Peez

Not until they had already replicated a lot.Gee, its amazing that anything is alive at all! Just how often do you think an aquatic amoeba is killed by "lightning, falling rocks, fires, meteors, (or) some unhealthy chemicals"? You sound like someone straining to find a reason to dismiss evolution, rather than someone interested in learning more to make an unbiased judgement.Based on what. Please explain how you came to this opinion.Ah, back to abiogenesis. Can I take it that you have given up on finding any flaw in evolution, then?Really? Those rainstorms must be far more dangerous to aquatic organisms than they seem to be.Abiogenesis. If you like, we can assume that the Invisible Pink Unicorn created trillions of nicely complex and reasonable well-adapted bacteria about 4 billion years ago. Now, can we discuss evolution?What theory? Even ignoring your attention to abiogenesis, the evolution of living things by descent with modification from common ancestors is not a theory, it is a fact.Scientists have tried millions of times to disprove the hypothesis of common descent, and have failed each and every time.Please explain.Meaningless until you define "optimum."Sadly, science does not exist just for the benefit of your belief. Science works by proposing naturalistic hypotheses, then testing them with empirical evidence, and forming theories that help to understand the results. It does not require "optimum" conditions or the "worst possible" conditions. Off hand, I can easily imagine conditions that would preclude life as we know it from ever existing. So what?Suppress your "unbelief"? Since you know very little about evolution in particular or even biology in general, this is hardly a big deal.

Peez

braces_for_impact

As a frequent browser (and seldom poster) to this forum I would like to personally thank all of those that contributed to this thread. This has definitely been one of the most informative threads I have read here in awhile. The proverbial 'light' came on over my head several times in your attempts to explain things to luvluv.

Also, thanks luvluv for asking some very poignant questions, some of which I have often wondered about myself.

Well done ladies and gentlemen!

luvluv

Peez:

Which is why I am here asking questions.

That all life evolved in a step by step process from a single ancestor. That everything about every organism can be explained without reference to a designer.

Whatever.

Wonder away. If you present a case I can't question, you will have proved me to have been either a truly open-minded person or a dyed in the wool young earth creationist.

So the quickest way to end this little mystery of my intentions is just to stick to proving your case, and not making snipy little comments on everything I say.

So there's no way to predict or estimate how often beneficial mutations are likely to happen? Then why would it be wrong for me to think they don't happen enough to account for the diversity of life?

My point was that since evolution happens so incrementally, I wonder if there's any real world advantage to most beneficial mutations at all.

I was saying that I doubt that an organism which has a photocell which is not hooked into it's central nervous system (in other words, it has a cell which reacts in some way to light but this reaction doesn't translate into any action on the part of the overall organism whatsoever) would fare any better than any other organism.

In my thinking, what reproduces and what doesn't reproduce has very little to do with such incredibly small and often insignifigant advantages for any organism. What survives to reproduce probably has more to do with pure luck.

I'm citing what is probably a non-existent case here to illustrate my objection. Say, in cat evolution, the first cat to have a tail has one which is only an eigth of an inch long. Does this cat really have such an advantage with such a functionaly useless appendage that he will significantly outreproduce his tail-less brethren?

Well, this is the problem. I'm still asking you questions about the scenario you drew up, and you just handwave all my questions away and say "I've already demonstrated this to you." I don't think you can say you've explained this until you've answered whatever objections I might raise.

Well, thanks. This is the first step in actually demonstrating to me how such a thing could happen. This is what I was talking about. How do you expect me to accept your scenario before I've had my questions answered.

See? I'm that much closer to believing in evolution now. And it didn't come about from you questioning my character, but from addressing my questions? How about that!

I still have some questions:

for b), what is signifigant about the lightwaves being absorbed rather than reflected?

for c) are you saying that a light-absorbing molecule (like rhodospin) IS bi-polar, or that in your scenario we have lucked onto a molecule which is both bi-polar and light absorbing?

for d) what meanest thou by "occuring in a nerve cell"? And I thought we were talking about unicellular organisms here? Do unicelluar organisms have "nerve cells" and "brains"? I might be lost, I thought you were talking about unicellular organisms.

You seem to be ignoring the fact that you haven't fully answered all of my questions. Until you have done so, my objections have a pretty firm foundation.

Our basic misunderstanding seems to be stemming from the fact that you believe you have answered questions which I don't believe you have answered. This probably stems from both my not understanding your answers, and from you not answering my questions.

