Experimental evidence for evolution
May 19, 2010 at 3:37 pm #13339
I have been reading about evolution recently in an attempt to understand it.
My question is whether there have been any experiments conducted that provide empirical support for macroevolution. Has there been any experiments that show an organism changing to something different?
I read about the fossil record and the theory in general but my question is about experiments.
May 19, 2010 at 4:14 pm #99803
I don’t know experiments, but there are some observations of evolution in nature (e.g. seeds of plants in wild and city; some birds etc.)
May 19, 2010 at 4:26 pm #99804
Thanks for the reply jack.
Are these observations considered to provide empirical validation for macroevolution?
What birds + plants are you referring to?
May 20, 2010 at 7:47 am #99812
There have been thousands of experiments carried out to explore the process of biological evolution. Since it takes numerous generations to create a new species, or anything close, most of these experiments have been done on micro-organisms or such things as fruit flies. These are rapidly reproducing organisms that go through many generations in a short time.
For example, culturing bacteria on nutrient agar, and slowly removing an essential nutrient to see if evolution will equip the bacteria to be able to develop new enzyme systems to manufacture that nutrient. It does, if the change is across enough generations.
Numerous similar experiments have shown the way bacteria adapt to the presense of antibiotics, and develop ways to neutralise them.
Experiments on large animals and plants are less common, and focus on smaller levels of change. For example : published in the New Scientist magazine (15 May 2010 issue, page 12) is an experiment in the Caribbean on lizard evolutionary change. Whole islands were isolated by surrounding them with nets, to manipulate the level of predation and competition to see what influence was most important in driving evolutionary change.
Cichlid fishes (from lakes in Africa) have been observed and manipulated to observe the process of evolution. At least one new species has been followed over a 100 year period, and recoerded as developing into a new species.
May 20, 2010 at 4:24 pm #99822
I’ve read about the bacteria and the fruit flies in several articles, but as you said those are examples of minor changes (micro-evolution)
I am particularly interested in the cichlid fish example though. How did it change to signify that what we observed was macro-evolution? Do you have any additional information?
May 20, 2010 at 7:56 pm #99823
The cichlid example was written up a few years ago in Scientific American. Cichlids in the fresh water lakes of Africa are amazingly diverse. Genetic or geographic isolation appears to be the key, leading to rapid speciation. These fishes have been observed and described by naturalists for at least 100 years, and at least one population has been observed over that time to become isolated and then change sufficiently so that it will no longer breed with its original stock.
May 21, 2010 at 9:32 pm #99847
If you found, in Nature, chihuahuas and mastiffs and poodles and spaniels, would you classify them as different species? It is artificial selection, which drives specific traits to extremes quickly, but it is kind of "proof of concept" results.
May 31, 2010 at 4:28 pm #99983
Dog breeding is not really something I would consider evidence for macroevolution.
My question pertains mostly to any evidence showing something changing to something novel or something drastically different if you like.
Is there any study/evidence for this?
May 31, 2010 at 7:22 pm #99986SelfishGeneParticipant
Observed instances of speciation:
This experiment may also interest you, however it is not speciation:
http://en.wikipedia.org/wiki/E._coli_lo … experiment
May 31, 2010 at 8:01 pm #99990
June 17, 2010 at 11:32 pm #100205
The Long Term Evolution Experiment (LTEE) has been going on since 1988.
By way of some background, Evolutionists debate a lot about how evolution works. Stephen Jay Gould suggested that sometimes mutations happen that have no immediate benefit; but those mutations remain in the gene pool because they are not harmful. Those mutations are just floating in the gene pool waiting to be used. Then a subsequent mutation that depends upon those previous mutations can occur that causes some benefit to the organism. In other words, a new mutation might depend upon other mutations that happened in the past. Scientists call this, “historical contingency.” “Historical contingency” simply means, “it depends upon something that happened in the past.”
Gould’s opponents say that the environment drives evolution to a particular solution, so it doesn’t depend on past accidents. Furthermore, a mutation that has no immediate benefit will likely disappear from the gene pool before it is eventually needed
They started out with 12 individual, identical E. coli bacteria and put each one in its own little Petri dish; and they grew into 12 colonies.
E. coli bacteria reproduce asexually. In simple terms, the bacteria grow bigger and bigger until they get large enough to split in half, so the parent cell turns into two identical child cells.. Although the division process nearly always produces two identical children, sometimes the process partially fails, producing mutant offspring.
It takes nearly 2 hours for E. coli bacteria to reproduce, so there are about 6.5 generations born every day. This is convenient for scientists because it allows them to study lots of generations in a reasonable amount of time.
So, if you start out with 1 bacterium, you will have 2 in about 2 hours, then 4 two hours later, then 8 two hours after that, then 16, then 32, then 64, and finally 128 in just over a day. It is very convenient that the colony grows by a factor of roughly 100 every day.
They fed them glucose and citrate, and gave them 12.2 times more citrate than glucose. This was critical because E. coli can’t digest citrate.. E. coli would die on a steady diet of citrate.
The goal of the experiment was to try to force the E. coli to evolve in such a way that they could digest citrate, like some other bacteria can.
They did this by giving the bacteria just enough glucose to keep them alive, and an abundance of citrate. The expectation was that if the E. coli did evolve into a form that could digest citrate, that new variety would flourish in the citrate-rich environment and drive the old variation to extinction.
One important caveat is this.
If you read the fine print, you will discover that E. coli can ALMOST digest citrate.
It took more than 30,000 generations to fully evolve a capability that was already almost there, and it only happened in 1 out of 12 populations.
Thirty-thousand generations isn’t a long time for a bacterium, but 30,000 generations for people is about 600,000 years.
They really had to try hard using all the evolutionary pressure they could muster, to produce this minimal change.
However there was one unexpected result from this experiment.
QUOTE from the paperquote :
One of the fundamental ideas behind the theory of Darwinian evolution is extinction. Natural selection allows the group that is more fit for survival to drive the less fit ancestors to extinction.
In this experiment, the new variety did not drive the old variety to extinction.
Presumably that is because there was enough food for both varieties. Hasn’t there always been enough food for just one transitional form to survive, at least long enough to leave some fossils?
The primary thing we learn from this experiment is how difficult it is to cause even the smallest amount of evolution.
The LTEE showed that after 20 years of extreme, relentless pressure, it is possible for a minimal improvement in digestion to occur (after just 30,000 generations ).
How many generations it would take to develop a whole digestive tract from teeth to anus.?
The experiment is still continuing having reached about 50,000 generations with no additional results.
June 21, 2010 at 4:13 pm #100266
The Long Term Evolution Experiment (LTEE) has been going on since 1988.
Some more detail of terms of the experiment.
When I stated in my last post that E. coli can ALMOST digest citrate” this was deserving of a little more explaination.
E . coli already has a number of enzymes that normally use citrate and can digest it . However, it lacks an enzyme called a citrate permease which can transport citrate from outside the cell through the cell’s membrane into its interior. All that was needed therefore to use citrate, was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there.
Lenski put it this way “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.
The team have not been able to track down the mutation(s), however the point that the paper emphasizes is the historical contingency of the new capability. The evidence shows that in only one of the 12 population lines, and after some 20,000 generations a “potential” ( potentiating mutation) occurred that allowed at least a second mutation after 30,000 generations to give rise to the new citric capability.
So Richard Lenski is affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.
If the development of many of the features of the cell required multiple mutations during the course of evolution, as this continuing experiment suggests, then this is another reason why Darwinian theory does not provide the answers to cell development.
June 21, 2010 at 4:20 pm #100267quote jevg:
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?
June 21, 2010 at 4:25 pm #100268quote jevg:
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?"
June 22, 2010 at 9:58 pm #100288
Thanks for your comments.
My response is as followsquote :
As I am neither a creationist nor any other “ist” I’m afraid this comment of yours escapes me.quote :
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.quote :
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 belowquote :
I’m a little bit tied for time to respond to your other comments but will do so very shortly
June 23, 2010 at 2:11 am #100289kamyarParticipant
has anyone done a computer model/simulation of evolution?
June 23, 2010 at 2:53 am #100290quote jevg:
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.
June 23, 2010 at 2:25 pm #100295quote jevg:
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?
June 25, 2010 at 10:16 am #100313
Hi robsabbaquote :
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
June 25, 2010 at 3:43 pm #100318quote jevg:
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.quote :
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…
June 28, 2010 at 2:47 pm #100341
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.phpquote :
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.
July 3, 2010 at 5:36 pm #100396
A further response to canolan’s last postquote :
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.htmlquote :
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.quote :
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.
July 21, 2010 at 10:36 am #100625
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.
July 21, 2010 at 11:57 pm #100631TheSymphofBiologyParticipantquote jevg:
This is something I’ve heard ID/Creationists say countless times.
July 22, 2010 at 6:33 am #100637quote jevg:
what the hell is current Darwinian theory???
Anyway, the 300k random mutations are not those SINEs and LINEs, but those making the genomes different, as you might notice, if you wanted. I think, that the retrotransposones are using some kind of homology insertion, so it’s pretty much not so surprising. And even more, it’s highly understandable, that these elements won’t be inserted into protein-coding areas, because that would be lethal in many cases and thus such mutations are eliminated by natural selection. Pretty nice, isn’t it?
July 22, 2010 at 3:28 pm #100642quote :
Hmm.. I thought I had made this clear in my précis in a previous post on this thread, however for the sake of clarity let me repeat.
“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.”
If you don’t find either mine or Simon Conway Morris’s précis sufficient, how about the description of the current ideas on evolution referred to as the Modern Synthesis, presented by Futuyma
"The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection; that most adaptive genetic variants have individually slight phenotypic effects so that phenotypic changes are gradual (although some alleles with discrete effects may be advantageous, as in certain color polymorphisms); that diversification comes about by speciation, which normally entails the gradual evolution of reproductive isolation among populations; and that these processes, continued for sufficiently long, give rise to changes of such great magnitude as to warrant the designation of higher taxonomic levels (genera, families, and so forth)."
– Futuyma, D.J. in Evolutionary Biology, Sinauer Associates, 1986; p.12
So as far as description goes, can we agree to be on the same page
I can then continue
July 22, 2010 at 6:31 pm #100646
you wrote about "current Darwinian theory", not about evolutionary theory…
July 23, 2010 at 2:14 pm #100657
So are we on the same page as to what theory is being discussed?
The current Darwinian theory that I am referring to is that which I qualified previously and for the sake of removing any misunderstanding I deferred to the Futuyma description.
Is it in order for me to respond to your comments now?
July 23, 2010 at 5:58 pm #100659TheSymphofBiologyParticipant
jevg, I think you misunderstood Jack. None of us know what the hell you’re referring to when you say "current Darwinian theory." There’s no such thing as "Darwinian theory."
July 23, 2010 at 7:35 pm #100660
You’re right there is no theory named as “Current Darwinian theory” anymore than there is an “evolutionary theory” as such.
There are different evolutionary theories around.
The standard theory known as the Modern Synthesis or Neo Darwinian Synthesis is the one I have referred to as the current Darwinian theory as described by among others Futuyma. I had thought I made that clear, but obviously not 🙂
Punctuated Equilibrium – not based on the gradualism of the Darwinian explanation
http://www.pbs.org/wgbh/evolution/libra … 35_01.html
Evo Devo – again not based on the gradualism of Darwinian explanation
And now the Post Modern Synthesis – You will find it here
The Modern/Neo Darwinian Synthesis is the current standard theory and the one I assume that you Jack and others refer to as evolutionary theory.
I hope this clears matters up
July 25, 2010 at 10:17 am #100673quote :
Interesting though your private hypothesis is, you are factually wrong when you say that the “300k random mutations are not those SINEs and LINEs”
Please read the paper carefully. In particular may I refer you to the section
Co-Localization of SINEs in Rat and Mouse
The very first sentence of that section reads :-
“Despite the different fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar: 300,000 copies.”
Gains and losses of DNA :- reads
“In addition to large rearrangements and segmental duplications, genome architecture is strongly influenced by insertion and deletion events that add and remove DNA over evolutionary time.”
The fact is that SINEs being retrotransposons are mutagens, their insertion/deletions are mutational events and by their very nature are therefore Random events.
