I certainly don't want to imply that I'm a biologist or by any means an expert, but I have seen a lot of examples (especially on/.) of people who clearly haven't done the work to chase down the relevant information before claiming that an entire field of science has done inadequate work. I'm afraid I've misinterpreted your efforts. I'm sorry about coming on as strong as I did.
You're exactly right, there are a lot of trolls and opinionated posters who don't do their homework. A lot more people would just drop this thread rather than admit they misinterpreted something. It says a lot about you that you didn't do that. Thanks.
Agreed. What I was seeing before is that to call something a "new gene" you seem to want it to appear all at once rather than adding to some existing (atlhough possibly not active) DNA. I think that we disagree here, since mutations can certainly be additive and must necessarily make use of (or rather, become part of) the DNA that's alredy there.
Actually, this is something that you have helped me to clarify. I was drawing a distinction between shuffling/transposition and "true mutation". Now I realize that my definition was wrong. Genetic changes are mutations. Period.
OK, if we did acquire the genes elsewhere, then that is certainly an alternative possibility to the idea that the accumulation of minor changes didn't do it. That would support an alternate theory, but I don't see how it casts too much doubt on mutation as a source of variation.
Looking back, I probably overstated this, but the point is still somewhat valid.
Do you have any idea how many times the old "start with a colony of clones that lack antibiotic resistence and watch antibiotic resistence emerge" experiment has been done?
I can't seem to find these papers. I found this one:
Science is not really equipped to study origins because the various underlying assumptions that are made cannot be proven by any repeatable experiment, but can only be assigned probabilities.
Also true of religion...well, except that religion doesn't even have the ability to assign probabilities.
The "mutation" you refer to is not necessarily the generation of new genetic code, but can very easily be the expression of existing code that wasn't active before.
You said:
That sort of implies that you had done some actual reading about the mutations I referred to. It's fairly clear that you haven't and you're dismissing the idea out of hand because you think that they could "very easily be" something else. So, the question again is, did you read the relevant material to see if they discussed the possibility, or are you assuming that you're the only person who had considered it?
"We have not yet determined the molecular events responsible for the genomic changes detected in our study. However, three lines of evidence suggest that they are mostly due to IS transposition and other types of chromosomal rearrangement."
Also:
"Finally, we observed significant changes in the copy number of certain IS elements (Table 2); these changes are most easily explained by transposition and deletion events that produce gains and losses of copies, respectively."
I'd say that those conclusions support my point. Yes, these are forms of mutation, but they are not generating new, novel functions, they are just copying and modifying existing functions. Microevolution, in other words. That's what I was trying to point out.
You've just proved my point for me. What you claim is impossible is _precisely_ what happens every time some germ develops immunity to a particular antibiotic
Let's be precise, please. I didn't claim anything was impossible. I made a statement, apparently too broad, that we cannot show that mutations lead to working genes. I stipulate that what you are talking about does, in fact, happen. What I was trying to point out is that broad new functionalities ("new genes" in my earlier statement) do not seem to appear in our genome based on mutations, but instead appear to come from transposition.
That is true of course, but what we consider a miracle today may not be tomorrow.
I saw someone's sig and it seems to fit here: "Any sufficiently advanced technology is indistinguishable from a rigged demo."
You haven't said anything in this post that I disagree with, but them's the rules. Everything starts with assumptions. If you can prove the assumptions wrong, you win. That's just the way science works.
Hmmmm... no I don't think that paper has a lot to do with my original point.
OK. You have made two reading recomendations for me then. The first was related to a talk.origins archive.
I think that all of this still goes back to a more fundamental misunderstanding on your part as to what constitutes a "new gene."
I don't disagree with you on the definition of a new gene.
That sort of implies that you had done some actual reading about the mutations I referred to. It's fairly clear that you haven't and you're dismissing the idea out of hand because you think that they could "very easily be" something else. So, the question again is, did you read the relevant material to see if they discussed the possibility, or are you assuming that you're the only person who had considered it?
First, I'm not dismissing anything. What I am doing is drawing a distinction. More about that later. I am constantly reading about this subject and trying to make sense of what I read. Have I read the papers you are talking about? I don't know. The one concrete reference you made, I haven't yet found. I stipulate that you are more knowledgeable about the subject than I am, and there simply isn't enough time for me to reach your level of knowledge before having this discussion. So we either have to accept that you can throw more specifics and continue the discussion anyway, or we can end it. Discussing this with you is a helping me to think through my positions. I am obviously in a position of ignorance compared to you. I still think that I have something valid to say. It doesn't appear that you agree.
Let me start with some things we both might agree on.
- A mutation is a change in a genetic sequence
- Evolution posits that mutations accumulate over time leading from a lack of genetic diversity to the genetic diversity we see around us
- For example, the chimp/human precursor accumulated enough different changes to divide into the two different species
Agreed?
My issue with evolution, and what I consider to be a weakness, is that while it is clear that these small changes (mutations) occur, it is not clear to me that they lead to new species. Yes, it's the old micro-evolution vs macro-evolution question. Mutations occur, but significant mutations, especially in higher plants and animals, are negative. Yes, I have considered the vast stretches of time involved, but it appears that all the mutations we have genetic evidence of (I know you'll feel free to correct me if I'm wrong!) are of the minor variety.
Let's return to the human/chimp divergence. If "we are our viruses" (Lynn Margulis, google it), then the accumulation of minor changes is not what made us human. We apparently received the genes that differentiate us from the chimps fully formed from somewhere else. I AM NOT SAYING THAT GOD DID IT!!!! I'm simply saying that it doesn't fit the accumulated minor changes model. To me this opens up the POSSIBILITY of intelligent design.
I'm enjoying this discussion and am learning from it. If you want to continue, great. If not, that's OK, too.
Actually, yes! Notice I didn't say that God doesn't exist, just that the study of God is religion, not science. And yes, there is a difference. Conjecture, backed up by the best evidence we can find, is what science is about. If you wish to study religion, go to it. If you want to study science, you have to give up miracles as an explanation.
I'm not sure what you're trying to say here, though. Does swapping of DNA across organisms somehow support ID? Maybe that's how the Designer is shining His Wisdom down onto us...