The basic flow of OUR conversation peez is that you shoot off an answer, I ask you a question about your answer, and you hand wave me away and say "I've already answered that.". I'll tell you ahead of time, I'm going to COMPLETELY scrutinize every answer you give me before I accept them. If this sounds like a conversation you don't want to be a part of, then I wouldn't blame you for taking your leave. It is a big thing to ask of somebody, and I realize that. You don't have any obligation to explain evolutionary theory to me. But understand that I am going to question everything, and I will be hard to convince. I'm not biased I'm skeptical, though the two attitudes would be hard to distinguish from each other in the course of this conversation. Honestly it's always been my opinion that everyone else is too credulous about evolution. If a possible scenario bridges a gap, even though it's nearly impossible to document and the odds against it occuring are astronomical, then that is what must have happened, case closed, don't ask anymore questions. I'm not like that, and if that is going to be too much of a hassle for you, maybe somebody else will take your place in this discussion.

Hold it. You tried to explain how it could appear (we're not done with that yet) you DID NOT address how it could spread. That was what I was questioning, and you never answered it. If it doesnt confer a reproductive advantage in it's incremental form EVER then it is just dumb luck that it survives in the genome. That is what the incremental evolutionary picture looks like to me, the survival of the luckiest, because the tiny advantages don't mean an awful lot in the real world of competition.

This is another reason why I have a hard time believing in evolution. It would be one thing if evolution worked by the appearance of real, practical advantages in one species. Then I could see unguided evolution leading to the specialized adaptations that I see around me. But when the advantages are so small that you wouldn't even expect it to confer an advantage, that means that what survives is not necessarily the fittest but the luckiest. And I don't see how you can get specialized organisms if what survives has nothing to do with who has the best adaptation. I don't believe species could evolve without real advantages confering clear, practical opportunities for the holders of these advantages to outreproduce their brethren. If that is not what is happening, if we are dealing with the survival of the luckiest and not the fittest, then how could evolution have any direction at all?

I'm not trying to argue it couldn't happen. Micheal Behe is what trying to argue that it couldn't happen looks like. I'm expressing my doubts and objections to the theory.

And I've explained that I meant that the MUTATIONS THEMSELVES were accidental, not natural selection. Nobody has questioned that, that I recall. That is an objection I have, not that mutations which confer an advantage will win out, but that the advantages will occur in a sufficient number in the first place.

I wasn't talking to you. I was talking specifically to someone whom I know to be an atheist.

Stick to responding to my general questions, or my questions directed at you, and this will go a lot smoother.

You haven't seen me get sarcastic yet, chief. If this got turned into a a**hole contest, you folks wouldn't stand a chance.

I would imagine that everytime lightning strikes in the water an aquatic amoeba is killed. Ditto for the rest of the phenomenae. If I understand correctly, this stuff was going on a lot more often, and with a lot more severity, on early earth than they occur now.

If you haven't noticed by now, I genuinely care not at all what you think about my internal biases. You can discuss this with me or you can take your leave. If you won't bring it up anymore, and will stick to helping me with the biological points, I will admit to whatever bias you would like me to admit to. If my claiming to be a Young Earth Creationist will get you to stick to the topic, just let me know. I'll do it. (For the record, THAT was me being sarcastic.)

Seriously, how many times are you going to say you doubt my biases? I think everybody here gets the point by now.

Wizardry

I think I'll try my luck at a couple of these:

Basically, absorbed photons cause a physical change in the molecules doing the absorption whereas reflected photons do not. Reflected photons don't do any work, they go off to do something else, whereas an absorbed photon can cause a change in a molecule (in this case, a protein).

Intro biology and physics to follow. My apologies if you know this already or if I get any of it wrong, but maybe it'll be good for the lurkers:

Proteins are rather large macromolecules consisting of one or more chains of amino acids. The specific order of the amino acids is referred to as a protein's primary structure. Proteins aren't long chains however, they are folded up on themselves based on polar bonding between different parts of the amino acids. Some of the more common structures are alpha-helixes (these are single helices, think of a spring) and beta-pleated sheets (folded like an accordian \/\/\/\/\/\/\/\/\/\/\/\/ ). Those formations are known as a protein's secondary structure. Proteins are folded up a bit more, with disulfide bridges and other bonds maintaining the three-dimensional structure that results, called tertiary structure. If multiple chains are involved, the interaction between them is the quaternary structure.

