User talk:Standonbible/Discussion of evolution

Discussions of Evolution | Standonbible !

Nylon Bacteria and Lungfish
You said: "new traits arising through random mutation are rarely observed at all"
 * You are deeply mistaken there. The speed with which new traits evolve surprised even the more conservative evolutionary scientists.  Nylon-eating bacteria are just one example of the top of my head that shows how quickly new traits evolve (the website also has rebuttals to creationist objections).  The evolution of the molecular machinery for eye sight (a huge amount of literature is out there) shows just how easily genome duplications produce utterly new traits (some not even related to sight).  Now, all these things have been observed only in the last 100 years.  But evolution had at least 3 billion years to happen.
 * The nylon-eating bacteria was a frameshift mutation that shifted a set of base pairs over X number of pairs. However, the bacteria always mutated this way when subjected to a certain environmental stress.  That is because the genetic code was already written for the nylon digestion enzyme but was hidden under a frameshift layering.  Either the Designer of the bacteria wrote this ability to mutate and reveal new abilities that were already there into the original DNA code, or this enzyme used to exist but an earlier frameshift mutation had temporarily hidden them.  For example: if your browser accidentally rendered www.microsoft.com backwards and it was an explanation of how to fix the problem with the browser, you wouldn't assume that such accidental renderings generate all self-help articles.  Rather, you would commend the designers of the Microsoft homepage for being able to design their source in such a helpful way - so that it would reveal new information when the new information was needed. standonbibleTalk! 03:47, 24 November 2006 (UTC)


 * So what you're saying is that it is more likely that a Designer exists, that the Designer foretold the eventual production of a synthetic compound (Nylon), and that the Designer saw it fit to equip a specific variety of bacteria with the ability to MUTATE INTO being able to metabolize it? And less likely the alternative that a random mutation, allowing the metabolization of Nylon and appears in an organism that multiplies more rapidly than most organisms on this planet, was selected as more fit for an environment containing Nylon? The problem with Intelligent Design is that the assertions being made by it (that the instruction for metabolizing nylon was placed, albeit incorrectly, in the DNA of the Bacteria by an Intelligent Designer) are totally untestable and therefore not falsifiable (ergo, not science). Furthermore, your strawman argument regarding the browser is irrelevant. The designer of a web browser is known, so saying that anomalous behavior like the renderings in a web browser is the product of design is tautological. And yes, in that scenario, that conclusion would be more acceptable than to say it was the product of random mutation of software code -- but again, living organisms ≠ computers.
 * Remember -- Evolution describes a system where mutations happen randomly (such as via frame shift) but effective ones are selected by the environment. This creates an illusion of design in the same way that an inclined plane creates an illusion of self-propelled movement when a ball is placed at the top of it.
 * If you're keen on getting your hypothesis about that enzyme being always there and just "showing up" in the presence of Nylon -- construct an experiment. How would you support that notion? More curiously -- why would a designer have the Flavobacteria metabolize Nylon? It seems like more of a stretch to think that pairing up those two is the product of design than to think that it happened by chance, and was selected for by fitness. Elecmahm (talk) 07:08, 30 March 2008 (UTC)


 * I would also like to point out that your statement "evolution had at least 3 billion years to happen" is an "argument from incredulity" - the same thing that proponents of ID are often accused of presenting. For example, often ID proponents show how large the odds of abiogenesis not happening are and say "look: it's so unlikely it can't happen".  This is an argument from incredulity.  However, saying "it had so long to happen" is the same kind of argument.  More on the rest of your argument later. standonbibleTalk! 03:47, 24 November 2006 (UTC)


 * I disagree -- this is not an argument of personal incredulity. An argument of incredulity would be something like "Look at the ridiculous amount of variations we see today, that HAS to prove Evolution is correct." But his statement was not making an argument that 3Gy somehow makes Evolution more or less plausible -- he was stating that the increases in complexity that we have observed have been within the past 100 years -- and that 3Gy is a far longer time. The implication is that More time = more potential for complex developments.