It is my point that swapping DNA across organisms weakens the strength of the evolution argument, especially when it occurs in eukaryotes. If, in fact, "we are our viruses", then we did not "evolve" new functions through random chance mutation. We received them, already working, from some other organism. If this is a common mechanism, as it seems to be, where did the original, functional genes come from?
This swapping negates, for example, the statement that an eye is so useful that it evolved 40 different times (Richard Dawkins). It was not necessary for any particular type of eye to "evolve" multiple times thereby proving that evolution works in parallel lines. It was merely necessary for the genes to exist and then get moved around by viruses to multiple organisms. It seems to me that the evolution argument is weak on this point, leaving open the possibility of a scientific intelligent design argument. I don't reject evolution, but I am willing to consider that it has weak points.
Do you have any idea how many times the old "start with a colony of clones that lack antibiotic resistence and watch antibiotic resistence emerge" experiment has been done? This is not new stuff. It's DECADES old. In a colony of clones, the only way for funny DNA sequences to show up is mutation.
As with your example of nylon metabolizing organisms, these involve minor changes to existing genes or the turning on or off of existing genes, not the creation of novel, working genes. I accept your statement as it stands, but a colony of clones can very easily contain unexpressed genes. The "mutation" you refer to is not necessarily the generation of new genetic code, but can very easily be the expression of existing code that wasn't active before. Genes are turned on and off regularly. That does not seem to meet my requirement of "generating a new gene".
Usually when somebody says, "No experiments have been done to demonstrate [insert fairly well accepted phenomenon]" it means that they haven't actually looked through the literature and they're repeating something that somebody else said
No, I'm not a working scientist, so everything I say is a repeat of something that I heard or read, or a logical extension of same. I consider myself to be a fairly well-read non-pro.
It could also be that there is one eternal, transcendent, intelligent being, GOD, who is self existent and is outside of all universes, including the one we are in. Why is it, strangely, the this "could be" is the one most disliked or fought against and why should this idea of GOD cause so much controversy?
Simple, because it is BORING as a scientific theory. What is there to study? God did it. That's religion, not science.
Life is way too complex for it to arise from random combinations and random circumstances thus it must have a designer. By ID's own arguments and reasoning, a creator/designer creating complex creatures like us must be also irreductibly complex.
Another form of life that we are not familiar with could have designed us. That form of life may not be irreducibly complex. If you hold that there has been time since the formation of Earth for us to evolve, you must agree that there has been time since the formation of the Universe for other forms of life to evolve. I don't buy into the ID/Creationist irreducible complexity nonsense, but your argument does not hold water.
Try postiting some sort of test for ID. If you can pull that off, we'll start thinking about calling it science.
Here's a simple test that will make Intelligent Design(the creationist stalking horse) and intelligent design (the scientific idea that maybe, just maybe, random chance isn't the driving force behind the creation of new genes) irrelevant:
A demonstration of random chance mutation generating a new gene under lab conditions, either in biological or artificial life.
As far as I can tell, we have never seen this. Our studies of the genome suggest that most adaptation takes plaace because of gene swapping, not because of random chance mutation. Try googling this quote by Lynn Margulis, "we are our viruses".
Artificial life research (computer simulations) always seems to start with good genes and then demonstrate that natural selection works to find good combinations of those genes, but, so far, no experiments that show the generation of new, working genes. Where do the working genes come from? I know that evolution says they have been generated out of millions of years of mutations being tested by natural selection. Showing this in action would, for me, make the idea of intelligent design unnecessary
None of them are well reasoned. They aren't science (they aren't falsifiable), they're bad theology (god of the gaps), and the proponents of all forms of ID lie, obfuscate and distort facts on a reular basis.
I can't agree with your statement. I accept a form of intelligent design (note the lower case) that does not require me to lie or distort facts. I believe that evolution's most serious weakness is that we have never been able to show that it is possible for mutations to lead to working genes. Yes, existing genes can be modified randomly to have slightly different functions, but I have a hard time accepting that all the genetic diversity we see around us comes from random chance mutation. If this is possible, why haven't experiments in computer code led to working code from random changes? A randomly generated series of characters will not compile into working code if the set of possible instructions includes many bad (non-working) possibilities. Artificial life research (it seems to me) always starts with a set of working instructions and goes on to prove that natural selection will select for the most appropriate combinations over time. Well, yes, but in the real world we have to deal with non-working instructions (bad mutations) being the norm rather than the exception.
Because of this, I accept that it is possible that some intelligent tinkering with our genome may have happened. Look how quickly we have gone from not even knowing about DNA to being able to manipulate genes. This proves that intelligent design of genetic structures is possible. We now know that much genetic variation among species on our planet comes from genes being swapped among organisms rather than by random chance mutation generating new genes. It appears that we may represent a pre-existing library of working genes and natural selection is responsible for finding working combinations. Is this theory falsifiable? Yes, all that is necessary is for experiments to show random chance mutations generating new, functional genes, either in living specimens or in artificial life. So far, I am not aware of that being shown. Almost all true mutations kill their recipients.
Please note that none of this argument requires "god of the gaps" or even religious arguments at all. Where did the pre-existing genes come from? I don't know, but I think that this is a resonable interpretation that doesn't require a series of mathematical miracles.
A good scientist will not let his beliefs get in the way of finding Truth. Should the newfound Truth disagree with what he believed, a true scientist would adjust those beliefs. Just as the religious majority was in time forced to acknowledge that the earth revolves around the sun.
Well said. I personally don't believe that you can scientifically describe the religious impulse, wherever it may come from.
I am a religious person (Christian, if you must know), but I still believe in a universe ruled by the laws of physics. My God is capable of violating them, but that's not my business. I can't violate them and to say "This is a miracle" is ultimately boring from a scientific perspective. My religion and my science are simply not related to each other. When they seem to conflict, I usually find that it is because I am applying the rules of one in the domain of the other. The Bible is a religious document, Principia Mathematica is scientific one.
Quoth Albert Einstein (again): "God does not play dice".
And it turns out ol' Albert was wrong. When you look at the universe at a quantum level, it is not deterministic, chance is involved, God does "play dice", figuratively speaking.
With all that said, there are still some problems with evolution, but that's another thread.
