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Blight
Social climber
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Oct 25, 2006 - 04:57am PT
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Aya, interesting posts.
Re: the Ara experiments: I can find nothing in any of the studies whih conclusively states that it was the new mutations which enabled the e.coli to adapt to temperature changes - that no e.coli was able to do this before. In fact, you said yourself that e.coli already have adaptaions which allow them to survive large temperature variations. Nor is there anything to indicate that the less able population didn't just progressively lose the ability.
In fact, all the studies I read (9) openly admitted that they didn't bother sequencing the end populations, nor did they examine the sustainability of the mutations.
This is a little unfair to the scientists in question though, since they weren't testing these hypotheses. Fascinating work though and remarkably rigorous, thanks so much for pointing me to it.
As for Barry Hall's work, I'm familiar with it. While it's controversial for a number of reasons, in the converstaion we're having it's just not very relevant: the hydrolysis of lactose is not a new function. It already exists.
As I've said before, any type of evolution depends on the idea that completely new functions, organs and limbs can spontaneously develop. Neither of the experiments you cited demonstrates this.
Thanks for your efforts though!
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raymond phule
climber
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Oct 25, 2006 - 05:28am PT
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"As I've said before, any type of evolution depends on the idea that completely new functions, organs and limbs can spontaneously develop."
I am not sure what you mean with your sentence. Is your meaning the same as in the sentence below?
As I've said before, any type of evolution depends on the idea that completely new functions, organs (like liver) and limbs (like wings) can spontaneously develop by a single mutation for an animal that didn't even have something similar before.
Have I understood you correctly?
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Blight
Social climber
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Oct 25, 2006 - 05:52am PT
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"As I've said before, any type of evolution depends on the idea that completely new functions, organs (like liver) and limbs (like wings) can spontaneously develop by a single mutation for an animal that didn't even have something similar before"
That's not how evolution works, Raymond.
Single mutations don't produce new organs and limbs for the simple reason that complex structures require large numbers of genes.
So such a structure would require many mutations to produce new genetic material, and would only appear after at least that number of generations.
This is pretty basic stuff, I'm sure you could find a web site to learn these fundamentals from if you're still confused.
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cintune
climber
Penn's Woods
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Oct 25, 2006 - 06:48am PT
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Hush, Blight, let the grownups talk.
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Blight
Social climber
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Oct 25, 2006 - 07:11am PT
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You really are deeply uncomfortable with anyone asking qeustions about science, aren't you cintune?
I'd have thought that if you were really sure about your beliefs, you'd be a little less insecure about them.
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raymond phule
climber
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Oct 25, 2006 - 08:35am PT
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Blight, isn't this the experiment you have been looking for
http://en.wikipedia.org/wiki/Luria-Delbruck_experiment
Seems to agree with all your 3 points below.
"1. Mutations are not new genetic material. They are replications of existing material. As an example, you can create a fly with 3 eyes. But that's not a new organ; flies already have eyes.
2. Changes need to be sustainable. In all cases to date, mutations either lead to sterility or they simply disappear.]
3. Changes must be net positive, and possible without interference."
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TradIsGood
Fun-loving climber
the Gunks end of the country
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Oct 25, 2006 - 08:47am PT
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"It's exactly as eeyonkee says, however: Darwin was concerned with the development of new species and was looking for an explanation. The explanation he came up with was natural selection."
Whether or not he was looking for an explanation, it seems to me that he did not really find one. See below
"Natural selection is an example of one evolutionary process. It is essentially the non-random difference in the rate of survival/reproduction of organisms. Certainly there are other evolutionary processes, and these processes can contribute to speciation as well."
My problem is that the theory seems at best to attempt to explain changes in phenotype populations. Unfortunately the explanation ends up seeming a bit circular. It basically boils down to an argument that the phenotypes that compete most effectively in the environment are those that procreate the most prolifically. So phenotype populations vary over time and that is caused by a differential in the rate of reproduction. Sure, there are examples, that are individually cataloged where advantages with respect to capturing food, avioding becoming food, and higher fertility offer the "competitive advantages". But in the end the theory basically really is a circular or tautological proposition.