Now please try to understand the section
Co-Localization of SINEs in Rat and Mouse
Francis Collins calculated there were some 300,000 mutational insertion/deletions in both the Rat and Mouse lineages.
What he found remarkable was that the resulting density patterns of each separate lineage
after all their individual histories were almost carbon copies of each other.
Now why, did he find the density patterns remarkable?
Because he looks at the data through the prism of the “Modern/ Neo Darwinian Synthesis” 🙂
According to that theory the Rat and Mouse had a Common ancestor and they diverged from that ancestor some 12-22 million years ago, forming the two separate species.
Since there was now two separate lineages with their own histories of mutational impacts over millions of years on their genomes, and again according to the theory, these mutational impacts were random and undirected, how is it that the data shows, not only were the density patterns highly Non Random but also, the individual patterns were almost exact copies of each other.
The other observation he noted was that the same patterns exist in the equivalent Alu (which are SINES) densities of the human genome. This pattern also exists in other mammalian genomes.
That is why he refers to the patterns as being remarkable.
Now it only requires a modicum of schoolboy logic to conclude that either the data is wrong or the prism through which that data is be interpreted is faulty.
Since some three hundred scientists have been involved in the project and they are satisfied with the veracity of the data, my conclusion is that the theory is wrong.
It is not wrong just at the peripheral edges, but right at its very heart.
Remember according to the theory.
Random undirected mutations in the genomes are what Natural Selection filters.
Now there is more that this study reveals but I think that is enough to be getting on with.
August 30, 2010 at 4:23 pm #101080
May I return to the Lenski experiment just to nail down this data on Non randomness.
http://myxo.css.msu.edu/lenski/pdf/2008 … t%20al.pdf
Please refer to the “Discussion and Future directions” of this paper (page6) and note the replays of the experiments from archived generations that are referred to.
Adaptations by mutations under stress are a well known phenomenon. If such adaptations are the result of totally random mutations as the theory teaches, then each resultant population must be different. However, repeating the final stages of this experiment on samples preserved from earlier generations of the original population, before it developed the citrate-feeding capability, resulted in identical citrate-feeding populations, all of which emerged after the same total number of generations.
How could the random mutations of each replay produce the same result. The answer is obvious. Those mutations were not random but highly Non Random.
This fact is also borne out by Raymond Huey et al. at the University of Washington in Seattle. They discovered that populations of fruit flies on three separate continents have independently evolved identical gene changes within just two decades (that’s 20 years, not 20 million years), apparently to cope with global warming.
http://www.newscientist.com/article/dn9 … rming.html
The fact that identical genetic changes as in Darwin’s finches were duplicated within a short time; the fact that the genetic changes in the fruit flies on three separate continents were identical; and the fact that many samples of early generations of E. coli produced the same adaptations and identical populations, prove that:
These genetic changes are not the result of random mutations. (If they were random, the results would not have been identical.)Therefore the ability to adapt must be pre-programmed into the genetic codes
September 1, 2010 at 1:08 am #101100
The mutations can still be random (I expect a tendency / predilection toward a particular TYPE of mutation – the inversions mentioned – might be involved, though), but selection can stabilize the same useful mutation when it appears in different populations dealing with the same environmental shift.
September 1, 2010 at 8:53 pm #101112
I find it difficult to follow your line of reasoning.
If something is random it is by nature unpredictable. There cannot be a “tendency / predilection toward anything if it is random. If there was this tendency then it is not random.
What is the difference between the expression you use and say, “random pattern or random order or random logic”?
I appreciate we all use oxymorons in everyday language. (One of my favourites in this economic climate is the term “rising deficits”). However to use an oxymoron to define data is not scientific.
Non-randomness explains the data quite easily does it not?
Why therefore is this not acceptable?
September 1, 2010 at 10:48 pm #101115
True randomness as a mathematical abstraction and life do not completely intersects. Mutation can be generated randomly but some things might directly impact the visible outcome:
– the mechanisms generating the mutations might act randomly but not be able to generate all type of mutations. For example DNA repair mechanisms can insert mutations, but will be constrained by the repair they make (ie replacing G oxidized to 8oxoG by T (IIRC), the location of the oxidation will still be random, the outcome will not)
– Some mutations will immediately be lethal, so you will never see them in the experiments, but because Lenski’s experiment deals with millions of bacteria, the death toll will not be visible in terms of growth rate
– Some mutations will provide an immediate and sensible advantage to the mutant, and will have a greater chance to be fixed quickly, and so appear to be more frequent than other mutations.
– Some physical characteristics of the DNA (frequency of translation and of replication, interaction with other proteins, physical location in the cell and accessibility to external mutagens…) might make some part of the genome more or less likely to see a mutation appear so the chance of mutations appearing in a given section of the genome are not equally distributed.
– And some path in the evolutionary landscape might be more likely and so appear favored (while not necessarily being the more efficient).
So my point is that the appearance of non randomness can be created by the accumulation of random events and that this appearance cannot be taken as a proof of design. The flow of water out of a tap is created by the mostly movements of billions of individual water (and other salts) molecules. The path of any individual molecule cannot be predicted with certainty. And yet the general movement can be accurately predicted and modeled.
September 2, 2010 at 12:33 pm #101126
May I correct you, randomness is not a mathematical abstraction.
If a sequence is unpredictable, we call it "random". Stated another way, outcomes which lack discernible patterns are said to be "random".
We don’t define randomness by what it is, but by what it isn’t. Of course an apparently "random" sequence may have an underlying order that we just haven’t yet understood.
The problem is, we are not finding apparently random sequences, the data is revealing, as you acknowledge, apparently non-random appearances.
If they are random as you seem to wish to assert then the onus must be on you to show how it is so.
With respect all you have done is to provide another hypothesis to support the first one of randomness. This is not evidence.quote :
Occam’s razor is a logical principal, it states that one should not make more assumptions than the minimum needed. It underpins all scientific modelling and theory. It admonishes us to choose from a set of otherwise equivalent models of a given phenomenon, the simplest one.
In any given model, Occam’s razor helps us to "shave off" those concepts, variables or constructs that are not really needed to explain the phenomenon. By doing that, developing the model will become much easier, and there is less chance of introducing inconsistencies, ambiguities and redundancies.
I am not providing proof of design.
I have been providing data that shows the non-random sequences that falsify the Darwinian concept of randomness. An essential requisite of any scientific theory is that it must be falsifiable.
So may I raise the question again
Non-randomness does explain the data quite easily, does it not?
Why therefore is this not acceptable?
September 2, 2010 at 3:54 pm #101132quote jevg:
I am not rapeseed 😉 although I guess you could probably get quite some oil if you were to press me… More seriously:quote jevg:
You are right, I only provided hypothesis to explain how apparent order could emerge from randomness. And I did not elaborate because I do not ave either the space or even the competences to do that here. However there are quite a few patterns by better than me that have demonstrated that simple conditions and randomness can lead to apparent order.
I could refer you to all the chaos theory, or more appropriately to Conway’s game of life.
So taking randomness in generation as a null hypothesis is far from being unreasonable. You are of course free to refute that, but in that case you have to at least offer an underlying explanation to the non-randomness. "It converges, so it cannot be random" is not enough. See that ties very nicely with the second part of the argument:quote jevg:
Non-randomness might explain the data quite easily, but it is not enough. If you want to argue non-randomness you have to provide an explanation or a source or something that direct this order. That would falsify the theory that mutation are randomly generated.
On the other hand, there are quite a lot of models that use random events to generate apparent order by using plausible and/or simple laws. So the simplicity of the model might be very relative, but you have to compare that to the implicit pre-requisites of non randomness and then use the razor adequately.
September 3, 2010 at 10:44 pm #101140
My sincere apologies, thank you for being so light hearted about it. I promise I will try not to press too hard. 🙂quote :
This is where a lot of confusion enters. May I explain
Chaos theory deals with the spontaneously forming of forms and order. All we have to do to observe spontaneous self-ordering is to pull the plug out of our bathtub drain (the flow of water as you have illustrated). Water molecules quickly self-order into a swirl (a vortex) from purely albeit complex physico-dynamic causes. This is mistakenly called self-organization. The vortex is not organized. It is only self-ordered. Now what is the difference?
No decision nodes are required for a bathtub swirl, or a candle flame to self-order out of a seemingly random Brownian movement. Proficient programming choices are not required for the heat agitation of water molecules to self-order into a vortex. No configurable switches have to be purposefully set, each in a certain way, to achieve self-ordering. No pursuit of a goal is involved. No algorithmic optimization is required.
This is totally different to the utility in functional Genetic Algorithms that contain all the above features. Cellular behavior cannot be accounted for in simply physical/chemical processes.
Sadly, for those of us who have not studied chaos or complexity theory in any depth, are fed with some rather sloppy definitions by those who should know better. Clear definitions in any scientific endeavor are an essential pre requisite to good communication.
All too often these or equivalent expressions “self ordering and self organization” are used synonymously, with all the resulting confusion.
I fully endorse that randomness, as a null hypothesis, is a perfectly reasonable and scientific position to take.
Darwin certainly put this whole subject on to a solid scientific footing and of course it was the null hypothesis for his day. Science has often progressed through the formulation of null hypotheses. Falsification though allows for the elimination of plausible hypotheses.
It is here where I disagree with your commentquote :
First just to be clear, I am not and have not stated that mutations are not randomly generated.
Mutations are randomly generated from different sources both internal and external.
What I am arguing is that these random mutations do not account for, or indeed are, the source of the functional utility that is observed in cellular processes and I have provided evidence to that effect.
I know of nothing in the scientific method that requires a theory can only be falsified if another was put in place, or that the source of any function must be known or explained in order for a theory to be validated, which if I understand correctly, you are suggesting.
You appear to be trying to shift the goalposts in this regard. However I would caution against that, because if what you say, is to be regarded as a criteria for a theory to be scientifically acceptable then you had better start re-evaluating, for instance, the theory of gravity.
Here is a theory of a force, who source we do not know, it violates the most fundamental law in physics, the law of conservation of energy, there is no explanation except that there is a manifestation that can be measured, and yet it is accepted, quite rightly, as a scientific theory.
(trust me I do know what I am talking about here, and would be happy to explain, but perhaps on another thread)
Alan Guth’s inflation theory, a fundamental part of the so called Big Bang theory, has no identifiable source or even explanation and yet it is regarded as a valid scientific theory and in many quarters as a fact.
So methinks it would be safer to put the goalposts back. 🙂
What I am trying to say is this non-randomness cannot be addressed by any law that we are aware of, or if it is even possible to have such a biological law.
Of course I could say that it is the Flying Spaghetti Monster wot did it.:)
The creationists would regard me as some manifestation from hell.
The Idists would not even touch me with a bargepole and you would probably pat me on the head, give me a lump of sugar and let me dribble away in a corner, while sending for the men in white coats. 🙂
There is though a serious point behind this little piece of nonsense.
If the evidence repeatedly shows any theory to be wrong, then still sticking to it would only echo the words of what Darwins brother Erasmus is reported to have said just before Darwin released his publication Origin of species.
"In fact the a priori reasoning is so entirely satisfactory to me that if the facts won’t fit in, why so much the worse for the facts."
Science is the victim when scientists ignore evidence in favour of some philosophical bias
September 3, 2010 at 11:18 pm #101141
My understanding of the driver behind evolution is change in the environment. This could be changes in predators of a species, prey or the species itself, and of course the habitat, weather conditions etc. In fact I could be here as long as the Lensky experiment listing all the possible drivers for evolutionary change.
As I understand it Darwin believed this too.
Does that make Darwin a gradualist or a punctured wotsitface?
In my book it makes him neither as well as both. He certainly believed in single step mutation which can redily explain the terms which were hijacked by a few scientists who wanted some publicity. Forgive my apparent insincerity above but it is wearisome reading people trying to stir up a controversy that doesn’t really exist.
September 3, 2010 at 11:44 pm #101142
Could those of you who say "Darwin was a Gradualist not a Punctualist" explain what he meant when he said this:
"the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form".
September 4, 2010 at 1:15 am #101143quote jevg:
I read a lot of what you say, and have even followed some of the links you posted but I have to say I don’t agree with many of your claims (such as the "Darwin was a gradualist not a punctuated equilibriumist…")
So can you AS CONCISELY AS POSSIBLE point out where you have provided evidence to support your claim above. If you think you have lots of sources, please just provide what you believe to be your most convincing ONE and we can discuss it’s merits.