"Genetic variation cannot give reptiles feathers or fish lungs"
 * Again, a very mistaken statement. Lung fish do exist (Lungfish), exactly as would be predicted by evolution.  To say that genetic variation cannot give fish lungs is a deeply ignorant and uneducated statement.  The lung fish are there and the genetic analysis shows them to be between the fish and the amphibians (exactly as evolution would predict).  Feathered reptile fossils have also been found (last year payed $50 bucks to see all those fossils in one place, the feathers are beautifully preserved) (Feathered dinosaurs.  I do remember the false fossil, but that took scientists less than two weeks to expose as such.  Now, these finding are only 20 years old.  Keep your eyes open for many more feathered reptile fossils.  The genetic evidence alone shows birds to be closely related to reptiles.  The research to find the genetic basis for feather has just started, so look out in the next couple of decades for more confirmation that reptiles indeed (over millions of years) grew feathers and beaks ;).
 * When I said "genetic variation cannot give fish lungs" I meant that natural selection cannot give the information for lungs to a creature without that information. If the information for lungs does not exist in a particular genome, genetic variation can't bring it out - you need a series of mutations.  That's all that I was saying. standonbibleTalk! 03:47, 24 November 2006 (UTC)
 * But it's a strawman to say that Evolution says the genetic information for lungs just popped up out of nowhere. I have not personally studied lungs in detail, so I can't speak of their physiological history -- but if you'd like to read one possible explanation, check [|this] out. In the case presented by madsci.org, lungs are derived from [|swimming bladders of fish] -- the mechanism for gas exchange could have developed later. Natural selection does not provide information -- it pares down the pool of organisms for those that are best suited to their environment. Mutations, alleles, and genetic drift are the source of information. Elecmahm (talk) 07:08, 30 March 2008 (UTC)

But I'm not here to argue about the validity of evolution (the 200,000 scientific articles published in the last 75 years can do that much better). I only advise you that next time you start a discussion over at Evolution to actually bring along verifiable sources.--Roland Deschain 17:40, 16 November 2006 (UTC)
 * Certainly. But now you know my position.  I suppose that if I brought a link to a peer-reviewed article from Ebscohost or something that stated "Mutations necessary for evolutionary progress happen only rarely" that would suffice?
 * I'll continue the conversation shortly - not for the sake of the Evolution article but just so that you know what I think about the examples you cited :-). Till then, 18:15, 16 November 2006 (UTC)
 * Don't get hung up on the rare beneficial mutation (I totally agree that beneficial mutations are rare). But rare mutation x 3 billion years x a vast vast vast number of organisms that have lived makes all the difference.  Michael Behe, the scientific front man for Intelligent Design (and a really smart guy) tried to use the rare beneficial mutation fact during the Dover trial to show evolution lacking.  Read up the transcript to see how that argument is destroyed.--Roland Deschain 19:10, 16 November 2006 (UTC)
 * Okay, so you have "rare mutations X 3,000,000,000 years X all the organisms that have ever lived = evolution". Fine.  Unfortunately, if the first factor is 0, it doesn't matter if you have 3 trillion years: evolution would still be flat.  You've mentioned one example so far: the nylon-eating bacteria.  And that information (for the new enzyme) was already in the gene because it had been designed that way; no matter how many times you subject the bacteria to that stress you still get the new enzyme.  As of yet I haven't seen any random mutations that actually increase the usable information in the genome (i.e. both have new alleles and provide an advantageous physical trait that will insure the new genotype is passed on through the population). standonbibleTalk! 03:47, 24 November 2006 (UTC)


 * But why would the first factor be zero? Are we shifting the debate into the realm of abiogenesis now? Mutation is a chemical, not a deterministic, process. Why would you think mutations wouldn't happen?
 * You really shouldn't make assertions like "the information for the new enzyme was already in the gene because it had been designed that way" because that argument is groundless. Where are you sourcing from? Personal conclusions? The Discovery Institute? I'm not attacking you here, but you are stating this particular point as an observed fact when in reality it is entirely fabricated.
 * And arguing that "since I haven't seen any random mutations that actually increase the usable information and provide an advantageous phenotype, then they must not exist" (which smacks of goal-post shifting) is quite clearly an Appeal to ignorance. What would be an acceptable random mutation that both increases usable information in the genome AND provides an advantageous phenotype? What would it do? What would it look like genetically? Most importantly: how would it be different than everything we have observed so far? I ask these as serious questions, because I'm wagering that NOTHING would be good enough for you to accept it sans-Designer. Am I right? Is there a scenario that would cause you to think: "OK, maybe intelligent design isn't right after all." Elecmahm (talk) 07:08, 30 March 2008 (UTC)