Not that it affects your point much, but if we get "out there" there will be a whole lot of places to look for bacteria. So many that ruling it out by exploration alone would be impossible. What if it was just one asteroid/whatever that came from a galaxy far, far away but its bacteria only came to Earth and deposited life nowhere else on the way? Then we'd have to get to that galaxy to prove it.
That is a good point. My assumption has been that if something like that were to happen, it would, of necessity, be a large-scale endeavor. But, yes, you are correct, we could find no bacteria and still not be able to completely rule out the possibility. Of course, extraordinary claims require extraordinary proof. So, for me, if we don't find bacteria easily, panspermia is mostly invalidated.
So, if we manage to figure out how to design a memetic framework that prevents us from going at eachother's throats physically, and convince the rest of the world to adopt that framework, then there may be some hope of near term contact
I'm guessing peace through superior firepower wouldn't fit the bill, eh? Honestly, I don't see much hope for this type of advance. The human race is violent and almost all attempts so far to meet aggression with peace have ended in disaster for the peaceful side. Alien intelligence farmers or not, I think we are pretty much stuck with the memes we carry now. Whatever the next step up on the evolutionary (or memetic) ladder** is, isolation would seem to be needed for it to gestate. With the "global village" we live in now, extraplanetary colonies would seem, to me, to be necessary before any serious "advance" could be made, either at the genetic or memetic level.
Nah I didn't call you an idiot, I said the statement was idiotic.
Yeah, I was baiting you a little to see if you would call me on it. I read your other post and it is interesting. Certainly speculative, but who's to say no? I've heard some speculation about periodicity in mass extinctions. But, as always, is it falsifiable? We'll know in a 100 million years or so.
As I've said in other posts, my favorite speculation about panspermia involves the creation of a library of useful genes, installed into hardy bacteria with some viruses to shuffle things around and launched into the cosmos. Once the bacteria established a beach-head on a likely planet, the shuffling of genes would generate complexity that would look a lot like !evolution!. Any intelligent descendants would be hard pressed to find proof one way or the other.
No more than I can prove evolution, because my background and field of knowledge is not in paleozoology, but I maybe can make a reasonable case.
Exactly. And it is a very reasonable case. I believe that even someone whose background is paleozoology could not prove it. They might be able to make an even more reasonable case. The history of science is littered with reasonable cases that later turned out to be incomplete or just not true. They were reasonable, but they failed when tested. Yes, I know, evolution has not failed any major test so far, but the big test, recreation of the process in lab or computer simulation has not been completed yet either.
However, even the most primitive single-celled deep trench life found so far still exhibits fairly complex genetic material.
A fact that was not predicted by Darwinian evolution. This doesn't invalidate evolution, but it does point out another weakness.
I was going to let this one go, but I can't, I just can't.
Heck, even the simplest cells we can study are the product of billions of years of evolution (Can you prove this? Phylomon) ...because anything more primitive probably has been completely obliterated through obsolence.
In this statement you are arguing from your assumptions. Since you start with the assumption that evolution has produced everything, you argue that evolution is too complex to understand easily. This, then, explains the lack of success in reproducing this part of evolution in the lab or computer. This is EXACTLY the same type of argument that the ID supporters make. They start from the assumption that God created everything and then argue that anything that can't be easily explained must be proof of God's existence. Both arguments are fallacies in this context. I am only disagreeing with the way you argue this point, not the validity of your assessment.
Please understand that I am enjoying this discussion. I hope you are, too. I do not intend to insult your beliefs or intelligence. If I've done so, please accept my apologies.
Up until the point where you called me an idiot I was enjoying what you said. If you are going to refer to my other posts, please try to be fair and not selectively quote. In almost all of my posts I have pointed out that Intelligent (ID) obviously pseudo-science.
Actually you have done no such thing. You have admitted in another post that direct genetic manipulation by humans has not resulted in the creation of new genes, just the manipulation of existing genes (usually by taking them from one species and inserting them in another).
This is a good point. Let me be more clear. In the short period of time that we as humans have been using the scientific method, we have gotten to the point of manipulating genes. I believe this proves that intelligent manipulation of genomes is possible, since we are already starting to do it ourselves. If something can be shown to be possible, that is a point in its favor, scientifically.
Actually there have been some examples of de-novo protein design for pharmaceutical use, but those have not been inserted into a species' genome to make it more successful in the wild (only for reproducing bacteria in pharmaceutical labs to produce the new proteins as drugs).
Thank you, you make my point for me. We are performing genetic modifications, thereby proving it to be possible.
To go from that to claiming that intelligent design explains the creation of complex structures like the mammalian eye is even more of a leap of faith than current expectations that evolution did the same. As far as I can tell that means that ID has no more supporting evidence about the possibility of intelligent creation of new genes supplementing evolution than Darwinian evolution does.
You are absolutely right. That is why I made no such assertion. I simply pointed out that being able to manipulate genes proves that genetic manipulation is possible. Let me say again, I think ID as it is being pushed by the religious right is garbage. But that does not change the fact that intelligent tinkering with genomes is possible and may have occurred. To say this does not make me a zealot, merely a realist.
As for simulations of artificial life and the demonstration of spontaneous creation of new genes through random mutation: We certainly don't understand fully how genes are expressed in complex cells, let alone multicelllar organisms, and until we do the accelerated simulation of evolution is not really possible.
Again, you make my point for me, Thank you. We cannot, at this time, prove that random chance mutation can produce working genes. Not in the lab, not in computer simulations. This is the major weakness of evolution as a theory. Notice, I never said it was wrong. I just said that we can't prove it to be possible, let alone prove that it was, in fact, the mechanism providing genetic diversity. I agree, it probably was. But it is not yet demonstrated.
However, assuming the next few generations of scientists don't have their analytical faculties damaged by intelligent design zealots or their research funding politically denied by similar fundamentalist religious zealots in political office, the days where you can make idiotic statements like the quote above are numbered.
I agree fully. I think, however, that to overreact, as you have done by calling my statements idiotic, is also a bad thing. Open-mindedness is important. ID zealots are pushing a political agenda, no question about it. But to insist that one must not criticize or point out weaknesses of evolution because of the ID zealots is harmful as well. There are other scientific alternatives.