September 4, 2010 at 12:59 pm #101145quote jevg:
Absolutely, so how do you explain ignoring the approx 3.5 million single step genetic mutations that lead to benefitial improvements in the Lenski experiment up to the 20,000th generation.
Also how do you explain ignoring the fact that the Lenski experiment showed the historic contingency could not be reproduced before the 20,000th generation.
Seems to me you have a philisophical bias of your own that you’re trying to convince yourself of.
September 4, 2010 at 1:52 pm #101149
Can you say in ONE sentence, WHAT is your point? Because you’re writing such long posts, I’m all tired about reading that (and apparently I’m not the only one) and it actually seems, that you agree with canalon…
September 5, 2010 at 8:54 pm #101168quote :
Darwin saw change not in terms of years but in terms of small modifications that gradually changed species. That is what your quote means.
There is no controversy that Darwin believed that evolution was driven by random mutations that gradually accumulated producing species change.
Just about every biologist I am aware of understands that, including ones on this forum. eg
by canalon » Fri Jun 25, 2010 3:43 pm (post no 20 I believe) 2nd page
…. I do not think that Darwin was anything but gradualist.
So there is no reason for you to become wearisome.
Perhaps before I respond to your other comments, this little bit of confusion can be cleared up.
September 5, 2010 at 8:58 pm #101169
My point in this regard is simply this.
Random mutations do not cause one species to change into another.
I don’t know what canalon believes so I don’t know if we are in agreement.
September 6, 2010 at 12:01 am #101170quote jevg:
It seems you missunderstood so I’ll quote Darwin again and this time add some emphasis for you:quote :
If you read the bits underlined as if one sentence, and ignore the "though long as measure in years", you will realise that Darwin was saying that species go through short periods of modification and long periods of stability.
The point is that gradualist is not mutually exclusive to punctuated equilibrium, in fact punctuated equilibrium embodies gradualism. However some advocates of punctuated equilibrium can also allow for other methods that drive change such as saltation, which is mutually exclusive to gradualist.
Also I’ll quote Stephen J Gould for youquote :
Read those two quotes by Gould and Darwin again and compare how similar they are.quote jevg:
Oh yes I know that one, wikipedia can be such an easy reference sometimes:quote :
Seems I’m getting closer to where your coming from now.
How about we rephrase your quote above and substitute "evolutionary scientists" for "Scientific creationists"?quote jevg:
But hold on.. the quotes from Gould and Darwin above.. and the other one from origin of species, you know, that famous one about the molluscs.quote :
So how is it you think that Darwin’s Gradualism is mutually exclusive with Gould’s Punctuated Equilibrium.quote wikipedia:
See there’s what you did, you confused Darwin’s Gradualism with Phyletic Gradualism. Don’t worry it happens all the time.quote jevg:
Canlon is indeed correct, Darwin was a gradualist, but as you can see from Darwins own words above, he was also a punctured equilibriumist, however he did not believe in Saltationism or Phyletic Gradualism.quote jevg:
Darwin believed this too.quote jevg:
Who are these opponents of Gould who say this? I know of many evolutionary scientists who believe natural selection drives out "bad" mutations and that a mutation that has no immediate benefit will likely disappear, but not always disappear, such scientists aren’t opponents of Gould. In fact most evolutionary scientists understand that many benefitial mutations will likely disappear too, just not as likely as a neutral mutation.quote jevg:
Lets hope so, I can’t wait to move on to this bit:quote jevg:
September 6, 2010 at 4:35 pm #101176
Origin of species – Chapter 6 Difficulties on Theory
http://embryology.med.unsw.edu.au/pdf/O … pecies.pdf
Darwin argues some of the difficulties experienced by his hypothesis. In this case the lack of transition fossils.
“These difficulties and objections may be classed under the following heads:-Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?…”
“Insensibly fine gradations” Does that sound like punctuated equilibrium or gradualism?
Chapter 4 (Natural selection)
“Natural selection will modify the structure of the young in relation to the parent, and of the parent in relation to the young. In social animals it will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change…”
Does this sound like he was advocating punctuated equilibrium?
Chapter 9 On the Imperfection of the Geological Record
“Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.”
If Darwin was advocating punctuated equilibrium why would he argue on the “extreme imperfection of the geological record”.
Gould and Eldridge argue that it is the geological record that supports their hypothesis.
Oh and by the way I don’t use wikipedia so please don’t attribute sources to me that I don’t use. Now when I use the expression “evolutionary scientists” I mean precisely that. You know ones like Gould,EldridgeShapiro,Dawkins,Coyne,Orr,Fordyke, Collins, Lenski etc. I could of course go on.
What I don’t use is the expression “Scientific creationists" so you see you would be no good as a spokesman for me. 🙂quote :
Well if you read Lenski’s own paper you need go no further than read the first three paragraphs after the Abstract to have your question answered.
Now as far as the evidence I have provided this forum with,may I will refer you to the following.
This particular thread from post 11 Thu Jun 17, 2010 11:32 pm
Also about17587-12.html from post 16 on Tue Aug 17, 2010 4:25 pm
Also about18849.html from post 6 Fri Jul 02, 2010 12:42 pm
Also about19377.html from post 4Mon Aug 30, 2010 6:47 pm
Happy reading 🙂
September 6, 2010 at 8:09 pm #101177quote jevg:
It sounds like what it is, insensibly fine gradations, i.e. small changes from one generation to the next. Which as I have pointed out previously is incorporated into punctuated equilibrium, or do you disagree?
In other words do you believe that punctuated equilibrium is mutually exclusive to gradualism? In fact I don’t need to ask this because you have already said as much but I’m asking anyway. So question for you:
Q. Do you believe that Puntured Equilibrium is mutually exclusive to Gradualism?quote jevg:
This paragraph was a set up for the next line which you so skillfully missed out so I’ve added it, and then if you read all together I’m sure you will agree (actually you probably won’t) that Darwin was really emphasizing that species do not adapt for the benefit of other species as was being argued by some people at the time ie the reason bees exist is to benefit flowers.quote :
This then begs a further question:
Q Do you believe that natural selection does not modify the structure of the young in relation to the parent, and of the parent in relation to the young?quote jevg:
Hold on, are you saying that because Darwin observed that the fossil record is extremely imperfect that he is not a punctured equilibriumist? Well there’s the next question then:
Q. Do you believe that the fossil record is extremely imperfect?quote jevg:
I wouldn’t and I didn’t, I was in fact pointing out where I had used wikipedia.quote jevg:
I’m not trying to be your spokesman, just trying to uncover your true philosphophical viewpoint.quote jevg:
I had done and I couldn’t find anybody who saidquote jevg:
but I could find the following:quote :
I think the translation of Morris and others towards the Lenski experiment is this:
Run the experiment long enough and a new species of bacteria will eventually start using Citrate.
Anyway while were on the subject of Lenski, could we clear up a few more of your errors?quote jevg:
Actually they didn’t feed them Citrate, the glucose was there as the sole source of carbon and energy.quote jevg:
No that was not the goal of the experiment at all. You really haven’t actually read Lenski have you? What you have been reading is someone elses version of it. Either that or your making your own interpretation up. I hope it’s the former.quote jevg:
There you go again, making stuff up. The appearance of the Citrate using bacteria was a complete surprise to Lenski’s team. They weren’t trying to breed a citrate using bacteria, but once it happened they went back and re-ran the experiments. Here’s what they found (you would know this if you actually followed the experiments and understood them);
- The neutral mutation (which allowed for a historical contingency) came about around 20,000 generations (ok I acknowledge you’ve spotted this).
The neutral mutation has to fix itself within the population, after this the next (random single step mutation) when it happened did so within 750-3700 generations.
What !?! I don’t like accusing people of blatantly lying so I’ll say this to you Jevg, you have been badly misinformed.
- The neutral mutation (which allowed for a historical contingency) came about around 20,000 generations (ok I acknowledge you’ve spotted this).
September 6, 2010 at 9:01 pm #101178
I apologise to the OP and readers in general for appearing to hijack this thread. It’s a fine line one takes when trying to put right a wrong. Does it help or hinder the audience? I don’t know, but I don’t want to take any chances. I’d suggest if Jevg wants to carry this on we "take it outside" (to another thread).
Maybe the subject could be "handbags at ten paces" or something similarly ludicrous.
September 7, 2010 at 10:22 am #101181
This discussion is sadly beginning to degenerate to the level of insults and that is regrettable. I am clearly causing you some distress and I have no wish to do that.
This thread was initiated by a simple question.quote :
Now what I and others have done is to try and answer that question. I have provided details of the LTEE experiment that is demonstrating how difficult it is for random events to effect even a small change in function. I have also directed attention to the Francis Collins paper calling in the research of some 300 or so scientists.
I have argued that this body of accumulating evidence supports my understanding that Random mutations whether gradual or punctuated does not lead to speciation. (commonly referred to as Macroevolution)
I have also argued that the evidence from Francis Collins raises serious doubts about the theory of common decent. (Another fundamental pillar of Darwinian theory classical or modern.)
I was about to move on to the question of natural selection and what part evidence is showing it plays in evolution. Your intervention has interrupted that, however I may be given the opportunity to put that as additional evidence to this original question.
Now you may wish to get into an argument over the finer points of a theory that in my opinion is being rapidly eroded by evidence. I have no desire to try and rearrange the tables on a sinking ship.
It should therefore come as no surprise to you, that I have no wish to trade handbags. 🙂
September 7, 2010 at 6:04 pm #101183
Macroevolution is just lots of microevolution.
September 8, 2010 at 8:48 pm #101198quote jevg:
If you feel insulted in any way I sincerely apologise, it was not my intention. Let me take the opportunity to say that personally I don’t feel in any way insulted by any of the comments you have made.quote jevg:
Thanks for your concern, however let me reassure you, your views cause me no concern whatsoever. They are your views and clearly you are entitled to hold them and express them. If my views differ, I too have taken the same opportunity.
Feel free to answer the 3 questions I posed to you, and address any points I raised in that post in any thread you choose….quote jevg:
… I would be particularly interested in your views on the points I made about your inaccurate references of the LTEE experiment.quote jevg:
Collins is an authority in his field, I note that when he was appointed to the Pontifract Academy of Sciences by the Pope it raised a few eyebrows particularly because he supports stem cell research. He is also open about his religious views for which he receives criticism from fellow scientists. This is unfair in my view because at least he’s being open about it. I mean, if someone is an atheist they don’t get criticised from fellow scientists.
I shall have to get hold of a copy of his book, according to USA today…quote :quote jevg:
…hopefully the rest of the forum will forgive my insolence and the delaying of the inevitable.
September 9, 2010 at 3:28 pm #101214
Thank you for your comments.
As we can now concentrate with questions that deal directly with the question in this thread, I will be very happy to deal with your questions and indeed any others. I have not ignored responding to serious and rational questions in the past and will respond as required in future.
I will however ask for a little patience at the moment as I am going to be away from my computer for about 36 hours or so. I will therefore respond sometime tomorrow evening UK time.
September 10, 2010 at 9:18 pm #101229
I will try to deal with the issues you raised that are connected to this experiment.
The LTEE experiment is named
Historical Contingency and Evolution of key innovation in an experimental population of Escherichia coli.
I introduced this paper to the forum in my very first post with the appropriate link for all to check against. To suggest that I have not read it and merely relied on someone else’s explanation I find somewhat curious.
To save any further confusion here it is again.
First sentence reads
“The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue.”
The purpose of the experiment therefore was to determine the validity of the hypothesis of “Historical Contingency”
(Page 1 para 4)
“They have since been propagated by daily 1:100 serial transfer in DM25, a minimal medium containing 25 mg/liter glucose as the limiting resource (2, 22).”
Under Materials and Methods (Page 7)
“The twelve populations have been propagated for almost 20 years by daily serial dilution in DM25, a minimal salts medium that has 139_Mglucose and 1,700_Mcitrate (2).”
“The various DMmedia used to grow cells in different experiments are all based on the same formulation as the DM25 used in the LTEE (1), with only glucose concentration varied. DM25 contains glucose at 25 mg/liter. DM500, DM1000, and DM2000 have 20, 40, and 80 times, respectively, more glucose than DM25, whereas DM0 contains no glucose.”