About my intro
You write in your intro: "Since no random gene duplication or polyploidy has been seen to actually increase the usable information in the genome or cause new traits to appear"
 * Now, I'll be the last to tell you to write what in your intro, but that statement is false. There are at last 5000 papers that I can find that deal with evolution as a result of gene duplication.  Here are some if you are interested:
 * 
 * Gene duplications and the origins of vertebrate development
 * Duplication and divergence: the evolution of new genes and old ideas.
 * The evolution of morphological complexity in zebrafish stripes

I write this because the above sentence is a favorite creationist argument. I might be totally wrong on this (I read the transcripts a long time ago), but that argument was used by the creationist in 1987 when the supreme court rules that creationism was unconstitutional. These papers weren't published at the time, but the known hemoglobin (allows transport of oxygen through blood) evolution, through gene duplication, was used to show that the above absolutist statement was false.--Roland Deschain 05:00, 17 November 2006 (UTC)
 * Okay, let's see here. The first article was a speculative description of how antibody-based immune systems might have come about - "This might have happened, that might have happened" but no example of an actual, observed mutation of the type we are talking about is given.  Likewise, the second is speculation about evolutionary history but lacks examples.  The fourth attempts to read the process of evolution in reverse in a particular area, but it has no examples.
 * The third article you gave looks like it would be rather interesting - a list of the occurrences and consequences of gene duplication. Unfortunately I can't get the actual article from it so I can't evaluate what it says past the abstract.
 * I think that the disagreement is over how "usable information in the genome or cause new traits to appear" is defined. I would like to see an example of a random mutation that gives a heritable, advantageous trait to the organism (in order for natural selection to "disseminate" new genetic information it must be both heritable and advantageous).
 * Oh - and the Supreme Court never ruled that creationism was unconstitutional - it struck down laws banning the teaching of evolution. Big difference. standonbibleTalk! 04:33, 24 November 2006 (UTC)

Some thoughts...
From what I can tell, much of what you say, standonbible, is based on your limited knowledge in the areas being discussed (disclaimer: I don't mean this as an insult and would point out that all of us have more ignorance than knowledge). The reason i mention this is that you did not seem to be aware, or disagree with the biological observation, that an increase in genetic information is possible. You had said we should continue on the talk page, so i am intersted to hear your perspective on this issue. I am reading with interest the discussion above and I think you are clearly very bright. With that in mind there are a few things I would like to point out to get us on the right track.
 * There is a misconception that evolution is about marching forward to improvement. The theory of evolution does not consider the quality of change. It only considers what survives.  The fittest is not always the best. Look at humans, they can't make vit C
 * A similarity between scientists and creationists is we all have more questions than answers!
 * A difference between scientists and creationists is that the scientists often have more information available to make informed analysis
 * I know a university lecturer in biology who is deeply religious and has a joint appointment in religious studies. Biologists are not all atheists and i think that says a lot more than any scientific argument for evolution.
 * With respect to the origin of life, simple cells on Earth are highly derived from an evolutionary perspective. In other words, no modern organism can be used as a model for the first cell since they are the end point of evolution. We need to consider their ancestors. The probability to come up with a modern cell is a different problem to calculating the probability of the first cell. Scientists have very little idea of what the first cell might have been and the few models that do exist are almost certainly wrong, however, that is the nature of science. The most important point I can make here, with respect to evolution and the origin of life, is that they are very different questions. The theory of evolution only addresses the diversity of life, it does not address how life began. Scientific models for evolution are not weakened by our huge ignorance with respect to the origin of life.

I think that this is enough for starters but these represent some common arugments that I come across from students in biology classes. David D. (Talk) 18:46, 16 November 2006 (UTC)
 * Hey David D. - I must say that I agree with the majority of your statements for the most part. No arguments - I understand that evolutionary progress is more about what survives than what gets better.  I would also state that I don't think a Christian can hold to a position that is contrary to that taught in the Bible if they understand the issues, but that is an entirely different discussion.
 * Obviously the debate was about evolution and not abiogenesis, but I'd be happy to tackle abiogenesis as well. According to a Nature article (I can't remember where it was but I can find it if I need to), scientists have decided that the minimum number of genes necessary to support reproducing, material-ingesting life is somewhere around 200 genes.  Absolute minimum.  A basic gene has around 1,000 base pairs, which means that 200,000 DNA base pairs must be in the right order for reproduction and ingestion of nutrients to take place.  Obviously a different type of code than DNA could have formed, but since we are talking about a certain amount of information the necessary odds would still apply.  Even if the right amino acids had formed randomly, they had somehow folded into proteins, and through a combination of hypercycles and clay crystal capsules had formed a DNA chain, it would still have only one out of 10120,412 possible combinations that would support life.  If every particle in the universe (1080) attempted to form into the right arrangement 10 times every second, it would still take 10188 years before you would be guaranteed to have the right combination.  The universe (by evolutionary standards) has only been around for 1010 years, which means the universe is 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,
 * 000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,
 * 000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 times too young to support abiogenesis - once.standonbibleTalk! 04:08, 24 November 2006 (UTC)