The important aspect of proteins is their three-dimensional shape, which is responsible for almost all protein activity. If some of the hydrogen bonding is disrupted, say by excessive salt concentration, a protein can loose all function, irrrevocably (which is why body temperature needs to stay within certain parameters). Enzymes for example bind to substrate molecules based on the physical shape of the molecule, in a kind of key-into-lock relationship. Teritiary structure is important, in many cases, a structural change on one side of a protein will cause a structural change in the functional parts of the protein (an allosteric effect). An inhibitor for example may bond to an allosteric site on an enzyme, which causes the enzyme's active site to be unable to bond to its substrate, negating its function. This is relevant because it demonstrates that seemingly minor structural changes can have far reaching effects on protein structure.

The cell membrane. This site explains it pretty well and has pretty diagrams. Simply, many proteins are embedded into the phospholipid bilayer that makes up the cell membrane with one end in the intercellular space, a middle part in the hydrophobic bilayer and another part in the cytoplasm. Some act as ion channels, allowing potassium and sodium through that normally couldn't make the transit through the nonpolar center of the membrane. Others, act as receptors for hormones, neuroreceptors, and other chemicals. Those chemicals induce changes in the structure of the protein on the cytoplasmic side of the membrane which causes a number of changes in the cell, causing it to respond appropriately to the stimulus.

Now to physics. Energy is quantized, meaning it can't be just any old value but has to be a multiple of some fundamental quantity. The same goes for the electrons orbiting the nucleus of an atom, they have to have certain orbital energies. In the normal, ground state, of the atom, all the electrons have the minimum amount of energy that they can have. That all changes whenever one of them is hit by a photon. When that happens, an electron becomes an excited and moves to an energy level farther away from the nucleus. This excited state of the atom is unstable and the electron will emit the excess energy and revert back to a lower energy state, eventually making it back down to the ground state. Such excitements disrupt the normal electronic structure of the atom, and if said atom is covalently bonded to another, the molecule as a whole.

Let's put it all together. Some of the light incident on the membrane of a cell hits an allotropic site of a protein embedded in it. This light excites an electron (or possibly a number of electrons), which leaps to a higher energy level. That causes all the atoms it's bonded to to shift its spacial arrangement, which in turn causes a temporary change in the tertiary structure of the protein activating an active site on the other side of the membrane. That sets off chemical reactions inside the cell that cause it to take appropriate action, say releasing neurotransmitters to the nearest nerve cell, or in the case of a unicellular organism, using cillia, flaggella or pseudopodia to move toward/away from the light source.

I hope that I answered your question somewhere in that overkill.

Well, as it turns out, rhodopsin does have a nonpolar region, as evidenced by the fact that in that nifty diagram, it is shown as a membrane protein.

By the way, you are misusing the term bipolar here. What we're looking for is a protein with both polar and non-polar regions. Polar regions have partial charges which may or may not be of the same charge, whereas non-polar regions do not have any parts that are consistantly postive or negative. For example, water is a polar molecule, the hydrogen ends tend to be positive and the area near the oxygen atom tend to be negative, whereas methane is completely non-polar.

from earlier, before all the confusion:

I was making a credibility argument. It seemed to me that sight was a response to light in the environment and thus could be broken into two parts 1)detecting light and 2)responding to it, and since neither was particularly hard to do, the combination would seem all that more probable. I tried to explain above how 1) might work, and as for 2), I reasoned that responding to a particular evironmental stimulus was something that was done in all sorts of blind organisms anyway. Rather primitive organisms will react to heat, physical contact and water salinity, so why not light? All that would have to happen is to have a salt sensitive protein to mutate in such a way that it also reacted to large amounts of photons incident upon it. Since said protein already caused the organism to alter its behavior, it would continue to do so and further modifications would refine the response.

Or, since whatever system employed by the kind of nonseeing organisms in which sight first arose allowed it to respond to a number of different stimuli, it would require only small modification to accomidate a new form of detection. That may or may not be true, but without further looking into it, it seemed plausible at the very least.

Principia

Posts like this, quite frankly, irritate me. It has the same tone of a 5 yr old brat endlessly reciting "why?" to parents or teachers for the sake of saying "why?" without taking anytime to absorb the lessons. If you're asking questions as fundamental as the role of mutations in evolution, luvluv, you really have no business posturing as an open-minded skeptic of evolutionary theory. Regardless of whether or not an evolutionist actually takes his time to bring you up to par from the intellectually deprived depths of Philip Johnson's rhetorical nonsense, you have only succeeded in showing why ID proponents ought not to be dictating how science is taught.