“Throughout the duration of the LTEE, there has existed an ecological opportunity in the form of an abundant, but unused, resource. DM25 medium contains not only glucose, but also citrate at a high concentration.” (page 2 para1)
Was the concentration of glucose deliberately chosen? — Yes
Why? — To provide selection pressure.(an ecological opportunity)
Are there variants of E coli that have the ability to utilize citrate?
Yes, they have been detected in the wild. Ref 44 and 45 in the paper provides the sources. It is found in pigeons, pigs, cattle and horses.
“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.” (page 2 para2)
Did the evolution of Cit+ come as a surprise? (as you have suggested)
“The long-delayed and unique evolution of the Cit+phenotype might indicate that it required some unusually rare mutation……” (page 2 para 4)
If an event is long delayed, it suggests to me that the event was anticipated or at least hoped for. Why you feel they were surprised is beyond me, especially when the ability of E.coli to use citrate already exists in other variants.
The experiment was designed to test the validity of Historical Contingency.
The populations were propagated (fed) in DM25 (a mixture of glucose and citrate) the ratio deliberately chosen for this experiment to provide selection pressure.
After 31500 generations the long delayed evolution of Cit+ arrived in one of the 12 populations. That is after a total of about 360,000 generations of “random mutations.”
It is now up to around 500,000 generations.
Remember this “new” trait only involved gaining the ability to transport the citrate through the cell wall. The ability to digest the citrate was already there.
It is with good reason that Lenski states:- (page 2 para3)
“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.”
It is also with good reason I posted the rather cryptic question.
How many generations would it take to develop a whole digestive tract from teeth to anus.? ( Let alone the whole organism)
The question is not whether evolution is a fact or not. It is a fact.
The question is.
Does evolution progress to the point of producing new species and is the driving force “random mutations”? Remember the mutations have to occur before natural selection can begin to operate.
After some now, 50,000 generations has a new species arrived?
Quite clearly no. It is still E.coli.
In summary this experiment has revealed that
1. Bacteria become fitter and get larger/
2. Most of the gain is in the first 2000 generations
3. Most of the gain comes from five different genes that have mutated.
4. After 20,000 generations, his group sequenced 918,700 bases from 50 isolates- they found 10 changes, all in ones with a “mutator” phenotype.
“It is clearly very difficult for E. coli to evolve this function. In fact, the mutation rate of the
ancestral strain from Cit- to Cit+ is immeasurably low; even the upper bound is 3.6 _ 10_13 per cell generation, which is three orders of magnitude below the typical base pair mutation rate.” (page 6 para. 2)
In English “immeasurably low” means – incapable of being measured.
“Nevertheless, one population eventually evolved the Cit+ function, whereas all of the others remain Cit_ after more than 40,000 generations. We demonstrated that the evolution of this new function was contingent on the history of the population in which it arose. ”
To establish their contention that historical contingency was the cause of the evolution they ran three replay experiments from the potentiated clones.
“Statistical Analysis of the Replay Experiments.
All three experiments show the same tendency for Cit+ variants to evolve more often from clones sampled in later than earlier generations of population Ara-3 “
I did unintentionally overstate the replay experiments results as described above when I stated that the replays “resulted in identical citrate-feeding populations, all of which emerged after the same total number of generations.”
Let me conclude with the question Lenski poses.
“Will the Cit_ and Cit+ lineages eventually become distinct species?
According to the biological species concept widely used for animals and plants, species are recognized by reproductive continuity within species and reproductive barriers leading to
genetic isolation between species (67) Although the bacteria in the LTEE are strictly asexual, we can nonetheless imagine testing this criterion by producing recombinant genotypes.….”
Why is the question left hanging?
Because the evidence simply is not there.
So you question me when you state
“so how do you explain ignoring the approx 3.5 million single step genetic mutations that lead to benefitial improvements in the Lenski experiment up to the 20,000th generation.”
I am not able to explain your assertion because I am unaware of the evidence you seem confident you have.
My question therefore is
What is the evidence you call on to support that statement? ( forget the 20,000 bit)
September 11, 2010 at 2:39 am #101233quote jevg:
When I asserted that "You really haven’t actually read Lenski have you? " you must forgive my generality. I was not suggesting that you hadn’t read that particular paper that you were citing. I was inferring that you hadn’t read any of the Lenski’s papers in which he outlined his reasons for the experiment and the way the experiment was carried out. I believe that if you had read any of these papers, understood them and didn’t doubt Lenski’s credentials then you wouldn’t have said the followingquote jevg:
Those statements are misleading. In many papers Lenski has outlined his goals for the experiment; providing data on historical contingency and establishing his own fossil record were two of his main goals but nowhere does he state his intention to force E coli to evolve Citrate digestion. As I have already pointed out, and again this comes from Lenski himself, they provided glucose as the sole source of carbon and energy.
People can look at your words and judge for themselves why you make such statements about the Lenski experiment. I personally try to see the best in people which is why I suggested that you had been seriously misled. If you wish to understand the LTEE more I suggest you visit their own website. There is a huge amount of data, if you are seriously interested in the experiment then you will be rewarded for your time and effort with a greater understanding of historical contingency and the benefits of having a more complete fossil record.
For your info the website is:quote jevg:
I know I open myself to the accusation of being lazy when I say this, but again I prefer to read what Lesnki says, and take his word for it when he states that when citrate using E coli evolved it came as a surprise. Again, you can infer what you wish if it suits your purpose but coupled with the fact that he never stated breeding citrate using E Coli as one of his goals and stating that it was a surprise to him and his team when it happened, I’m happy to say your statement is misleading.quote jevg:
I’d go even further than that and say not only do they have to occur but also they have to take hold in the population before natural selection can do it’s thing.quote jevg:
Not according to Lensky et al;
"Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial"
Genome evolution and adaptation in a long-term experiment with Escherichia coli
Jeffrey E. Barrick1,7, Dong Su Yu2,3,7, Sung Ho Yoon2, Haeyoung Jeong2, Tae Kwang Oh2,4, Dominique Schneider5, Richard E. Lenski1 & Jihyun F. Kim2,6
Glad to hear it, hopefully you will acknowledge the same regard towards your other misleading comments on the LTEE regarding their goals and use of Citrate. How you interpret the results of the data is your own business but I hope you agree you haven’t represented the LTEE correctly in your assertions of their running of the experiment.quote Jevg:
The way I read it Lenski is posing a possible hypothesisc for future testing, I don’t think anyone is arguing that the evidence is there. It obviously isn’t until experiments can be run to test it.quote jevg:
I looked at the data back when the 20,000th generation was new and since then we have now passed 50,000 generations. Zachary Blount is responsible for co-ordinating testing to establish benefitial single genetic mutations, last I knew he had personally tested 40 trillion e coli cells, then there are others either in the LTEE team or in labs around the world who support their work.
The data to support my statement is contained in the research published on the LTEE website and in fact is more likely to be even greater than this number now which is why I added "approx", in hindsight I should probably have chosen "at least".
The following papers are those that I know cover benefitial single genetic mutations: 122, 140, 155, 166, and 178
What the LTEE has shown is that there have been at least 3.5m instances of e coli cells mutating in a single gene and this mutation leading to improved fitness.
September 13, 2010 at 10:40 am #101258
So apart from the rhetoric on the periphery of this question
We are agreed, random mutations and natural selection can make an organism fitter and larger (bacteria in this case) and more adaptive in an existing environment that in more general parlance is referred to as micro evolution.
So lets return to the question that initiated this thread.quote :
Can we also agree then that this 22 year long experiment by Lenski (which as I have stated before is what good science is all about and whose website I have been following for some time now) has not produced evidence that supports a hypothesis that new species emerge as a result of this “Darwinian mechanism”.
The term the macro-evolution is used in the question and again is general parlance for speciation.
In other words there is no empirical evidence that provides support for a continuum between micro-evolution and macro-evolution.
September 13, 2010 at 12:45 pm #101259quote jevg:
Absolutely agreed, I only wish you had said this at the beginning. I would be pretty certain that if an experiment could be conceived that would breed a new species in an extremely short amount of time (and I mean that in the same sense that Gould and Darwin both used it) it would receive both praise and criticism in equal measure. It would certainly be headline news.
As it stands all we have to satisfy ourselves are clues such as the existence of ring species, an extremely incomplete fossil record and multiple experiments to push the boundaries of micro evolution.
What we have is a smoking gun, some empty bullet cases, lots of blood but unfortunately no body. Again thats just my view of it.
September 15, 2010 at 9:05 pm #101283
This is what I wrote on June 25 Page 2 of this thread.quote :
Anyhow at least there is some measure of agreement now.
I did say I would go on to the question of natural selection but that will have to wait till the
weekend as I am rather busy with other matters till then.
September 16, 2010 at 12:23 am #101288
You said a heck of a lot more than that. Bygones I suppose.
I’m actually looking forward to seeing how you tie up historic contingency and non randomness, which is I think where your heading?quote :
I’d say this is different enough from the OP’s question to be in it’s own thread by now. Otherwise your going to find people discussing the OP popping up in the middle of some discussions over what you postulate.
September 21, 2010 at 4:48 pm #101395
Apologies for the delay. I was away longer than anticipated.
The experimental evidence to date does not show random mutation/variation as a driving mechanism that leads to the formation new species. That is now fairly clear.
What variation that does occur does so within species.
The Darwinian hypothesis majors on (environmental) Natural selection as being the main driving mechanism causing speciation.
The question therefore is whether this fundamental pillar of the hypothesis is borne out in experimental evidence.
A 30 year project carried out by K.Gartner is reviewed in his 1990 paper found here
Part of the summary reads
“Utilizing methods established in twin research, only 20-30% of the range of the body weight in inbred mice were directly estimated to be of environmental origin. The remaining 70-80% were due to a third component creating biological random variability, in addition to the genetic and environmental influences. This third component is effective at or before fertilization and may originate from ooplasmic differences. It is the most important component of the phenotypic random variability, fixing its range and dominating the genetic and the environmental component.” ( my emphasis)
These finding are endorsed by D.L.Lajus & V.R. Alekseev in their 2004 paper
This is how they introduce their paper
“It is commonly thought that phenotypic variation in the wild population of most bisexual species is determined by two factors. The first is the genotypic difference between the individuals. The second is caused by diversity of environmental conditions during the formation of the phenotypic trait and manifests itself as phenotypic plasticity. Therefore different environments may result in different phenotypes even if genotypes are the same.
Most studies focus on genotypic variation because this kind of variation provides the basis for population’s adaptive response to change in environmental factors by
means of selection. Much less attention is usually paid to the non-genotypic component. But some experiments have shown that even when both genetic and environmental causes of phenotypic variation have been accounted for, variation still exists.”( my emphasis)
In 2005 Albert H.C. Wong et al confirmed the above.
http://hmg.oxfordjournals.org/cgi/conte … uppl_1/R11
They write (under PHENOTYPIC VARIATION IN GENETICALLY IDENTICAL ANIMALS: ‘THE THIRD COMPONENT’)
“In an elegant series of experiments designed to explore the relative contributions of genes, environment and other factors to laboratory animal phenotype, Gartner (17 ) was able to demonstrate that the majority of random non-genetic variability was not due to the environment. Genetic sources of variation were minimized by using inbred animals, but reduction of genetic variation did not substantially reduce the amount of observed variation in phenotypes such as body weight or kidney size. Strict standardization of the environment within a laboratory did not have a major effect on inter-individual variability when compared with tremendous environmental variability in a natural setting.
Only 20–30% of the variability could be attributed to environmental factors, with the remaining 70–80% of non-genetic variation due to a ‘third component…effective at or before fertilization’” (17 ).(my emphasis)
There are clearly built in mechanisms that cause probably most of the variation we see within species.
So what the experimental evidence and genetic research is showing is fairly clear.
The Darwinian mechanisms for speciation, so often touted as fact, are really not supported by experimental/empirical evidence.
Research in Developmental biology is probably causing the greatest stress to these hypothetical mechanisms.
So returning to the original questionquote :
Yes there is empirical evidence and NO it does not support “macroevolution”.
In fact all the available evidence is serving to falsify this Darwinian (neo or classical) hypothesis.