 * I have had many an argument about evolution/abiogenesis with creationists, and decided I couldn't put up with the same sort of ignorance that is normally associated with it. I have since removed this stress from my life. Luckily, I live in a country where I don't have to put up with it. You seem to have a brain, however, and it may be of worth to have a discussion.
 * Your entire argument above is largely flawed. I would like to read the Nature article you are speaking of, as I would like to draw interpretation from the source directly rather than through the interpretation of another.
 * Firstly, DNA was not the first code of life. It was much more likely RNA. How all the bases for RNA first formed is unknown, but there is obviously research into this. Secondly, you need to understand how much the biochemistry of life is actually chemistry. The very beginnings of "life" is not the same as how life works now. The beginnings of life would have been a small mixture of chemicals, possible one chemical (RNA). The difference with this chemical was that it could split, and form two of itself. A sort of reproduction of a simple chemical. Unlike modern DNA and RNA, there were no mechanisms by which it could assure perfect replication of a sequence, so there would be high levels of "mutation". Most of these new, mutated, chemicals would have reacted with something, and "died" into an unreactive, organic molecule which could not "reproduce".
 * RNA, however, has one more feature (which DNA does not have). It has the ability to make many shapes, and structure, and act as a sort of protein. It is still used in modern life within many proteins to help with structure. As the early RNA mutated, it would have mutated new chemicals which had different structures, and survived through different means. Once the diversity of these chemicals was greatly increased, mutualism between chemicals would have allowed interactions which increased their survivorship. This would have eventually led to a simple cell, which would have been an evolutionary innovation, which led to great diversification of cells, and the eventual evolution of complex life. DNA would not have evolved for an extremely long time. It has very many advantages over RNA for storing information, but only within the cell.
 * There is no giant step in this explanation. 1) Formation of reproducing chemical 2) diversification of simple chemicals 3) mutualism between chemicals 4) evolution of simple cell 5) diversification of cell etc. etc.
 * The use of RNA as information storage would not have occured for a long time. Some protein like chemical would have evolved to be able to read it, and used it for very simple means. Again, this is an evolutionary innovation which would have quickly spread and diversified throughout all life, as it is veryuseful. If the Nature article is talking about DNA based organisms, evolution was already well underway. It is pretty much like saying the chances of humans evolving (based on the arrangement of their DNA) is too small to have ocurred. That is because that is not how it ocurred. --liquidGhoul 15:45, 24 November 2006 (UTC)
 * You mentioned hypercycles and random protein formation via RNA. I had already factored those in.  The problem with the step-process that you gave is the definition of "reproducing" - hypercycles do not count as reproduction because there is no information pool that can be operated upon. standonbibleTalk! 16:32, 24 November 2006 (UTC)
 * Can you elaborate on that? I don't understand what you mean by "information that can be operated upon". --liquidGhoul 23:36, 24 November 2006 (UTC)
 * Certainly. When I say "that can be operated upon", I mean that the information pool (the DNA, code, RNA, whatever) exists separately from the "life" of the organism itself.  If the organism is just hypercycles, there is no population in which natural selection can operate.
 * Generally, abiogenesists "bridge the gap" of life by saying "if we have a stable, reproducing system, then natural selection and mutations can operate on it to make it more and more complex...." Then they cite hypercycles, which are (for the benefit of other readers) proteins that attract other proteins in a specific orientation that then attract other proteins.  This creates a cycle from protein to protein.  However, this cannot "be operated upon" by natural selection because for natural selection to differentiate gene structures in a population the genetic code must be independent of the organism.  In a hypercycle, each protein leads to another protein and there is no way for genetic variation to take place without changing the structure of the "organism" - natural selection/mutagenesis requires a stable organism whose genetic code can be slowly modified and spread out over a population. standonbibleTalk! 00:40, 25 November 2006 (UTC)
 * Not true. You are extrapolating the processes by which natural selection occurs now, to how it would have occured at the beginnings of life. If you really want, you can call it molecular selection, as it is a different process, but it still makes sense. We have a group of replicating molecules (do you agree this is possible?). If there is a change which causes a conformational change in the molecule (which could easily occur by changing of base sequence, do you agree?). Those which are too reactive will react and never be seen again. Those which are not, will not react, replicate, and will be seen again. This causes diversity in the molecules, as there are a lot of different molecules with alot of different conformations. This doesn't mean they have any function whatsoever, they are just unreactive enough to allow replication to occur. By chance, some of these molecules may be able to work together to stay unreactive for longer, and replicate more. Once some of these mutualistic relationships produce a proto-cell membrane, the evolution of life is underway. --liquidGhoul 01:12, 25 November 2006 (UTC)