Beyond that, however, we need to decide whether Darwin actually proposed a method relating to changes in the number of species in particular and not just phenotype population changes. I would hold that he has no prescription for the development of new species at all. The nice part of that is that it is not in conflict with any fundamentalist issues. In particular, since no mechanism for changes in species is advanced, there really is no support for the thesis that man ever existed in any other form (from Darwin's results - not paleontological records.)
To be sure, more modern work has examined extensively the chemistry and role of genes. But if we exclude this from the Darwin Evolutionary Model (it came significantly later), the model remains a conundrum. It leaves one making hand-waving post hoc arguments about populations in a chaotic ecological universe. See, for example, the discussion of viruses above.
Allowing in modern developments in understanding of genetics is key. Suppose we do that. And further, let us suppose that the genetic trees mentioned above do imply special change, i.e. that modern species did in fact evolve over time from entirely different species. Geneticists can very readily make statistical inferences about the development based on the "distance" (size of the differences) between one species and another. They can even show the evolution of "races" or phenotypical changes of a species in many cases.
Now the problem facing us is to demonstrate that such changes are plausible in the time frames suggested by the data. Doing this is the really and truly interesting science. And it is the one key test of the theory. It is one thing to speculate that species A evolved from species B based on the same number of chromosomes but different DNA sequences. It is another thing entirely to propose a mechanism that allows for the change in the required amount of time allowing for the stochastic processes involved. In other words, there needs to be an explanation for the development of a new genetic sequence (mutations, and other mechanisms) that is biologically and chemically supportable and physically probable enough to occur in the time required.
In short, I think the theory is a nice start, but the mechanisms of change are not well understood even today. To me, The Selfish Gene just does not cut the mustard, but is simply a fancy way of saying the same thing that Darwin said - which is not to say that he was wrong - but simply saying again, that he did not find anything that explains the "origin of species".
This book has been around awhile, though not as long as the Selfish Gene. It does attempt to explain research into how species evolved and suggests that biologists today may be too specialized to find the answers!
Margulis, Lynn and Dorion Sagan, 2002, Acquiring Genomes: A Theory of the Origins of Species, Perseus Books Group, ISBN 0-465-04391-7
Are they right? Don't ask me. But it is more thought provoking IMO than Darwin or Dawkins. And it seems to address the question that everybody really is trying to understand, i.e. whether and how these evolutionary trees occured. :-)
60 posts or so...
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Blight
Social climber
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Oct 25, 2006 - 10:04am PT
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"Blight, isn't this the experiment you have been looking for"
No, but thanks for looking it up.
This experiment fails to meet the first criterion: that mutations should create new traits or structures. Viral resistance is not a new trait.
It is however an excellent illustration of how natural selection works on mutations, which is why they won the prize for it.
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eeyonkee
Trad climber
Golden, CO
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Oct 25, 2006 - 10:06am PT
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The Selfish Gene just does not cut the mustard, but is simply a fancy way of saying the same thing that Darwin said..
I would heartily disagree with this statement. The focus on the fitness of the gene as compared to the fitness of the organism is a big one and has lots of rather subtle ramifications. Also, I think that speciation is well-enough understood. One way in which you could undoubtedly create two species out of one is to suddenly transport some members of a parent population to another part of the world, completely cut off from the first. After some tens of thousands of years, those (now) two populations will have changed sufficiently that they will not be able to interbreed and they will be two separate species. This exact thing has happened several times in the past because - the most obvious following the break-up of large continental masses such as the breakup of Pangea and Laurasia/Gondwanaland etc. This is not the only was to form new species, but some sort of geographic isolation in addition to a bottleneck in the total genome of the soon-to-be new species will almost always play a part.