September 22, 2010 at 4:04 am #101400quote jevg:
Now please don’t bombard me with links and other data but can you succintly explain to me where the empirical evidence that supports your view* on speciation is?
You reject evidence on the basis that its not direct observation of speciation and then post links to experiments which are… you guessed it.. not direct observations of speciation.
* I don’t know if you’ve actually explained your view. I think I’ve got it, reading between the lines but can you just come out and say it so we can all be clear where your coming from?
September 23, 2010 at 4:15 pm #101448
The whole statement readsquote :
Now if that is not clear enough then may be it is the English language that has the problem 🙂
Look I understand your need to use rhetorical devices to veer away from what the evidence is revealing.
If it is your view (although I am not sure what your view is) that the Darwinian mechanism is real and explains speciation, then likely it is a very ingrained viewpoint.
This however is science and science requires evidence. The evidence I have repeatedly pointed to shows that the Darwinian mechanism does not explain speciation.
That is where I am coming from.
However, there is a more fundamental principle that Developmental biology raises against this mechanism.
Please bear with me, if only for the purpose of some education.
Embryological evidence has long shown that DNA does not wholly determine morphological form. This suggests that mutations/variations in DNA alone cannot account for the changes required to build a new body plan, which is what speciation requires.
( I can point you to the evidence both in the wild and experimental, but I wont push my luck 🙂 )
DNA directs protein synthesis. It also helps regulate the timing and expression of the synthesis of various proteins within cells.
DNA alone though, does not determine how individual proteins assemble themselves into larger systems of proteins, still less does it alone determine how cell types, tissue types, and organs arrange themselves into body plans.
Other factors, such as the structure and organization of the cell membrane and cytoskeleton, play important roles in determining developmental pathways that give rise to body-plan formation during embryogenesis.
For example, the shape and location of microtubules in the cytoskeleton influence the shape and form of embryos. Arrays of microtubules help distribute the essential proteins used during development to their correct locations in the cell.
Now microtubules themselves are made of many protein subunits. These protein subunits in the cell’s microtubules are however identical to one another. But neither they nor the genes that produce them account for the different shapes and locations of microtubule arrays that distinguish different kinds of embryos and developmental pathways.
What matters in development is the shape and location of microtubule arrays, and (this is important) the shape and location of a microtubule array is not determined by its units.
An analogy may help explain
Electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But these lower-level components do not determine their own arrangement in an integrated circuit.
Biological systems also depend on the hierarchical arrangements of parts.
Genes and proteins are made from relatively simple building blocks, nucleotide bases and amino acids, arranged in specific ways.
Cell types are made of, among other things, systems of specialized proteins.
Organs are made of specialized arrangements of cell types and tissues.
And body plans comprise specific arrangements of organs. ( I hope you can see the hierarchical nature of the cell arrangement.)
Clearly therefore the properties of individual proteins (or indeed the other lower-level parts in the
hierarchy generally) do not determine the organization of the higher-level structures and organizational patterns or forms.
It follows, then, that the genetic information that codes for proteins does not determine these higher level structures either.
James Shapiro uses the analogy of Lego-like assemblies regarding this arrangement.
The above consideration poses but just one challenge to the sufficiency of the neo-Darwinian mechanism.(there are others)
Why does this pose a challenge?
Because neo-Darwinism seeks to explain the origin of new information, form, and structure as the result of selection acting on randomly arising variation at a very low level within the biological hierarchy, namely, within the genetic text.
Yet major morphological (form and shape) innovations depend on the specific arrangement at a much higher level of the organizational hierarchy that DNA alone does not determine.
So if DNA is not wholly responsible for the body-plan ,(which is a fact) then DNA sequences can mutate indefinitely and still not produce a new body plan.
But speciation requires a new body plan.
These mutations could and do produce variations at the lower levels and that is what the experimental evidence I have referred to shows.
Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian radiation.
September 24, 2010 at 12:03 am #101452
My view is quite simple.
Evolution has happened, and that is a fact.
Natural selection is happening, that is also a fact.
Whether natural selection alone explains new species is unknown, for the simple reason that observing new species is so difficult. Hey for all we know all this random mutation and natural selection may serve only to improve a species, maybe even to set the conditions for the creation of a new one, but maybe not create a new one.
Anyone who holds a view that something causes new species does so on a basis of faith because, to quote one of your favourite lines, "the evidence is simply not there".
September 24, 2010 at 8:15 am #101457Julie5Participant
Hi, not sure if this has been discussed here, but cancer provides a compelling demonstration (even if not proof!) about how mutations in DNA can create a new ‘surviving unit’ (ie, cancer cell/tumour) which evolves by continuing mutation, so that a ‘late cancer cell’ can be considerably different in genome from an early one, and which, moreover, has spread into other eco-niches (ie, metastasised), and which also demonstrates survival of the fittest, as chemo will kill off vulnerable cancer cells, whilst some, with different genotypes, will survive to continue to increase their population in the host body and colonise more and more habitats (lungs, bones, brain, liver, peritoneum etc etc etc….)(until the host dies, of course….)
The only evolutionary barrier cancer faces is, of course, the death of the host, except starting again from scratch in a new host for those particular cancers that are familial and inheritable.
But, in a microcosm, each patient’s cancer does seem to demonstrate rather a lot of the tricks and traits that evolution uses to increase populations, colonise new habitats, and improve fitness (ie, survivability).
By the way, the death of the host situation that limits cancer could also be a pretty good mirror of the death of the host situation that global warning/earth destruction by humans presents as a grim limit to our own species….
September 24, 2010 at 4:46 pm #101460
I fully agree with you and it is good to be at one on this.
This is something that both empirical evidence and research supports and is good sound science.
There are things that science is unable to answer and it becoming clear that species origin is one of those things.
Science however can and often does show what cannot be.
Species origin by the Darwinian mechanism of random variation and natural selection cannot be, and I hold that the accumulating and now indeed the overwhelming evidence of actual science, demonstrates this. The last two of my posts simply summarises that evidence.quote :
Nice to have agreement again.
What is very problematic though, is the reality in the scientific community that Darwin’s Origin of Species hypothesis which is a faith based view (and it is) is paraded as fact, to the point that any other faith based view is regarded as unscientific (which they are) and considered irrelevant and often ridiculed.
Julie5 » Fri Sep 24, 2010 8:15 am
What you say is demonstrably true.
Remember though that there is a great deal of difference between the concept of “survival of species” and the “arrival of species”
The full Title of Darwin’s publication is very revealing.
“On the Origin of Species by Means of Natural Selection, or the Preservation of
Favoured Races in the Struggle for Life.”
Darwin himself recognized that he was using one hypothesis (preservation) supported by observable evidence to support his philosophical view of an entirely different process (origin).
September 25, 2010 at 1:37 am #101464quote jevg:
Not quite.. when you sayquote :
That is indeed a fair point of view to take, however you then shift your viewpoint without any further prompting towards…quote :
in order to conclude…quote :
So firstly you interpret data to support a viewpoint (A suggests B is not true), but then suddenly state that viewpoint as if it were a fact (ie B is not true).quote jevg:
Darwin’s hypothesis was that evolution has happened and that natural selection drives it. Whether natural selection drives alone is the debateable point, but the amount of evidence in support of natural selection’s role means that anyone who suggests it isn’t even in the car is being unscientific.
I don’t think that the scientific community regards faith based views as irrelevant and I certainly don’t see any ridicule that isn’t justfied. Examples of justified ridicule would be the conservapedia/Lenski dialogue, demanding samples of E Coli was just plain asking to be ridiculed. On the other hand Shapiro’s treatment by some members of the scientific community is unwarranted, but these people represent a minority and certainly don’t represent the science community in the same way that Conservapedia don’t represent people of faith.
You have previously likened neo-darwinism to being a sinking ship, one only has to type the following words "neo darwinian sinking ship" in to a search engine to see the types of unscientific people who hold those views. Only you will really know whether your part of that community or the scientific one.
September 26, 2010 at 6:33 pm #101492
When I statedquote :
I was stating a fact. I resisted the urge to provide evidence simply because of your stated request for me not to keep referring to evidence
However may I repeat
Changes in DNA alone do not produce new body plans. That is a fact supported with evidence.
I also stated that the Darwinian mechanism of random mutations/variations and natural selection can and do produce variations at levels lower than speciation.
From your comments I rightly or wrongly assumed that we are in agreement
However if I assumed wrongly and you have evidence to challenge that view then please present it so that a rational debate can continue.
However I am not going to engage with you on peripheral issues. If you disagree with me on the matter of ridicule then that is ok with me.
We are dealing with opinion on this matter and it’s always good to have variety, so long as it does not lead to animosity.
September 27, 2010 at 1:14 am #101496quote jevg:
I guess the only explanation for my failure to be overwhelmed by such evidence is that I can’t see the wood for the trees. Seriously though, you can hold whatever opinion you wish, but know this; if what you say were true then I’m sure we wouldn’t be having this debate because it would be accepted by major sections of the scientific community.
The way I see it, one small but growing section of the scientific community (evolutionary developmental biology, a relatively new field) is currently undergoing a debate over interpretation of it’s own findings. You seem to liken this to the sinking of the darwinian ship, whereas I suggest it’s merely a few raised voices in one corner of the foredeck. I guess what I’m saying is that I think you’re overreacting.quote jevg:
There is evidence in support of this viewpoint but of course this is down to interpretation. There is overwhelming evidence that genes are responsible for body plan changes, such as the loss of limbs that lead to snakes. Darwins own observation of the beaks of finches was later confirmed to be the result of genetic expression alone.
Whether you believe that phenotypic evolution conflicts with neo darwinism or extends it is a point of view. I guess I take the view that it extends it (rather like Einstein extended Newton). But then again, I believe in the evidence which supports natural selection and the extension of that viewpoint is that DNA, whether directly or indirectly, is responsible for embryological development.
Well we’ve had Darwinism and Neo-Darwinism, I guess "Post Modern Darwinian Development" might be the new watchword in years to come. 😀
September 27, 2010 at 8:53 am #101506Julie5Participant
This is probably a can of worms, but I’ve personally never really undrestood why some faiths don’t like evolution. Huge numbers of religious people have no problem with E by NS (eg Catholics, Anglicans), and simply reconcile the science with their theology – ie, that God used the mechanism of E by NS to produce the living world, and good old Homo.sap to do whatever He/She are here to do.
If some religious people say they don’t like E by NS because it implies that it’s chance alone that produced Homo sap, then they don’t really get the concept of divine omniscience and omnipotence. If they seriously think God can’t set up a universe in which particular genes are subjected to particular mutuations by particular mutagenic events at particular times which eventually result in Homo sap, then they believe in a pretty puny God to my mind! (When you are God, random doesn’t exist!)
As for the moral objection to E by NS, that species come and go without any divine care of them, well, Nature, like it or not, is red in tooth and claw, and no amount of Creationism is going to get round that moral problem.
Finally, it is my personal belief that the reason dinosaurs came and went is because God thought they were a pretty neat idea, and got a lot of fun out of them (After all, we already know He/She has an inordinate fondness for beetles….). More utilitarianly, of course, He/She needed dead dinosaurs to form our modern oil reserves, which are necessary to get Homo Sap into a state of civlisation where we are wealthy enough so we can FINALLY sort ourselves out and put a stop to poverty, illness etc etc, and built that City of God that is our Divine Task (ie, for those who are of a religious disposition.)
And, whether or not we are religious, making people happier and healthier is a clear moral imperative for all of us.
September 27, 2010 at 8:58 am #101508quote jevg:
That’s definitely not true. You can have plenty of mutations causing basically nothing, but you can have like one mutation, which changes "everything"
October 1, 2010 at 1:30 pm #101594
When you say “everything” I have to assume you mean “speciation or novel body plan” because that is what this question is all about.
Can you therefore point me to evidence that shows how one mutation, as you put it, can change “everything”.
There seems to be a problem here in separating science from religion.
This question is about whether there is any experimental evidence that supports speciation.
It has nothing to do with faith or religion. That said though, peoples faith can and often does impact on their world view.
In a book review by Danny Yee on the book
Bones of Contention:
Controversies in the Search for Human Origins Roger Lewin, he made this comment.
“And anyone who still holds to a naive belief in the clear-cut objectivity of science and scientists will find it an eye-opener.”
That comment carries a lot of merit.