Not irrelevant and not incorrect. You'll notice I didn't use the word "scientists", I said science oriented individuals. And I notice that you did not answer the question. So, let me ask again. What scientific evidence would it take for you to be convinced that evolution had been falsified? If something irreducibly complex were found, would you then be convinced? Would it take a message encoded into the genome from some Progenitor race? Would evidence of bacteria raining down from outer space convince you? I'm not asking you to abandon your scientific principles, just to fantasize a little. Or, perhaps, to admit the there is not much chance that you could ever be convinced that evolution had been falsified.
All scientific theories are falsifiable, so at least some thought went into how they could be falsified. Evolution is considered to be a fairly reliable theory because it has managed to not be falsified so many times. Since you cannot know what it is that you do not know, evolution is evaluated every time new evidence is found. So far, no new evidence has failed rationalization with the theory of evolution.
This is a fair enough statement, but it is tangential to the question. The question is a speculative one. What piece of evidence would convince you that evolution had been falsified?
What you see as verification is actually attempted falsification.
With all due respect, you seem to be making a lot of assumptions about what I think and see. And, to set the record straight, I am familiar with the scientific process.
There are weaknesses in evolution and the big one is that nobody has been able to prove that random chance mutation can generate functional genes. Yes, it's a reasonable assumption. Yes, the evidence seems to fit. But science is about reproducing results and, so far, nobody has reproduced that part of evolution. Not in the lab, not in computer simulations.
It's interesting. I don't really disagree with anything you say, but we seem to be coming to different conclusions. A couple of points:
From where do you get 500 years?
I was trying to encompass the industrial revolution, Mendel, Darwin plus a large fudge factor. Nothing magical about the number except that in that short period of time we have come so far. Even using your time period of tens of thousands of years, it's just not a very long period of time. And yet, here we are, modifying genomes. I think that proves the point that intelligent tinkering with genes is a very real possibility.
Your discussion of the plant pot made of legos is well-made. I think any disagreement we had on that has been cleared up. To summarize, we seem to agree that just about anything is possible, but it might take a very long time for it to happen. Agreed?
Whoa there, you're getting ahead of yourself. Who said anything about dumbing down the instruction set?
With all due respect, you did. You said:
If you consider a simple enough instruction set, it is easy to generate valid programs randomly. If every possible value for the order field represents a valid operation, then there can never be an invalid order and hence the validity of a program only depends upon it not producing an overflow condition
The genome is not a simple instruction set. My original point was that if I use a random character generator, I will not get working programs. Let me amplify this a little. I work with C# sometimes. I could set up my random character generator to create text output and then try to compile it as a C# program. While it is theoretically possible that someday I may get random output that compiles and does something useful, it is staggeringly unlikely.
What you proposed is that we create a simple instruction set in which every possible random string is a valid instruction. I would call that "dumbing down" the address space of possible instructions. I think my analogy is closer to the real world of DNA. There is a huge address space of possible strings of amino acids to be woven into a strand of DNA. Only a small set of them produces "working code" when "compiled" into proteins inside a cell. I don't disagree with your example, I just don't think it is close as mine to the real world that we are discussing.
Now you're just moving the goalposts closer and closer together.
Yes, I am. This is because I think there is a difference between using existing code and creating new code. This is the distinction that I am trying to illustrate. To continue with my C# example, if I create new programs by using existing objects or cutting and pasting other people's code, I am not creating new code, just remixing code that already exists and is known to work. While this can creat novel functionality, it is not the equivalent of writing code the old-fashioned way, from scratch; it does not create new strings of working code, just reshuffles the code that already exists.
With regards to the genome, we see what appears to be increasingly complex code throughout geological time. The question is, "Where did that new code come from?" So far, I have not seen convincing proof that random chance mutation, even across geological timeframes, can produce new, working code. Yes, it is a reasonable explanation, but it has not been proven to be possible.
At this point, most people I discuss this with throw up their hands and say, "You're here, aren't you? That proves that it must work." This is a logical fallacy. Existence of an object does not prove what method was used to create that object. Yes, random chance mutation may be the source of new, working DNA code. But, so far, nobody has actually been able to reproduce that process in the lab or on a computer without doing what you proposed (what I referred to as "dumbing down" the instruction set).
I want to say that I am enjoying this discussion and do not mean any disrespect of your beliefs and/or logic. If something I say comes across as dismissive or condescending, please forgive me in advance.
Finding his example with transponsons would still be pretty ugly for evolution, but as you indicate it could be explained as a freak transfer event for two reasons.
I'm not even sure that I would call it a freak transfer. According to Lynn Margulis, a prominent, main-stream bioligist, "Viruses today spread genes among bacteria and humans and other cells, as they always have... We are our viruses". She said this in a book written in 1998. For me, transposons of just about any stripe would not falsify evolution, with the following exception:
If you found the same viral DNA insertion in whales and in humans - and in fact found it inserted in precisely the same location - and it was absent in chimpanzees - that would be a huge problem for evolution. The insertion of the same viral DNA at the exact same location cannot reasonably be dissmissed as a random occurance, and finding multiple such examples would be overwhelming evidence.
That would, for me, be strong evidence of intelligent tampering with the genome. I don't expect to find that, though. IF we do someday find evidence of design, I think it will be along the lines of a genetic "terraforming package". A library of a lot of useful genes, with some viruses to shuffle them around, loaded into some hardy bacteria and seeded into the cosmos. I think this model has the potential to explain what we see around us without requiring a miracle and without completely invalidating evolution. This theory (panspermia) has the added benefit of being falsifiable. If we get out there and don't find bacteria, it obviously didn't happen that way.
You mentioned common descent. I'm not so sure, with what we now know about transposition, that common genetic descent is a requirement. We have already found strange bits of DNA where they have no right to be. Eukaryote genes in prokaryotes and the like. Chlamidia trachomatis, for example, contains more than 30 eukaryotic genes.
Slashdot Mirror
I certainly don't want to imply that I'm a biologist or by any means an expert, but I have seen a lot of examples (especially on /.) of people who clearly haven't done the work to chase down the relevant information before claiming that an entire field of science has done inadequate work. I'm afraid I've misinterpreted your efforts. I'm sorry about coming on as strong as I did.
You're exactly right, there are a lot of trolls and opinionated posters who don't do their homework. A lot more people would just drop this thread rather than admit they misinterpreted something. It says a lot about you that you didn't do that. Thanks.
