells, certainly well below the mutation frequencies I have measured in E. coli of about four mutations per every 100 to 1000 cells. (my emphasis)
In addition to proofreading systems, cells have a wide variety of repair systems to prevent or correct DNA damage from agents that include superoxides, alkylating chemicals and irradiation (33). Some of these repair systems encode mutator DNA polymerases which are clearly the source of DNA damage-induced mutations and also appear to be the source of so-called "spontaneous" mutations that appear in the absence of an obvious source of DNA damage (34). Results illustrating the effectiveness of cellular systems for genome repair and the essential role of enzymes in mutagenesis emphasize the importance of McClintock’s revolutionary discovery of internal systems generating genome, particularly when an organism has been challenged by a stress affecting genome function.”
Darwinian or neo Darwinian theory was for it’s day, however with the advances in our knowledge of cell machinery those ideas really don’t stand the test of experimental evidence.
I would like to add some further evidence to this thread to support the view that the current Darwinian theory is in serious trouble.
Support for the gradualism of the standard theory is definitely declining.
This is most obvious among developmental biologists who are promoting a “New Evolutionary Synthesis”. There is an online book on the National Center for Biotechnology Information website
You can read this new theory in Chapter 22 “New Evolutionary Synthesis”
Now it is often stated that the human genome contains about 25,000 genes. This actually represents, according to various estimates, from about 2-5% of the total genome. Most of the rest of these are regarded as junk DNA, leftovers from evolutionary process and the bulk of the standard neo Darwinian synthesis concentrates on these 25,000 or so called “coding genes”. These are the ones that code for protein and regarded by Dawkins, for example, as the fundamental unit of evolution, in his “selfish gene” hypothesis.
In the last few years we have learned that over 90% of our genome transcribes into RNA sequences at some development stage in cells and tissue. They form part of an incredibly complex regulatory system.
“The eukaryotic genome as an RNA machine” is the title of a recent paper that discusses this.
http://www.sciencemag.org/cgi/content/a ... /5871/1787
Most, if not close to all, of our chromosomal DNA consists of different types of genes that
have only recently been discovered.
The number in the human genome is now estimated to be 25000 protein coding plus an additional about 450,000+ RNA transcribed genes.
The vast majority of the genome therefore is transcribed, either into protein-coding genes or into regulatory RNA’s.
Some of these RNA gene range in length from only 20 or so genetic letters to millions
of letters long.
In 2004 Francis Collins co authored a paper entitled
“Genome sequence of the Brown Norway rat yields insights into mammalian evolution”
http://www.nature.com/nature/journal/v4 ... 6.html#a56
Have a look at some of the images in this paper, 2 of which are worth a close look (I haven't yet obtained permission to post images direct to this forum)
For ease of reference open the url in a new tab
http://www.nature.com/nature/journal/v4 ... 26_F9.html
Figure 9d of the paper shows the relative densities of SINE’s (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements).
Both these elements are types of mobile DNA known as Retrotransposons and together comprise about half of the mammalian genome.
Without worrying too much about the technical details just focus on the relative densities of these elements.
What we have here are the relative densities of LINEs and SINEs along 110,000,000 DNA letters of Rat chromosome 10 (From Fig. 9d of reference 1.)
The x-axis represents the sequence of letters in DNA and the blue line indicates where SINEs occur.
What is clear from the figure, LINEs (pink boxes) tend to peak in abundance where SINEs (blue boxes). taper off and vice versa There is therefore a compartmentalization of LINEs and SINEs in a kind of a bar code structure along the chromosome.
Now the paper then goes on to show the comparison between this density pattern on the Rat as compared with the Mouse chromosome.
Have a look at Fig 9c
The similarity of these two patterns is quite remarkable, as Francis Collins himself notes
“Despite the different fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar:” (my emphasis)
The problem this evidence poses for Darwinian theory is this.
According to the theory the Mouse and the Rat diverged from each other from the last common ancestor (LCA) i.e. they became separate species. This took place about 20 million years ago (perhaps 12-22 million years).
So a natural question is:-
How could two separate lineages with their separate histories of random mutations (the paper suggests over 300,000 mutations) produce two almost identical patterns.
300,000 random mutation events in the mouse have to somehow match the 300,000 random mutation events in the rat.
Is that a realistic scenario ?
The fact is that these density patterns are highly Non Random.
Incidentally the same pattern occurs in the human genome.
The other fact is that these elements accumulate around the protein coding genes and are clearly now being seen to have a regulatory function.
In the light of all this emerging evidence it comes as no surprise that development biologists are openly questioning the standard dogma.
There is a lot more evidence but this I am sure is sufficient for the moment.
This is something I've heard ID/Creationists say countless times.
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