May I remind you what you yourself wrote on the Fri Sep 24, 2010 12:03 amquote :
You now writequote :
You appear to be (and I would conclude unintentionally) blurring the distinction between variation within species (ie darwin@s finches) and speciation.
You also refer to the loss of limbs in snakes as overwhelming evidence for body plan changes by genes.
This of course raises quite a controversial topic on the origin of the snake. However whichever side of the argument you are on, none of the discussions address, what to many is the fundamental question about snake evolution in the first place:
Why should an animal with legs evolve into one without them?
Legs seem to be quite a useful bit of equipment; every other terrestrial vertebrate has them.
The Darwinian hypothesis of natural selection rests on the selective advantage for survival. The snake seems to me to be disadvantaged by the removal of it’s limbs.
Now a biblical scholar pointed me to the Genesis account Chapter 3 verse 14, which reads in reference to the serpent.
“Because you have done this you are accursed more than all the cattle and all wild creatures. On your belly you shall crawl……”
So the account states that all the animals were put into a state of disadvantage (cursed) but the snake more than the rest, in that it lost it’s limbs.
Now I may not be a creationist, but this explanation has more logic to it than Darwinian selectivity.
What do you think?
October 1, 2010 at 1:59 pm #101595quote jevg:
The fact that you do not see the advantages of the loss of limbs does not prove anything. Maybe it makes it easier to crawl into small holes/spaces, or maybe something else that cannot be seen but was advantageous for the snake’s ancestor. Remember that reversion is not always possible, and once something is lost, it might not be possible to get it back. So the evolution has to work on what is there now, not on what was previously there.
The famous example by S.J. Gould is the Panda’s thumb. Bear lost it, but a thumb is useful to eat bamboo shoots, but the thumb structure cannot be recreated, however another solution emerged (i refer you to the book, he writes better than me).
And the "curse" solution however better it looks to you have so much implicit complexity (necessity of a creator, possibility of curses etc…) that I suggest that you take Occam’s razor and use it. But once again remember the implicit assumptions behind your scenarii.
October 2, 2010 at 10:43 pm #101607
I asked a simple question “what do you think?
You raise an interesting scenario.quote :
May I refer you to Richard Ellisin’s book AquaGenesis where he puts it this way on page 158
“Although the fossil record is too sparse to make any definitive statements (always dangerous in paleontology anway), many paleontologists have done exactly that. After two groups of scientists examined fossil snakes from the same area, two scenerios emerged. Scanlon, Lee, and Caldwell have proposed that snakes are derived from water-dwelling lizards (mosasaurs), and emerged from the water to become the terrestrial species that we know today. “
“the other group of scientists, Tchernov et al. (2000), believe that modern snakes are the descendants of small, burrowing, terrestrial lizards.
. . . As for the legs, which Scanlon et. al. cited to demonstrate that snakes are descended from lizards, all they mean to Tchernov’s group is that ancestral lizards lost their legs, became snakes, evolved into snakes with legs, and as of now have become (mostly) snakes without legs. They acknowledge that this is a less parsimonious explanation, but it nevertheless "remains a possibility, given the incompleteness of the fossil record of snakes and the recognition of multiple loss of limbs among squamates in general."
This excerpt simply highlights the different views.
Notice that with the “land hypothesis”, the originators Tchernov et.al. acknowledge that their explanation is “a less parsimonious” one, the hypothesis that you appear to be supporting.
Excerpts from Page 155
. . . None of this discussion addresses what to many is the fundamental question about snake evolution in the first place: Why should an animal with legs evolve into one without them? Legs seem to be quite a useful bit of equipment; every other terrestrial vertebrae has them. Only the fishes are legless; the whales, to adapt to the fishes watery environment, have lost their hind limbs completely and their forelimbs have evolved into paddles. Perhaps the sea snakes are a more advanced form of snake, for only in aquatic animals does leglessness confer an advantage — or at least, it does not handicap the animal. . .
You will notice that my question is a direct lift from Ellisin’s book. So it is Ellisin who does not see the advantage of loss of limbs. In fact he goes further and states that “only in aquatic animals does leglessness confer an advantage — or at least, it does not handicap the animal. . .
My guess is he knows more about this subject than you or I and it could even include Geokinkladze
You suggest I use Occams razor and I am very happy to apply that principle.
Here is the principle http://pespmc1.vub.ac.be/occamraz.html
“The principle states that one should not make more assumptions than the minimum needed. This principle is often called the principle of parsimony. It underlies all scientific modelling and theory building. It admonishes us to choose from a set of otherwise equivalent models of a given phenomenon the simplest one. In any given model, Occam’s razor helps us to "shave off" those concepts, variables or constructs that are not really needed to explain the phenomenon. By doing that, developing the model will become much easier, and there is less chance of introducing inconsistencies, ambiguities and redundancies.”
So which idea do I apply Occams razor to
The aquatic hypothesis
The land hypothesis
Or the “someone removed the legs intentionally” hypothesis. 🙂
Well since I have played “devil advocate” by introducing the creation or “someone removed the legs intentionally” hypothesis I will apply occam’s razor to it.
Remember one should not make more assumptions than the minimum needed.
We know that during the late 50’ and early 60’s thousands of women took the drug Thalidomide to combat morning sickness. This resulted in the terrible tragedy of thousand’s children being born with deformed or missing limbs.
So it proved that direct intervention (whether intentional or not) during the embryo stage of development can produce loss of limbs.
The only assumption that therefore needs to be made is that the cell mechanism can be directly altered to make this change heritable.
Therefore just one assumption is required.
Less than one could make it a fact.
How many assumptions are needed for the “land hypothesis” ?
How many for the “aquatic hypothesis” ? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626205/
Please read just the Conclusion of the paper and count the number of assumptions. Also remember that the land hypothesis is less parsimonious than the aquatic hypothesis.
Now I am only playing “devils advocate” here, but the creation hypothesis wins, simply on the basis of the occams razor principle which you have introduced into this discussion.
I have studied Gould’s essay on the Panda’s thumb and I would ask you to count the number of assumptions he has had to make before he arrived at where he wished to go.
We are dealing here with belief systems not with the scientific method.
The boundary between belief and science is being blurred to the point that beliefs are being presented as fact and that, I strongly argue, is not good science.
October 4, 2010 at 5:57 pm #101633quote jevg:
I would not call a "top of my head hypothesis" a support for any hypothesis. I have absolutely no clue about what made the loss of limb useful to be honest. I was just trying to point out that the fact that you (or anyone else for that matter) do not see the advantage does not mean that there are none.quote jevg:
Actually you were the first one to bring it in, and I will once again repeat what I told you: the implicit complexity of the creator is much higher than any hypothesis that we could do based on that event happened randomly, and that one, and that other… because if you take the thalidomide example to get there you needed the full evolution of human, the development of a civilization and of a chemical industry etc to get to that molecule. So one little pill/step with a lot more hidden complexity than a series of mutations by mechanisms that are known and do not require external forces.
This is in this hidden complexity that you have consistently refused to acknowledged that lies the opposition to any external creator in modern science.
October 5, 2010 at 1:31 am #101639quote jevg:
Ok give me YOUR universally accepted definition of a species. In other words YOUR definition of a species, that is also universally accepted as THE definition of species. Now I’m not interested in your definition that is accepted by the people who read the same books as you, I’m talking about THE universally accepted definition. I could be asking the impossible, maybe miracles happen?quote jevg:quote jevg:
Firstly I think you’re a creationist. Now that’s not meant as an insult so please don’t take it as one. I guess that’s just my opinion. The only reason I say it is that you say you’re not, but it’s become fairly obvious to me that you are.
Secondly, with regard to the snake: Limbs have a resource cost that requires maintenance. Limbs would adversely affect digestion. Limbs would snag on twigs and branches. They would provide an easier target for predators and prey. In return what advantages would they provide? I guess that as random mutation and natural selection have led to them disappearing then the advantages must have been outweighed by the disadvantages.
October 5, 2010 at 7:48 am #101642
I am just now joining this long and interesting thread, so please forgive me if I’m repeating information others have already covered.
jevg says "the Darwinian mechanism does not explain speciation." This statement is true if by "Darwinian" jevg means the theory as explicated in Darwin’s On the Origin of Species in 1859. Darwin did a good job of explaining adaptation, but despite his ambitious title, he didn’t provide much insight into the process of speciation.
But current evolutionary theory — called the "modern synthesis" because it integrates Darwin’s theory with Mendelian genetics — explains speciation quite well. And evolutionary biologists have amassed considerable evidence to support this view.
For an excellent review of this evidence I refer you to Chapter 7 of Why Evolution Is True by Jerry A. Coyne. Because speciation generally takes millions of years, it cannot be observed directly. But the fossil record, embryology, and genetic analysis show that species diverged from common ancestors.
The most common type of speciation involves geographic isolation. The theory of geographic speciation predicts that species on either side of a geographic barrier will be more closely related to each other than to species on the same side of the barrier. This is exactly what evolutionary biologists have found. Coyne writes:quote :
Evolutionary theory also predicts that after a period of geographic isolation, diverging species will become reproductively isolated. This reproductive isolation has been shown many times in nature. And using flies, which have short generation times, scientists have been able to produce reproductively isolated populations in the lab.
Coyne also describes another type of speciation that can be studied directly. Polyploidy, or the production of extra copies of chromosomes, can cause speciation in as little as two generations. This type of speciation happens often in plants and occasionally in animals. In some plants, biologists have been able to reproduce these speciation events in the lab, to the extent that the lab varieties can mate successfully with the species that evolved in nature.
Thus Darwinian theory, as it is currently understood by evolutionary biologists, is extremely well supported by scientific evdience.
October 5, 2010 at 8:40 pm #101657
Your honesty is very refreshing, and this is in no way a patronising comment.
I agree that because I don’t see an advantage does not mean there is none.
What I disagree with is the a priori position that speciation is a product of some Darwinian mechanism and that position is a scientific fact. If it were a fact then the evidence would point to it.
I have been consistent in pointing out that the experimental evidence does not point in that direction. In fact it contradicts that position.
Now nobody has managed to refute that evidence and with good cause because this controversy is not about science but about two opposing belief systems.
Neither of these belief systems can be supported by science.
Science by it’s very nature, must operate within the realms of natural law, and natural law does not and indeed cannot explain the arrival of the cell or life or species.
This is the situation whether we like it or not.
Let me explain ( Please think about this)
All known life depends upon genetic instructions. No hint of metabolism has ever been observed independent of an oversight and management information/instruction system.
We use the term "bioengineering" with good reason.
Genes are literal programs. They are sent from a source by a transmitter through a channel within the context of a viable cell. They are decoded by a receiver and arrive eventually at a final destination.
At this destination, these messages catalyze the needed biochemical reactions.
The cell is in fact a biochemical communication system.
Genes have undeniable "meaning" which is shared between source and destination. (Fact)
Noise pollution of this "meaning" is greatly minimized in the cell by ideally optimized redundancy coding and impressive biological repair mechanisms. (Fact)
A noisy channel is one that produces a high corruption rate of the source’s signal.
Now signal integrity is greatly compromised during transport by randomizing influences. (Fact)
In molecular biology, various kinds of mutations introduce the equivalent of noise pollution of the original instructive message. (Fact)
Communication theory goes to extraordinary lengths to prevent noise pollution of signals of all kinds. (Fact)
So given this longstanding struggle against noise contamination of meaningful algorithmic messages, does it not seem curious to you that the central dogma of biology today attributes genomic messages themselves solely to "noise."?
Without algorithmic programming to control options, the number of possible paths in sequence space for each needed biopolymer is truly enormous.
But when multiple biopolymers must all converge at the same place at the same time to collectively interact in a controlled biochemically cooperative manner, I argue that faith in this "self-organization" becomes "blind belief."
No empirical data exists for such a metaphysical leap.
Darwinism (in all its forms) and Creationism (in all its forms) are both belief systems, trying to explain this arrival with both claiming theirs is truly scientific. The fact is that neither of them is.
Isn’t it about time a start is made to at least acknowledge this.
October 5, 2010 at 10:01 pm #101659quote StevePush:
You are half right, it’s certainly long. It’s been fun while it lasted but unfortunately I shall have to take my leave and do other things. I’ll hope to check back now and again to see if there’s an answer to the question: why are leaves green? see: http://www.biology-online.org/biology-forum/about675-48.html which is originally what brought me here.