Agreed. What I was seeing before is that to call something a "new gene" you seem to want it to appear all at once rather than adding to some existing (atlhough possibly not active) DNA. I think that we disagree here, since mutations can certainly be additive and must necessarily make use of (or rather, become part of) the DNA that's alredy there.
Actually, this is something that you have helped me to clarify. I was drawing a distinction between shuffling/transposition and "true mutation". Now I realize that my definition was wrong. Genetic changes are mutations. Period.
OK, if we did acquire the genes elsewhere, then that is certainly an alternative possibility to the idea that the accumulation of minor changes didn't do it. That would support an alternate theory, but I don't see how it casts too much doubt on mutation as a source of variation.
Looking back, I probably overstated this, but the point is still somewhat valid.
Do you have any idea how many times the old "start with a colony of clones that lack antibiotic resistence and watch antibiotic resistence emerge" experiment has been done?
m axtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=g enomic+evolution+antibiotic&searchid=1138477885820 _2558&FIRSTINDEX=0&journalcode=pnas
I can't seem to find these papers. I found this one:
http://www.pnas.org/cgi/content/full/100/17/9658?
But it seems to say that the antibiotic resistance was already there, only not being selected for.
Science is not really equipped to study origins because the various underlying assumptions that are made cannot be proven by any repeatable experiment, but can only be assigned probabilities.
Also true of religion...well, except that religion doesn't even have the ability to assign probabilities.
I said:
The "mutation" you refer to is not necessarily the generation of new genetic code, but can very easily be the expression of existing code that wasn't active before.
You said:
That sort of implies that you had done some actual reading about the mutations I referred to. It's fairly clear that you haven't and you're dismissing the idea out of hand because you think that they could "very easily be" something else. So, the question again is, did you read the relevant material to see if they discussed the possibility, or are you assuming that you're the only person who had considered it?
I direct your attention to this paper http://www.pnas.org/cgi/content/full/96/7/3807 , a study of 10,000 generations of E.coli in which Papadopoulos, et al, conclude:
"We have not yet determined the molecular events responsible for the genomic changes detected in our study. However, three lines of evidence suggest that they are mostly due to IS transposition and other types of chromosomal rearrangement."
Also:
"Finally, we observed significant changes in the copy number of certain IS elements (Table 2); these changes are most easily explained by transposition and deletion events that produce gains and losses of copies, respectively."
I'd say that those conclusions support my point. Yes, these are forms of mutation, but they are not generating new, novel functions, they are just copying and modifying existing functions. Microevolution, in other words. That's what I was trying to point out.
You've just proved my point for me. What you claim is impossible is _precisely_ what happens every time some germ develops immunity to a particular antibiotic
Let's be precise, please. I didn't claim anything was impossible. I made a statement, apparently too broad, that we cannot show that mutations lead to working genes. I stipulate that what you are talking about does, in fact, happen. What I was trying to point out is that broad new functionalities ("new genes" in my earlier statement) do not seem to appear in our genome based on mutations, but instead appear to come from transposition.
That is true of course, but what we consider a miracle today may not be tomorrow.
I saw someone's sig and it seems to fit here: "Any sufficiently advanced technology is indistinguishable from a rigged demo."
You haven't said anything in this post that I disagree with, but them's the rules. Everything starts with assumptions. If you can prove the assumptions wrong, you win. That's just the way science works.
Hmmmm... no I don't think that paper has a lot to do with my original point.
OK. You have made two reading recomendations for me then. The first was related to a talk.origins archive.
I think that all of this still goes back to a more fundamental misunderstanding on your part as to what constitutes a "new gene."
I don't disagree with you on the definition of a new gene.
That sort of implies that you had done some actual reading about the mutations I referred to. It's fairly clear that you haven't and you're dismissing the idea out of hand because you think that they could "very easily be" something else. So, the question again is, did you read the relevant material to see if they discussed the possibility, or are you assuming that you're the only person who had considered it?
First, I'm not dismissing anything. What I am doing is drawing a distinction. More about that later. I am constantly reading about this subject and trying to make sense of what I read. Have I read the papers you are talking about? I don't know. The one concrete reference you made, I haven't yet found. I stipulate that you are more knowledgeable about the subject than I am, and there simply isn't enough time for me to reach your level of knowledge before having this discussion. So we either have to accept that you can throw more specifics and continue the discussion anyway, or we can end it. Discussing this with you is a helping me to think through my positions. I am obviously in a position of ignorance compared to you. I still think that I have something valid to say. It doesn't appear that you agree.
Let me start with some things we both might agree on.
- A mutation is a change in a genetic sequence
- Evolution posits that mutations accumulate over time leading from a lack of genetic diversity to the genetic diversity we see around us
- For example, the chimp/human precursor accumulated enough different changes to divide into the two different species
Agreed?
My issue with evolution, and what I consider to be a weakness, is that while it is clear that these small changes (mutations) occur, it is not clear to me that they lead to new species. Yes, it's the old micro-evolution vs macro-evolution question. Mutations occur, but significant mutations, especially in higher plants and animals, are negative. Yes, I have considered the vast stretches of time involved, but it appears that all the mutations we have genetic evidence of (I know you'll feel free to correct me if I'm wrong!) are of the minor variety.
Let's return to the human/chimp divergence. If "we are our viruses" (Lynn Margulis, google it), then the accumulation of minor changes is not what made us human. We apparently received the genes that differentiate us from the chimps fully formed from somewhere else. I AM NOT SAYING THAT GOD DID IT!!!! I'm simply saying that it doesn't fit the accumulated minor changes model. To me this opens up the POSSIBILITY of intelligent design.
I'm enjoying this discussion and am learning from it. If you want to continue, great. If not, that's OK, too.
So imagining alternate universes is less boring?
Actually, yes! Notice I didn't say that God doesn't exist, just that the study of God is religion, not science. And yes, there is a difference. Conjecture, backed up by the best evidence we can find, is what science is about. If you wish to study religion, go to it. If you want to study science, you have to give up miracles as an explanation.
Did you read the papers? Probably not.
http://www.talkorigins.org/faqs/fitness/
Is this what you are suggesting that I read?
I'm not sure what you're trying to say here, though. Does swapping of DNA across organisms somehow support ID? Maybe that's how the Designer is shining His Wisdom down onto us...