Hi!
I noticed you on the evolution page and I thought I would say hi. You are doing well by trying to inject some rationality into the discussion and help people work constructively. Although creationists are always looking in speciation for evidence of a Creator (which I do not think is particularly fruitful), I thought I would compile a short list of suggested other places to look for evidence of God in science. These are far harder to consider because they require more thought and investigation. However, they are far more likely in my estimation to have positive results than hashing over the same old speciation ground that everyone has beat to death for more than 150 years. Plus, the science involved is very cool. You can find a cursory list of these areas on my homepage. If you want to know more, let me know.--ReasonIsBest 07:53, 22 November 2006 (UTC)
 * Hi Reason! Thanks for the vote of confidence; I am sure that we both have similar goals for Wikipedia.  Unfortunately your characterization is not exactly correct; I don't go around looking for evidence for a Creator.  Romans 1:20 says that God created the entire universe as a testimony to His creative power - and that people who ignore this are without excuse.  The Bible is self-proving and it is supported by science.  I am not trying to shove God into well-established scientific ideas; Darwin formulated the speculative hypothesis of universal common descent by natural selection as a way of rejecting God (his daughter had died at a very young age and his journal entries reflect his anger towards God).  Darwinian evolution fell flat after we understood genetics, but the scientific community recreated it using mutation theory.
 * You will notice that I have not mentioned God on the evolution page because I am not trying to shove the supernatural into science; rather I am trying to make the article more informative so that people can see the large flaws in evolutionary theory for themselves.
 * Anyways, thanks for the comment. I checked out your list on your home page and it looks pretty interesting - I'll have to look at it further.  Thanks and happy editing! standonbibleTalk! 13:26, 22 November 2006 (UTC)
 * Well some people are looking for evidence in science to "prove" or support their beliefs. I am sure you are aware of some in creation science or intelligent design who are. Some are like me. We know that there is no physical evidence for certain beliefs, we just choose to have them, by faith. We don't worry about the physical evidence, which might not exist. If we are wrong, so what? Evolution of course has been altered in significant ways since Darwin proposed it. There are even Lamarckian ideas being introduced into it in some ways. I would not expect it to stay the same for the next 500 years, or even next 50 years. The theory is going to be forced to incorporate new evidence. It might eventually be superceded or replaced of course. All scientific theories are on the potential chopping block. But in the meantime, many parts of evolution are extremely well established. And also, the theory of evolution appears to have incredible powers of prediction, or at least it is believed to have them. And since it is useful, or it is felt to be useful, it is widely accepted and prominent.  I compiled the list of ideas because I feel that a lot of effort is being "wasted" in trying to find holes in evolution by religious people. Some want to support their faith, some want proof of their faith, some want to prove the bible is "right", or some other holy book, some have decided that evolution is satanic somehow, etc. However, creationists are unlikely to find holes or problems with evolution after 150 years of intense effort. Much more well-trained scientists are frantically looking for holes themselves, since if one can find evidence of something that evolution can not explain, they will make their careers. It is not blindly accepted. It is tested and studied over and over and over by an army of scientists. It is extremely well-established. However, if a person wants to look at an area which is far more fecund with possibilities for investigating evidence of a creator, then there are many of them. Off the top of my head, I made a short list. These are all mysterious areas, and not well understood at all, and  areas in which even scientists and atheists of various stripes will seriously contemplate the existence of a creator or what might be viewed by some as "supernatural" influences (although it might not be called "supernatural" of course). The only drawback is that to study these is very very difficult. It is also exciting, because the science in these areas is far more intricate and compelling than something as deadly dull as random mutations feeding into natural selection (sorry I am not a biologist). I would be glad to discuss them with you further.--ReasonIsBest 16:49, 22 November 2006 (UTC)