Hopefully if anything comes of this thread then it will be that viewers will realise it’s better to prevent your religious views from clouding your rational ones. Science is attempting to answer the big questions via a series of small incremental steps, sometimes there are periods of stasis, other times there are periods of rapid discovery, quite a lot of theories become extinct (sound familiar anyone?) 😉
Stephen Hawkings is currently doing the rounds with his new book, he says that God isn’t necessary to explain the creation of the universe. I agree wholeheartedly with that one. Anyone who tries to prove or disprove the existence of God by scientific means should be treated with caution.
October 6, 2010 at 4:23 am #101661quote jevg:
I agree with regard to creationism. It is not falsifiable and thus not scientific.
Darwinism, on the other hand, is scientific, and your own posts prove as much. You claim to have presented experimental evidence that cotradicts Darwinian theory. I disagree that the studies you cite contradict Darwinism, but the fact you can articulate such an argument proves that Darwinism is falsifiable.
The fact that Darwinists are unconvinced by your arguments does not in itself render their views to be blind faith. As long as they can make predictions that can potentially be proven false, their views are scientific.
October 6, 2010 at 10:18 pm #101684
The theory of evolution as we know it is scientific as it lays hypothesis on how it work, makes predictions and allow verification of them, or falsifications. Creationism is based on faith only. That is the main difference.
Now in light of your analysis of facts, I hope you won’t mind if I ask whether you are an engineer. For curiosity’s sake…
October 11, 2010 at 7:17 am #101761
Sorry for the delay but have been otherwise occupied. Life outside this forum you know 🙂
I am a Radio/Radar Engineer (now retired).
I agree with your last comment. Creationism is based on faith and cannot be subjected to scientific enquiry. Where I would add to your comment is that Darwinism which was and could have been regarded as null hypothesis originally has now, in my view, taken on the mantra of a faith based system.
Darwin tried to explain the origin of Species scientifically and indeed put forward a plausible hypothesis while honestly recognising it’s flaws. Those flaws have in the light of evidence turned out to be quite profound and that is why I argue the way I do.
October 11, 2010 at 7:46 am #101762
I hope my response to canolan explains more my position.
My whole point is that Darwinism is falsifiable and the evidence is showing it to be so. Since it is being falsified with evidence, and at the same time still being regarded as a scientific theory (indeed as fact) this is what has turned this hypothesis into a belief system.
You referred me to Jerry Coyne’s book.
I have read a lot of it though not all and would be very happy to discus it further. This book actually proves my point and I will be quite happy to demonstrate it.
October 12, 2010 at 6:32 am #101777quote jevg:
I would be pleased to read your thoughts on why you believe the theory of evolution has been falsified.
October 12, 2010 at 8:42 am #101782
you’re saying, that darwinism/theory of evolution was disproved, but these are not equal. The theory of evolution was here even before Darwin, he just came up with the mechanism.
October 13, 2010 at 6:34 pm #101819quote jevg:
Because several days have passed since jveg offered to elaborate on jveg’s critique of Darwinian theory, I have looked to past posts for the evidence jveg has offered to provide. One study jveg cited was the long-term evolution experiment, or LTEE (See http://www.pnas.org/content/105/23/7899.full.pdf+html).
Jveg’s interpretation of the LTEE misstates what the data from the experiment actually show. The experiment was designed as a test of two alternative hypotheses: the rare-mutation hypothesis and the historical contingency hypothesis. As the name suggests, under the rare-mutation hypothesis a new trait arises as a direct result of a rare mutation. In that case the probability of acquiring the new trait remains constant over time. Under historical contingency a new trait is contingent on one or more past mutations that do not give rise to new traits by themselves but make it more likely that subsequent mutations will give rise to the new trait. In that case the probability of a new trait will start out low but rise substantial after the appearance of the “potentiating” mutation(s).
The data from the LTEE study support the historical contingency hypothesis. But since both of these hypotheses are Darwinian, the results do not falsify Darwinian theory. Even though the experiment was not designed to test Darwinian theory, the fact that a new trait arose confirms a key element of the modern synthesis of evolutionary theory.
Jveg notes that a small new trait arose in only one of 12 cultures and only after more than 30,000 generations. He estimates that would equate to 600,000 years in human generations and questions how the entire human digestive system could evolve so quickly. (That’s not a good estimate because many of our ancestor species probably had generation times shorter than 20 years.) In fact, our digestive system has had a thousand times longer than that to evolve. The earliest know chordate fossil dates from 550 million years ago, and it would have already had a functioning digestive system to survive. What’s more, the field of evolutionary development has shown that small genetic changes that affect early developmental stages of an organism can have enormous effects on form and function.
Jveg also notes that the population with the new trait did not drive the parent population to extinction. Darwinian theory does not hold that the mere appearance of a new form of life necessarily means its parent population will go extinct. Closely related species and populations can coexist indefinitely. In the LTEE, the new population did not drive the parent population to extinction because the parent population was a superior competitor for glucose. What Darwinian theory does say is that over time, as environments change, some forms become extinct. The LTEE has confirmed one way in which nature generates the variation that enables such selection to occur.
October 13, 2010 at 9:00 pm #101822
First, I would like to thank you to add data to the Salem hypothesis I was curious and it is not really related to the thread, so I will not discuss further.
As for the rest of your argument, other have once again demonstrated, and better than I would, that your understanding of the experiments that demonstrate the falsification of the theory of evolution is slightly out of touch with what others (including the author of such work) think they mean.
And I would suggest that the theory of evolution by natural selection is still not perfect, and there are a lot of things that are not understood, but scientist are working on that and expanding and improving our understanding of how individuals are changing. All in all the theory is the best model we have, it makes predictions that er generally verified, and I would be curious if you had any other system that would perform better. As T. Kuhn in the ‘structure of scientific revolution’ you need more than just pointing problems to overturn a model that work because scientist will keep adding epicycle to make it work, you need to provide a whole model that work better. I am still waiting for a hint of that. For the moment you have limited yourself to say that the creator hypothesis is as credible as random mutations fully ignoring the hidden complexity. So what else do you have in store, besides "I refuse to understand and listen how it works, I refuse to admit it, you biologists are wrong"?
October 18, 2010 at 11:49 am #101882
My apologies for not responding to the last few posts.
I have been otherwise engaged not the least of which is a back injury I have sustained. However I am back again. I will catch up with the posts and continue shortly. I notice Stevepush has put up an appraisal of the LTEE experiment . I will study it and respond.
btw I am glad to add data to the Salem hypothesis. Always good to be of help 🙂
October 18, 2010 at 2:09 pm #101884
I’m so sorry to hear about your back injury. I’m glad you’re feeling better.
October 19, 2010 at 6:12 pm #101914
Thanks very much for your kind thoughts. Happily my wife is a nurse although she does come over as matron more often than not. 🙂quote :
Apart from the first line 🙂 I agree with you. My first post demonstrated this. (page 2)
My appraisal about this experiment was to point out how difficult it is to even arrive at a new trait, let alone a new species. (Defination : in biology a taxonomic group potentially capable of interbreeding)
Remember this was simply a modification (which is already known to exist in the wild) of transport through the cell wall into an already operating digestive system.
This experiment demonstrates only variation (either by historical contingency or rare mutation) and only that.
Nobody that I am aware of disagrees with this level of evolution (microevolution)
It does not demonstrate a continuing progress towards speciation.
Although generations is a more accurate way of describing the process of evolution most commentary focus on timeline,and that is why I equated the number of generation in years and in human terms.
It shows in human timelines how long a process, even a minor variation, takes.
Hence my question “How many generations it would take to develop a whole digestive tract from teeth to anus.?”
Now, however we may differ as to interpretation, one fact is clear. The variation that this experiment has shown is variation within the species. It in no way demonstrates the speciation that Darwinian theory predicts. Lenski himself acknowledges this point with a question.quote :
This is quite a fundamental point to focus on because many cite this kind of “microevolution” as evidence of “macroevolution”. There is no evidence of a continuum between these two concepts.
If I may I would like to take up on Jerry Coyne’s book in my next post shortly.
October 19, 2010 at 11:05 pm #101923quote jevg:
I have the feeling that your quote from Lenski is not complete. Because he is a microbiologist and there is one thing that I am pretty sure ho knows, and this is that the common definition of species based on genetic isolation is quite useless when talking about bacteria. Those promiscuous bugs can take DNA from many sources without much problems. The definition of a bacterial species is quite a difficult one and that you might be interested to read that paper:
published in 1999, so only 20000 generations, and yet enough divergence accumulating to come close to define a new species.
October 20, 2010 at 3:30 am #101927
It is a mistake to over-interpret the data. The experiments in the paper we are discussing were designed to distinguish between Darwinian hypotheses. These particular experiments are not a test of whether natural selection can result in speciation. It’s as if I said to a YECist, the Bibical account of creation cannot be true because Exodus does not explain how God created the world.
Nevertheless, I would be concerned if the LTEE produced some data that were incompatible with Darwinian theory. If I understand your position, you are saying that, because it took more than 30,000 generations for one of the E. coli populations to display a new trait, it’s not possible for evolution to have occurred during the history of the Earth. But in fact the LTEE data are compatible with Darwinian theory, for the following reasons:
1) The LTEE has been under way for about 20 years. According to evolutionary theory, life on Earth began about 4.5 billion years ago. Thus evolution has occurred over a period that is 225 million times longer than the LTEE.
2) New traits do not necessaily arise one at a time. Over evolutionary time, organisms have become more complex, with larger genomes. Multiple new traits can be evolving in the same organism simultaneously.
3) The environment of the LTEE is stable. Evolution occurs most rapidly when environments change dramatically, as has happened many times during the history of life on Earth.
4) In nature, there are factors other than mutation that contribute to genetic change: sexual reproduction and other forms of recombination, polyploidy, the incorporation of whole new genomes, as when mitochrondria became part of eukaryotic cells.
5) The field of evolutionary development has shown that even small genetic changes can result in major changes in form and function.
6) Speciation has been demonstrated in many other experiments involving bacteria, plants, and animals. (See http://www.talkorigins.org/faqs/faq-speciation.html)
October 20, 2010 at 3:43 am #101929quote :
Your feeling is correct, Patrick. The paper goes on to suggest experiments that could determine whether the Cit+ population is evolving into a new species.
October 20, 2010 at 11:06 pm #101942
Just to clarify
I was responding to the question which you probably may not have fully appreciatedquote :
The Lenski experiment that I introduced into my answer is in my opinion what good science is all about.
The background I initially provided demonstrates that I was in no way trying to read more into the experiment. Since however it is the best experiment to test what happens to an organism under stress conditions I considered and still do consider it an appropriate experiment to provide information on the question.
On the matter of speciation it is Lenski himself who brings up this point. And my direct quote from the paper shows this.
You are quite right that Lenski probably has an understanding of the biological concept of species in bacteria that may be different from that which I defined, but the point is that whatever definition we apply Lenski himself did not consider that speciation had taken place.
It is also clear that historical contingency is a theory that provides the drive towards speciation. So this experiment is about the mechanism of speciation. After all Darwinian theory is about speciation.
And my point was, that this experiment which is probably the most extensive one yet, has not shown that speciation can occur in this manner. Will it as time goes on – well that is currently an unanswered question and therefore science as yet, using the scientific method, has not answered this question.
Therefore the Darwinian mechanism is not a proven theory and I simply argue that it should not be presented as a fact as it so often is.
Just to also clarify we are not talking about 30,000 generations. Please remember that there are 12 populations and the experiment has now proceeded past 50,000 generations for each population. That makes 600,000 generations so far.
I have read somewhere (I will look it up in a follow up) that it is considered bacteria became settled in about the first billion years.
As regards YEC’s
I have had discussions with them, and clearly they have a misunderstanding of the text they place their belief in.
Genesis 1 – 2:4 is a historical narrative and not a scientific postulate. It actually says so itself.
Here is what it says at the conclusion in Gen 2:4
“These are the generations (history) of the heavens and of the earth when they were created, in the day that the Lord God made the earth and the heavens.”
Notice the use of the word generations which means history in the original language.
Notice also the fact the day in this verse refers to all the creative days mentioned previously.