It is my point that swapping DNA across organisms weakens the strength of the evolution argument, especially when it occurs in eukaryotes. If, in fact, "we are our viruses", then we did not "evolve" new functions through random chance mutation. We received them, already working, from some other organism. If this is a common mechanism, as it seems to be, where did the original, functional genes come from?
This swapping negates, for example, the statement that an eye is so useful that it evolved 40 different times (Richard Dawkins). It was not necessary for any particular type of eye to "evolve" multiple times thereby proving that evolution works in parallel lines. It was merely necessary for the genes to exist and then get moved around by viruses to multiple organisms. It seems to me that the evolution argument is weak on this point, leaving open the possibility of a scientific intelligent design argument. I don't reject evolution, but I am willing to consider that it has weak points.
Do you have any idea how many times the old "start with a colony of clones that lack antibiotic resistence and watch antibiotic resistence emerge" experiment has been done? This is not new stuff. It's DECADES old. In a colony of clones, the only way for funny DNA sequences to show up is mutation.
As with your example of nylon metabolizing organisms, these involve minor changes to existing genes or the turning on or off of existing genes, not the creation of novel, working genes. I accept your statement as it stands, but a colony of clones can very easily contain unexpressed genes. The "mutation" you refer to is not necessarily the generation of new genetic code, but can very easily be the expression of existing code that wasn't active before. Genes are turned on and off regularly. That does not seem to meet my requirement of "generating a new gene".
Usually when somebody says, "No experiments have been done to demonstrate [insert fairly well accepted phenomenon]" it means that they haven't actually looked through the literature and they're repeating something that somebody else said
No, I'm not a working scientist, so everything I say is a repeat of something that I heard or read, or a logical extension of same. I consider myself to be a fairly well-read non-pro.
It could also be that there is one eternal, transcendent, intelligent being, GOD, who is self existent and is outside of all universes, including the one we are in. Why is it, strangely, the this "could be" is the one most disliked or fought against and why should this idea of GOD cause so much controversy?
Simple, because it is BORING as a scientific theory. What is there to study? God did it. That's religion, not science.
P.S. How do you explain viruses (which don't have DNA)?
Viruses do have DNA. They just don't have the mechanisms for reproducing. They need a living cell to reproduce.
Life is way too complex for it to arise from random combinations and random circumstances thus it must have a designer. By ID's own arguments and reasoning, a creator/designer creating complex creatures like us must be also irreductibly complex.
Another form of life that we are not familiar with could have designed us. That form of life may not be irreducibly complex. If you hold that there has been time since the formation of Earth for us to evolve, you must agree that there has been time since the formation of the Universe for other forms of life to evolve. I don't buy into the ID/Creationist irreducible complexity nonsense, but your argument does not hold water.
Try postiting some sort of test for ID. If you can pull that off, we'll start thinking about calling it science.
Here's a simple test that will make Intelligent Design(the creationist stalking horse) and intelligent design (the scientific idea that maybe, just maybe, random chance isn't the driving force behind the creation of new genes) irrelevant:
A demonstration of random chance mutation generating a new gene under lab conditions, either in biological or artificial life.
As far as I can tell, we have never seen this. Our studies of the genome suggest that most adaptation takes plaace because of gene swapping, not because of random chance mutation. Try googling this quote by Lynn Margulis, "we are our viruses".
Artificial life research (computer simulations) always seems to start with good genes and then demonstrate that natural selection works to find good combinations of those genes, but, so far, no experiments that show the generation of new, working genes. Where do the working genes come from? I know that evolution says they have been generated out of millions of years of mutations being tested by natural selection. Showing this in action would, for me, make the idea of intelligent design unnecessary
None of them are well reasoned. They aren't science (they aren't falsifiable), they're bad theology (god of the gaps), and the proponents of all forms of ID lie, obfuscate and distort facts on a reular basis.
I can't agree with your statement. I accept a form of intelligent design (note the lower case) that does not require me to lie or distort facts. I believe that evolution's most serious weakness is that we have never been able to show that it is possible for mutations to lead to working genes. Yes, existing genes can be modified randomly to have slightly different functions, but I have a hard time accepting that all the genetic diversity we see around us comes from random chance mutation. If this is possible, why haven't experiments in computer code led to working code from random changes? A randomly generated series of characters will not compile into working code if the set of possible instructions includes many bad (non-working) possibilities. Artificial life research (it seems to me) always starts with a set of working instructions and goes on to prove that natural selection will select for the most appropriate combinations over time. Well, yes, but in the real world we have to deal with non-working instructions (bad mutations) being the norm rather than the exception.
Because of this, I accept that it is possible that some intelligent tinkering with our genome may have happened. Look how quickly we have gone from not even knowing about DNA to being able to manipulate genes. This proves that intelligent design of genetic structures is possible. We now know that much genetic variation among species on our planet comes from genes being swapped among organisms rather than by random chance mutation generating new genes. It appears that we may represent a pre-existing library of working genes and natural selection is responsible for finding working combinations. Is this theory falsifiable? Yes, all that is necessary is for experiments to show random chance mutations generating new, functional genes, either in living specimens or in artificial life. So far, I am not aware of that being shown. Almost all true mutations kill their recipients.
Please note that none of this argument requires "god of the gaps" or even religious arguments at all. Where did the pre-existing genes come from? I don't know, but I think that this is a resonable interpretation that doesn't require a series of mathematical miracles.
A good scientist will not let his beliefs get in the way of finding Truth. Should the newfound Truth disagree with what he believed, a true scientist would adjust those beliefs. Just as the religious majority was in time forced to acknowledge that the earth revolves around the sun.
Well said. I personally don't believe that you can scientifically describe the religious impulse, wherever it may come from.
I am a religious person (Christian, if you must know), but I still believe in a universe ruled by the laws of physics. My God is capable of violating them, but that's not my business. I can't violate them and to say "This is a miracle" is ultimately boring from a scientific perspective. My religion and my science are simply not related to each other. When they seem to conflict, I usually find that it is because I am applying the rules of one in the domain of the other. The Bible is a religious document, Principia Mathematica is scientific one.
Quoth Albert Einstein (again): "God does not play dice".