Here's a great snippet from Dawkin's "River Out of Eden"
(Starts off with a quote from a physicist) Peit Hein captures the classically pristine world of physics. But when the ricochets of atomic billiard balls chance to put together an object that has a certain, seemingly innocent property, something momentous happens in the universe. That property is the ability to self-replicate; that is, the object is able to use the surrounding materials to make exact copies of itself, including replicas of such minor flaws in copying as usually arise. What will follow from this singular occurrence, anywhere in the universe, is Darwinian selection and hence the baroque extravaganza that, on this planet we call life. Never were so many facts explained by so few assumptions. Not only does the Darwinian theory command superabundant power to explain, its economy in doing so has a sinewy elegance, a poetic beauty that outclasses even the most haunting of the world's origin myths.
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raymond phule
climber
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Oct 25, 2006 - 10:09am PT
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One thing that is clear from this thread is that no expert on evolution participate in the discussion.
It makes it on some what the same level as mountain mans global warming threads. The opinion of someone with no knoweledge on the subject is not very interesting. Many people here know much more than MM but the idea is the same.
It can be fun to discuss a theory but that a couple of laymen should decide if a theory is correct or not is kind of ridiculous.
I dont even think that hardcore IE people from the discovery institut like Behe agree with Blight's criticism. They try to convience people by going even further into microbiology where very few people have any knoweledge. The propaganda method seems to be that the people they want to convience dont understand the arguments. Then is it just word against word about who is right and it doesn't seem to be that difficult to make people belive in lies if both sides say that they are correct. Look at the current US admininstration for an example.
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cintune
climber
Penn's Woods
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Oct 25, 2006 - 10:09am PT
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"You really are deeply uncomfortable with anyone asking qeustions about science, aren't you cintune?
I'd have thought that if you were really sure about your beliefs, you'd be a little less insecure about them."
 Settle down, laddie. Go play with your imaginary friend.
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raymond phule
climber
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Oct 25, 2006 - 10:14am PT
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"Viral resistance is not a new trait."
Ok, what is a trait for a bacteria?
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 10:33am PT
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Blight, if you've actually read the studies and looked at the data in the Bennett et al studies, you'll see that it is very evident that the ability to survive at novel temperatures increased over generations (rather than being progressively lost).
E. coli are able to survive at wide temperatures, yes. However, with each successive generation, they were able to survive better than the previous ones. How do you explain this, if you dismiss the idea that mutations arose in the bacteria's genome that allowed it to live better at these new temperature regimes? Please keep in mind that the bacteria were originally all identical.
Also, if you want to say that the old populations progressively lost the ability to live at higher temperatures (you'll need to explain how this would work a little better, since the original populations were frozen, so did not change, while the other populations were growing in the new environments).
Finally, and most to the point, they most certainly did sequence the genomes of these bacteria, and found multiple mutation events - so I'm not sure which studies you read? Here is a link to one of their studies which is available online. Several of these gene duplication events were coincident with statistically significant increases in fitness. Again, how would you explain this result?
I suppose that you might dismiss these results because the mutation events they found were replications and deletions, rather than the spontaneous appearance of completely new DNA sequences - which is the "proof" (please recall that there is no such thing as absolute proof in science) you requested. Yes or no?
Re: Barry Hall. The point in that case is that the E. coli he started with could not hydrolyze lactose. "It already exists" is true - but not of the cells he was studying.
The lactose matabolism pathway that these cells evolved was completely novel - i.e. it did not exist in the original cells, nor does it exist in other E. coli that are able to metabolize lactose (via a different pathway).
There are plenty of other examples, of course, such as the mutations in certain Flavobacterium and Pseudomonas strains which allow the production of enzymes which degrade nylon. Nylon is a manmade substance, the bacteria are not normally able to digest it. The mutation (it's been sequenced) that arose allowed them to utilize nylon as a food source. This was a new gene sequence that coded for a new protein that allowed the digestion of a new food source. Here is a link to one of the papers showing the results of sequencing the mutation.
There are lots of other examples of bacteria with mutations that allow the digestion of new, manmade compounds. Quick google searches will yield these.