So the bible itself does not equate the word day as a 24 hour period, but yet many fundamental religionists believe it as a fact.
October 21, 2010 at 1:36 am #101943
We’ll just have to agree to disagree about the LTEE. I still think you’re trying to extract a conclusion from that paper that is not supported by the data.
But even if the populations in the LTEE never became distinct species, that result in a single experiment would not falsify Darwinian theory. The theory does not predict that every genetic change will lead to a speciation event. But there are many studies that do document speciation events. The three web pages below provide dozens of examples:
If you are really trying to make a fair assessment of Darwinian theory, you should weigh all of the evidence.
October 21, 2010 at 2:38 am #101945quote jevg:
Your answer surprised me, so I went to look for the paper, and I am indeed surprised by the quote. The paper I linked to and that he co-authored compares the different lineages and uses some of the criteria used to define species in bacteria. It was done long ago and I would not be surprised if even more divergence had accumulated since.
But in the paper you cite Lenski is making a point that should not be ignored. in the LTEE there is little to no sex between the bacteria. That is something very different with what is observed in real life. Exchange of genetic material is probably very important, although quite hard to observe. But I have worked on said subject, and I can tell you that horizontal gene transfer in the larger environment are probably quite important.
And I must say that I find you very polite with regards to YECs.
October 21, 2010 at 3:44 pm #101961
I don’t know if you have actually checked the papers themselves that Chris Stassen has referenced to show speciation as he claims.
His first example is here
Now if you wish to read the entire paper and fry your brain as it has mine please go ahead 🙂
However may I refer you to the summary on page 14.
But before that Dobzhansky and Pavan state very clearly that they are dealing with at least 5 races within the species Drosophila pcrulistorum. This experiment was about determining the cause of sterility in one of the strains during hybridization, as I understand it. They could not establish the actual cause, however they hypothesize that it may be the result of some symbiotic relationship between Drosophilia and a virus or other microorganism. The summary below confirms this.quote :
Now you will notice in the summary that they refer to the “new Llanos” as a strain of the species but hypothesize that the process is one of speciation.
In the Appendix that follows Costas. D. Kastritsis in his analysis – well let him explainquote :
This is an examination of hybrid sterility within the species. The “new Llanos strain is still Drosophila.
If more confirmation is needed then here is another paper.
Now I have not checked out the other examples he cites but my instinct tells me that the Fireweed still remains Fireweed, the Faeroe Island house mouse still remains a Faeroe Island house mouse and so on.
Really Chris Stassen is pushing the envelope out a bit to cite these as examples of speciation.
October 21, 2010 at 3:57 pm #101962quote jevg:
It is admirable that the authors showed restraint and did not immediately declare the Cit+ population to be a "distinct" species. But it probably is a new species. Since E. coli reproduces asexually, the two populations are effectively isolated. (Even if they weren’t, the Cit+ population is isolated from the other 11 cultures.) Unless the entire Cit+ population reverts back to the Cit- genotype, it is a new species. In other words, we now have two kinds of bacteria that differ in both genotype and phenotype and descended from a common ancestor.quote :
I’m not sure what point you are trying to make here. Historical contingency is a proposed mechanism of Darwinian evolution. The LTEE study supports the hypothesis that historical contingency was important in this particular evolutionary change. It does not, however, establish that historical contingency plays an important role in evolution generally. But even if the importance of historical contingency does become established, that would not falsify Darwinian theory; it would reveal in greater detail how Darwinian evolution works.quote :
I would not use the term "proven." Darwinian theory (or more precisely, neo-Darwinian theory) is one of the most well-confirmed theories in science and thus ought ot be taught in science classes. Evolution, on the other hand, is a fact. Even before Darwin, scientists recognized that organisms change over time. They just didn’t know how it occurred.quote :
My take on these numbers is just the opposite of yours. The first bacteria on Earth that could exploit an abundant energy source would have undergone explosive growth, since there would have been no competitors. Within a short time, the numbers of these bacteria would have dwarfed the number in the LTEE’s 12 small cultures. If the LTEE shows evolutionary change in 30,000 or 50,000 generations, I would expect such changes to have occurred much more rapidly in the much larger population that probably existed billions of years ago — or for that matter in the larger natural populations that exist today.
It is also a mistake to generalize from the mutation rate in the LTEE, because mutation rates vary greatly. My evolution textbook has a table showing various mutation rates per 100,000 cells or gametes. These range from 0.00004 for streptomycin resistence in E. coli to 12 for yellow body in fruit flies and 4.2-14.3 for achondroplasia in humans. (Source: Evolution by Douglas J. Futuyma, 2005, Sinauer Associates, p. 171)
October 21, 2010 at 4:04 pm #101963
I wouldn’t argue with you regarding the exchange of genetic information in real life. You have the real life experience, I don’t.
I can only refer to the papers by biologists themselves.
Why Lenski has not sought out a real life environment, only he can answer. I expect it has to do with control of the process.
My experience has shown me that peoples’ views are most often sincerely held. So although they may not be in accord with the facts I feel that the people holding them should be treated with respect. It can sometimes be very frustrating though. 🙂
October 21, 2010 at 7:54 pm #101967
The main objective of the cited article is indeed an investigation of hybrid sterility among subspecies of Drosophila paulistorum. This topic is interesting because it elucidates an important aspect of speciation: Sexually reproducing species must be reproductively isolated.
The evidence you seek is mentioned only briefly in this paper. On page 152 the investigators wrote, "The Guianan [group of Drosophila paulistorum populations] is the most distinctive, and seems to deserve being regarded a species of its own." A year later the researchers published another paper documenting why the Guianan subspecies had evolved enough to be regarded as a separate species, which they called Drosophila pavlovskiana. I have not been able to find this paper free on the Web, but the first page, including the abstract, is available at http://www.jstor.org/pss/2423385
According to the Encyclopedia of Life (http://www.eol.org), Drosophila pavlovskiana is still recognized as a separate species.
October 21, 2010 at 8:43 pm #101968quote jevg:
There is quite a lot of data available on Horizontal genetic transfer (HGT), as it is known in bacteria. I encourage you to look at it. The evidence of genetic instability are there.
The main problem is that we know very little of the life of bacteria outside of the lab. take a gram of soils, and you will be able to identify 1000’s of bacterial species. But bacteria can acquire DNA from dead cells (whatever they were) or from phages, which are estimated to be 10x more numerous than bacteria. Moreover the ability of bacteria to pick-up foreign DNA and to keep it is directly dependent of the environment. So the LTEE is a reductionistic view of what is happening in real life. Lenski has made the choice to observe what happens to isolated populations of E. coli if left for thousands of generation. It is a good way to estimate the importance of accumulation of point mutations. He is dong his analysis of his strains and point to the things that he finds interesting. As I have mentioned earlier, others have had a look at his strains and have demonstrated some interesting side effects, notably re speciation, something that Lenski seems not to have seen worth pursuing. But it is only a very tiny ray of light in the immensely complex unknown that bacterial communities are representing. Taking this experiment as a benchmark to estimate the rate of evolution in the real world is quite frankly foolish.
Maybe you could have a look at some of the work by (for example) Ivan Matic, François Taddei, Miroslav Radman and Erick Denamur on the mutator phenotype.
October 22, 2010 at 7:56 pm #101973
You raise the real life scenario and quite rightly so, but what is this real life scenario demonstrating.
HGT is a major factor here. However what does it say about one of the central doctrines of Darwinism, Common Descent.
It took Carl Woese decades to have his views of a separate domain of Archaea accepted.
Why such resistance?
One of the reasons was that it contradicted the Darwinian view of common descent, a single tree of life, the simple illustration so often depicted in textbooks. This was one of the early things I was taught in biology class at college.
Ofcourse there is no single TOL. It’s now beginning to be regarded as more of a bush – I would argue as more of a forest. And you rightly point to the importance of HGT that is so prominent in this regard.
Also you quite rightly point out that the Lenski experiment is a good way to estimate the importance of accumulation of point mutations. But what has he discovered about these point mutations?
Well let him answer. ( Please note carefully)quote :
“..each population tried every typical one-step mutation many times.”
So even in this most highly selective environment point mutations with or without historical contingency, the simple variation in a trait requires literally hundreds of thousands of generations. So as I asked previously how many generations would be required for a full digestive tract to be produced.
Now you rightly say to use this experiment, as a benchmark to estimate the rate of evolution is frankly foolish. I would say it is frankly ridiculous. There is no way to use this as a benchmark for something that isn’t happening.
Please bear in mind why this even modest change is so difficult – because of the rigid control the cell exercises during division. Clearly the cell legislates against random changes or biological noise as a communications engineer would describe it.
So in the wild we see the role of HGT (at the very least) compromising the idea of common descent.
In the lab we are getting direct evidence on the very weakness of point mutations to drive speciation.
That leaves natural selection, and Darwin himself acknowledged that NS is not the only mechanism to speciation. Natural selection can eliminate a species that is not adapted to it’s environment but it has no power to modify it’s form. It can only work on what is already there.
So of the three fundamental pillars of Darwinism , random variation/mutation, natural selection and common descent, I see only, possibly one third of one pillar that has potential.
In 1999 Ernst Mayr (one of the founding fathers of the modern synthesis) received the Crafoord Prize from the Royal Swedish Academy of Science and gave a lecture, and which in part he saidquote :
He goes onquote :
And againquote :
I am arguing against a philosophy, not science and I have no less an authority than Ernst Mayr himself promoting that view and with pride.
All I ask is not to confuse philosophy with empirical science. This confusion is all too apparent in, for instance Jerry Coyne’s book “Why evolution is true” that Steve referred to and I would be only too happy to discuss it, to demonstrate my point.
October 23, 2010 at 7:39 am #101978
It says that in addition to the genes of their immediate ancestors, organisms sometimes carry genes form other branches of the tree of life. Recent genetic analysis suggests that all life descended from a single ancestral gene pool.quote :
It took more than a century for the Copernican model of the universe to be accepted. New discoveries sometimes take awhile to gain widespread acceptance. Usually this is for good reasons (e.g., not enough data yet).quote :
Woese didn’t challenge the tree; he rearranged it.quote :
None of those metaphors is perfect.quote :
What digestive tract? Human? Probably on the order of tens to hundreds of millions of generations. Along the way, more primitive digestive tracts evolved in fewer generations.quote :
If you believe evolution does not occur, what alternative do you support?quote :
Yes, cells repair DNA damage, deactivate viral genes, etc. Despite these mechanisms, genetic variation is an empirical fact.quote :
You have misinterpreted the Mayr quote. He was speaking of the "philosophy of biology," that is the branch of phiosophy that studies how biology is done. He was not saying that biology is unscientific. It is, in fact, as rigorous as any other field of science.
October 25, 2010 at 7:20 am #101989WDWParticipantquote :
I’m unaware of an experiment that provides empirical support for macro-evolution above the species level. However, there are claims of new species produced from existing ones. With much debate over the meaning of the word "species" and over methods of species identification, its difficult to find consensus on the matter. Its possible that some of these "new species" may simply be variations within the species itself. In other cases, it appears the new species are a type of hybrid limited by reproductive postzygotic barriers.
March 30, 2012 at 10:48 am #110404einfopediaParticipant
i think that it is very informative for you and you also find the your answers in this paragraph..
Sperm competition, when sperm from different males compete to fertilize a female’s ova, is a widespread and fundamental force in the evolution of animal reproduction. The earliest prediction of sperm competition theory was that sperm competition selected for the evolution of numerous, tiny sperm, and that this force maintained anisogamy . Here, we empirically test this prediction directly by using selective breeding to generate controlled and independent variance in sperm size and number traits in the cricket Gryllus bimaculatus. We find that sperm size and number are male specific and vary independently and significantly. We can therefore noninvasively screen individuals and then run sperm competition experiments between males that differ specifically in sperm size and number traits. Paternity success across 77 two-male sperm competitions (each running over 30-day oviposition periods) shows that males producing both relatively small sperm and relatively numerous sperm win competitions for fertilization. Decreased sperm size and increased sperm number both independently predicted sperm precedence. Our findings provide direct experimental support for the theory that sperm competition selects for maximal numbers of miniaturized sperm. However, our study does not explain why G. bimaculatus sperm length persists naturally at ∼1 mm; we discuss possibilities for this sperm size maintenance.
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