And it turns out ol' Albert was wrong. When you look at the universe at a quantum level, it is not deterministic, chance is involved, God does "play dice", figuratively speaking.
With all that said, there are still some problems with evolution, but that's another thread.
Not that it affects your point much, but if we get "out there" there will be a whole lot of places to look for bacteria. So many that ruling it out by exploration alone would be impossible. What if it was just one asteroid/whatever that came from a galaxy far, far away but its bacteria only came to Earth and deposited life nowhere else on the way? Then we'd have to get to that galaxy to prove it.
That is a good point. My assumption has been that if something like that were to happen, it would, of necessity, be a large-scale endeavor. But, yes, you are correct, we could find no bacteria and still not be able to completely rule out the possibility. Of course, extraordinary claims require extraordinary proof. So, for me, if we don't find bacteria easily, panspermia is mostly invalidated.
So, if we manage to figure out how to design a memetic framework that prevents us from going at eachother's throats physically, and convince the rest of the world to adopt that framework, then there may be some hope of near term contact
I'm guessing peace through superior firepower wouldn't fit the bill, eh? Honestly, I don't see much hope for this type of advance. The human race is violent and almost all attempts so far to meet aggression with peace have ended in disaster for the peaceful side. Alien intelligence farmers or not, I think we are pretty much stuck with the memes we carry now. Whatever the next step up on the evolutionary (or memetic) ladder** is, isolation would seem to be needed for it to gestate. With the "global village" we live in now, extraplanetary colonies would seem, to me, to be necessary before any serious "advance" could be made, either at the genetic or memetic level.
**I know, teleological, but go with me on it
Nah I didn't call you an idiot, I said the statement was idiotic.
Yeah, I was baiting you a little to see if you would call me on it. I read your other post and it is interesting. Certainly speculative, but who's to say no? I've heard some speculation about periodicity in mass extinctions. But, as always, is it falsifiable? We'll know in a 100 million years or so.
As I've said in other posts, my favorite speculation about panspermia involves the creation of a library of useful genes, installed into hardy bacteria with some viruses to shuffle things around and launched into the cosmos. Once the bacteria established a beach-head on a likely planet, the shuffling of genes would generate complexity that would look a lot like !evolution!. Any intelligent descendants would be hard pressed to find proof one way or the other.
No more than I can prove evolution, because my background and field of knowledge is not in paleozoology, but I maybe can make a reasonable case.
Exactly. And it is a very reasonable case. I believe that even someone whose background is paleozoology could not prove it. They might be able to make an even more reasonable case. The history of science is littered with reasonable cases that later turned out to be incomplete or just not true. They were reasonable, but they failed when tested. Yes, I know, evolution has not failed any major test so far, but the big test, recreation of the process in lab or computer simulation has not been completed yet either.
However, even the most primitive single-celled deep trench life found so far still exhibits fairly complex genetic material.
A fact that was not predicted by Darwinian evolution. This doesn't invalidate evolution, but it does point out another weakness.
I was going to let this one go, but I can't, I just can't.
...because anything more primitive probably has been completely obliterated through obsolence.
Heck, even the simplest cells we can study are the product of billions of years of evolution (Can you prove this? Phylomon)
In this statement you are arguing from your assumptions. Since you start with the assumption that evolution has produced everything, you argue that evolution is too complex to understand easily. This, then, explains the lack of success in reproducing this part of evolution in the lab or computer. This is EXACTLY the same type of argument that the ID supporters make. They start from the assumption that God created everything and then argue that anything that can't be easily explained must be proof of God's existence. Both arguments are fallacies in this context. I am only disagreeing with the way you argue this point, not the validity of your assessment.
Please understand that I am enjoying this discussion. I hope you are, too. I do not intend to insult your beliefs or intelligence. If I've done so, please accept my apologies.
Up until the point where you called me an idiot I was enjoying what you said. If you are going to refer to my other posts, please try to be fair and not selectively quote. In almost all of my posts I have pointed out that Intelligent (ID) obviously pseudo-science.
Actually you have done no such thing. You have admitted in another post that direct genetic manipulation by humans has not resulted in the creation of new genes, just the manipulation of existing genes (usually by taking them from one species and inserting them in another).
This is a good point. Let me be more clear. In the short period of time that we as humans have been using the scientific method, we have gotten to the point of manipulating genes. I believe this proves that intelligent manipulation of genomes is possible, since we are already starting to do it ourselves. If something can be shown to be possible, that is a point in its favor, scientifically.
Actually there have been some examples of de-novo protein design for pharmaceutical use, but those have not been inserted into a species' genome to make it more successful in the wild (only for reproducing bacteria in pharmaceutical labs to produce the new proteins as drugs).
Thank you, you make my point for me. We are performing genetic modifications, thereby proving it to be possible.
To go from that to claiming that intelligent design explains the creation of complex structures like the mammalian eye is even more of a leap of faith than current expectations that evolution did the same. As far as I can tell that means that ID has no more supporting evidence about the possibility of intelligent creation of new genes supplementing evolution than Darwinian evolution does.
You are absolutely right. That is why I made no such assertion. I simply pointed out that being able to manipulate genes proves that genetic manipulation is possible. Let me say again, I think ID as it is being pushed by the religious right is garbage. But that does not change the fact that intelligent tinkering with genomes is possible and may have occurred. To say this does not make me a zealot, merely a realist.
As for simulations of artificial life and the demonstration of spontaneous creation of new genes through random mutation: We certainly don't understand fully how genes are expressed in complex cells, let alone multicelllar organisms, and until we do the accelerated simulation of evolution is not really possible.
Again, you make my point for me, Thank you. We cannot, at this time, prove that random chance mutation can produce working genes. Not in the lab, not in computer simulations. This is the major weakness of evolution as a theory. Notice, I never said it was wrong. I just said that we can't prove it to be possible, let alone prove that it was, in fact, the mechanism providing genetic diversity. I agree, it probably was. But it is not yet demonstrated.
However, assuming the next few generations of scientists don't have their analytical faculties damaged by intelligent design zealots or their research funding politically denied by similar fundamentalist religious zealots in political office, the days where you can make idiotic statements like the quote above are numbered.
I agree fully. I think, however, that to overreact, as you have done by calling my statements idiotic, is also a bad thing. Open-mindedness is important. ID zealots are pushing a political agenda, no question about it. But to insist that one must not criticize or point out weaknesses of evolution because of the ID zealots is harmful as well. There are other scientific alternatives.