Here, let me give you a clue, luvluv -- evolutionists don't have all the answers. As intellectually curious individuals, they can simply answer "I don't know" to any one of your questions, and science will proceed uninhibited. Why? Because science has a well established method for attacking the unknown. It doesn't relabel "I don't know" with equally ambiguous terminology such as "design" or "irreducible complexity" or "complex specified functional information" and leave it at that.

You may, with all of our leave, keep asking your questions. But, what is distinctly absent from your posts is an alternative approach of answering them -- something that is distinctly different from methodological naturalism. As such, you have offered nothing of substance to the discussion.

Try me.

PS: Oh, oops, I just realized that RBH made observations of a similar nature earlier in the thread.

Doubting Didymus

If everyone could try and lower their hackles, that would be just nice. If this does turn into an arsehole competition, it will be cut down in its tracks before anyone fires their first volley. I, for one, would consider that no small shame.

I'll address one small point, as it relates to my own specific hypothetical scenarios.

Wizardry has already pointed out that rhodopsin is in fact in posession of a non polar region. However, in my example, we've been looking at a mutation in a gene that already coded for a membrane protein. (by 'membrane protein' we're always talking about proteins with the appropriate nonpolar bits). I envisioned a heat sensor already being manufactured for the cell membrane, being duplicated and then mutated. So we aren't trying to do this from scratch, we have raw material to work with. A mutation that makes the second copy unstable, making it open in response to the drop of a hat, or a photon, would then give you a primitive photoreceptor in one easy step.

Now, on a related note, I happen to know that proteins that are ancestors of modern opsins are present in bacteria. I've tried to find information on their function, but without any luck. Does anyone watching have any idea? Are they actually light receptive, or is their function different? Are they located in the membrane?

Peez

luvluv
That all life evolved in a step by step process from a single ancestor.[/b][/quote]Good, we can focus on this.Actually, evolution does not make this claim. Evolution (in the sense of "all life evolved in a step by step process from a single ancestor") does not make any claim about how it happened. It is a scientific fact that life evolved by descent with modification from a common ancestor, just as it is a scientific fact that the earth orbits the sun (another "sweeping claim" of science).Does this mean that you cannot address the points I raised?I don't follow you there.[quoteSo the quickest way to end this little mystery of my intentions is just to stick to proving your case, and not making snipy little comments on everything I say.[/quote]First, nothing in science is ever "proved" in the sense of being established with complete certainty. Second, if you are as biased as some of your posts have suggested, then no amount of evidence would change your mind. On the other hand, I could be wrong about you, and anyway there are others who might benefit from the explanations given here. Finally, you may characterize my comments as "snipy" but the fact remains that you have decided that certain things couldn't evolve before even knowing how they work or how evolution works.O.K., but you seem to be making a general point: If you wish to communicate privately with someone, you may do so with private messages. This is an open board exactly so that everyone may participate.Banging your chest solves nothing, and is unlikely to impress anyone here.Sorry, I should have explained. Even if every lightning strike killed 1,000 amoebas, this would not appreciable affect amoeba populations in the ocean. Note that lighting does strike, and the amoebas are doing fine. Now, let us leave the surface of the ocean and swim down to some thermal vents about one mile below. Are you under the impression that lightning kills a lot of organisms down here?

Peez

Peez

My apologies, DD, for my part in escalating things. Also, I apologize to luvluv for any excessively confrontational comments. I stand my the substance of what I have posted but I realize that the tone has been degenerating and I accept some of the blame.

Peez

Doubting Didymus

Triffic. Now what do bacterial precursors of opsin proteins do?

MrDarwin

luvluv, one thing I've learned in the course of my research is that large morphological differences can result from small genetic differences. In the context of "new information" I had asked you about two groups of plants, one with narrow red hummingbird-pollinated flowers, the other with large green bat-pollinated flowers. Where I was going with this is that although these species were so different that they were classified as different genera, they are interfertile. Not only can they be crossed, but the hybrid seedlings are fertile and breeding them further has demonstrated that the differences are due to a small number of genes that are inherited by very elementary Mendelian principles. Based partly on my research, another scientist reclassified these species in the same genus. Since then, molecular systematic studies have confirmed that these species are very closely related. I believe that even using YEC criteria, they would be considered the same "kind."

Now, this is not an isolated case! Dozens of similar examples are being published every year. Major differences are not difficult to produce by mutation. We know it. We can demonstrate it. It is a non-issue for biologists. And there is no reason not to apply what we know about organisms living today to those that lived in the past: the differences between the very first tetrapods, and the fish that gave rise to them, are not much greater than those between living species that we know are closely related. The large differences accumulated bit by bit, over time, and these gradual changes over time are documented in the fossil record.