Please explain how these studies don't show the development of new processes via mutations?
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eeyonkee
Trad climber
Golden, CO
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Oct 25, 2006 - 10:44am PT
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I'm curious, Raymond, what's your background?
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 10:48am PT
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Now, regarding Lynn Margulis: she first states that Darwin's theory is essentially a tautology - google is great because you don't have to write stuff yourself! I found this page talking about that statement.
The rest of it basically seems to suggest that what Darwin proposed is useless as a mechanism for speciation because he did not know about genes, mutation, etc. That's a rather silly statement, really - and I suppose she mostly makes it because the rest of that book probably goes on to try to support her endosymbiosis theory?
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Blight
Social climber
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Oct 25, 2006 - 11:13am PT
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Aya, what you've posted certainly looks more convincing. I appreciate your hard work, I guess this is using up almost as much of your time as mine!
However, I still have the same problem with what you've posted: if completely new traits and structures can emerge, why do all the experiments referenced just deal with existing ones?
The ability to survive temperature variations, metabolize lactose, or to produce enzymes, is not new. It's been seen before. Even the abstract of the nylon-eating bugs paper states that it's a preexisting sequence.
This goes all the way back to what I first asked for: evidence of the development of a new trait or structure in an existing species. I don't think any of what you've posted demonstrates that, and without that process, there can be no evolution.
And one more time: I'm not saying evolution is wrong. I'm saying that I think our understanding of it is wrong. I'm not a creationist, or an ID proponent. I'm just someone who doesn't swallow what I don't properly understand without questioning it.
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Aya
Uncategorizable climber
New York
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Oct 25, 2006 - 11:21am PT
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What you're essentially saying, then, is that cats were to suddenly evolve horns, that would not be evolution because cows have horns?
The mutations were new.
The nylon mutation was created by a frameshift mutation. The previous sequence was moved over, and suddenly encoded for new proteins. How the new sequence emerges (insertion, replication, deletion, frameshift, etc.) is irrelevant: the fact of the matter is that it is now a new sequence that codes for new proteins.
If you cannot see this, then once again, your dismissal of evolution is essentially irrelevant because you aren't undserstanding its underlying mechanisms .
As for time: it's time I would have spent this morning having a leisurely breakfast and watching Charmed and ER on TNT. My guilty pleasure shows. Instead, I watched Charmed and ER, had a leisurely breakfast, and got to root around my brain for all the crap I shoved in there when I took prelims... of course, now, I should probably go to the library to see if I can't cram some organic chemistry in there.
You still have not answered my questions.
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raymond phule
climber
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Oct 25, 2006 - 11:32am PT
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"I'm curious, Raymond, what's your background?"
I am PhD student in engineering. I have read a couple of Dawkings books and a couple of other "popular" science books.
I have very limited knowledge about biology though.
I consider the way people think about creation/evolution, religion, global warming, politics etc interesting. The use of propaganda and how it effect people. There are no problem to found people on both sides with some kind of PhD saying that the other side is incorrect.
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Blight
Social climber
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Oct 25, 2006 - 11:34am PT
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"What you're essentially saying, then, is that cats were to suddenly evolve horns, that would not be evolution because cows have horns?"
Er, I think that would bring problems of its own.
The nylon mutation was created by a frameshift mutation. The previous sequence was moved over, and suddenly encoded for new proteins. How the new sequence emerges (insertion, replication, deletion, frameshift, etc.) is irrelevant: the fact of the matter is that it is now a new sequence that codes for new proteins.
It's very relevant, and I think that dismissing any part of the process as "irrelevant" smacks of not wanting it looked at too closely.
The ability of that sequence to encode for different proteins already existed, in fact that's what it does (and always did). It was not new.
If you cannot see this, then once again, your dismissal of evolution is essentially irrelevant because you aren't undserstanding its underlying mechanisms
So unless i agree with you I must be wrong? Oh well, I can live with you thinking that. Please don't waste any more time on me.
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