Irrelavent and incorrect.
Not irrelevant and not incorrect. You'll notice I didn't use the word "scientists", I said science oriented individuals. And I notice that you did not answer the question. So, let me ask again. What scientific evidence would it take for you to be convinced that evolution had been falsified? If something irreducibly complex were found, would you then be convinced? Would it take a message encoded into the genome from some Progenitor race? Would evidence of bacteria raining down from outer space convince you? I'm not asking you to abandon your scientific principles, just to fantasize a little. Or, perhaps, to admit the there is not much chance that you could ever be convinced that evolution had been falsified.
All scientific theories are falsifiable, so at least some thought went into how they could be falsified. Evolution is considered to be a fairly reliable theory because it has managed to not be falsified so many times. Since you cannot know what it is that you do not know, evolution is evaluated every time new evidence is found. So far, no new evidence has failed rationalization with the theory of evolution.
This is a fair enough statement, but it is tangential to the question. The question is a speculative one. What piece of evidence would convince you that evolution had been falsified?
What you see as verification is actually attempted falsification.
With all due respect, you seem to be making a lot of assumptions about what I think and see. And, to set the record straight, I am familiar with the scientific process.
There are weaknesses in evolution and the big one is that nobody has been able to prove that random chance mutation can generate functional genes. Yes, it's a reasonable assumption. Yes, the evidence seems to fit. But science is about reproducing results and, so far, nobody has reproduced that part of evolution. Not in the lab, not in computer simulations.
It's interesting. I don't really disagree with anything you say, but we seem to be coming to different conclusions. A couple of points:
From where do you get 500 years?
I was trying to encompass the industrial revolution, Mendel, Darwin plus a large fudge factor. Nothing magical about the number except that in that short period of time we have come so far. Even using your time period of tens of thousands of years, it's just not a very long period of time. And yet, here we are, modifying genomes. I think that proves the point that intelligent tinkering with genes is a very real possibility.
Your discussion of the plant pot made of legos is well-made. I think any disagreement we had on that has been cleared up. To summarize, we seem to agree that just about anything is possible, but it might take a very long time for it to happen. Agreed? Whoa there, you're getting ahead of yourself. Who said anything about dumbing down the instruction set?
With all due respect, you did. You said:
If you consider a simple enough instruction set, it is easy to generate valid programs randomly. If every possible value for the order field represents a valid operation, then there can never be an invalid order and hence the validity of a program only depends upon it not producing an overflow condition
The genome is not a simple instruction set. My original point was that if I use a random character generator, I will not get working programs. Let me amplify this a little. I work with C# sometimes. I could set up my random character generator to create text output and then try to compile it as a C# program. While it is theoretically possible that someday I may get random output that compiles and does something useful, it is staggeringly unlikely.
What you proposed is that we create a simple instruction set in which every possible random string is a valid instruction. I would call that "dumbing down" the address space of possible instructions. I think my analogy is closer to the real world of DNA. There is a huge address space of possible strings of amino acids to be woven into a strand of DNA. Only a small set of them produces "working code" when "compiled" into proteins inside a cell. I don't disagree with your example, I just don't think it is close as mine to the real world that we are discussing.
Now you're just moving the goalposts closer and closer together.
Yes, I am. This is because I think there is a difference between using existing code and creating new code. This is the distinction that I am trying to illustrate. To continue with my C# example, if I create new programs by using existing objects or cutting and pasting other people's code, I am not creating new code, just remixing code that already exists and is known to work. While this can creat novel functionality, it is not the equivalent of writing code the old-fashioned way, from scratch; it does not create new strings of working code, just reshuffles the code that already exists.
With regards to the genome, we see what appears to be increasingly complex code throughout geological time. The question is, "Where did that new code come from?" So far, I have not seen convincing proof that random chance mutation, even across geological timeframes, can produce new, working code. Yes, it is a reasonable explanation, but it has not been proven to be possible.
At this point, most people I discuss this with throw up their hands and say, "You're here, aren't you? That proves that it must work." This is a logical fallacy. Existence of an object does not prove what method was used to create that object. Yes, random chance mutation may be the source of new, working DNA code. But, so far, nobody has actually been able to reproduce that process in the lab or on a computer without doing what you proposed (what I referred to as "dumbing down" the instruction set).
I want to say that I am enjoying this discussion and do not mean any disrespect of your beliefs and/or logic. If something I say comes across as dismissive or condescending, please forgive me in advance.
Finding his example with transponsons would still be pretty ugly for evolution, but as you indicate it could be explained as a freak transfer event for two reasons.
t /full/1998/1022/1 membership required
8 1023txt A short synopsis here
I'm not even sure that I would call it a freak transfer. According to Lynn Margulis, a prominent, main-stream bioligist, "Viruses today spread genes among bacteria and humans and other cells, as they always have... We are our viruses". She said this in a book written in 1998. For me, transposons of just about any stripe would not falsify evolution, with the following exception:
If you found the same viral DNA insertion in whales and in humans - and in fact found it inserted in precisely the same location - and it was absent in chimpanzees - that would be a huge problem for evolution. The insertion of the same viral DNA at the exact same location cannot reasonably be dissmissed as a random occurance, and finding multiple such examples would be overwhelming evidence.
That would, for me, be strong evidence of intelligent tampering with the genome. I don't expect to find that, though. IF we do someday find evidence of design, I think it will be along the lines of a genetic "terraforming package". A library of a lot of useful genes, with some viruses to shuffle them around, loaded into some hardy bacteria and seeded into the cosmos. I think this model has the potential to explain what we see around us without requiring a miracle and without completely invalidating evolution. This theory (panspermia) has the added benefit of being falsifiable. If we get out there and don't find bacteria, it obviously didn't happen that way.
You mentioned common descent. I'm not so sure, with what we now know about transposition, that common genetic descent is a requirement. We have already found strange bits of DNA where they have no right to be. Eukaryote genes in prokaryotes and the like. Chlamidia trachomatis, for example, contains more than 30 eukaryotic genes.
URL:http://sciencenow.sciencemag.org/cgi/conten
URL:http://www.panspermia.com/whatsne4.htm#%209