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# Questions on Evolution.

Author Topic:   Questions on Evolution.
Rrhain
Member (Idle past 1145 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003

 Message 16 of 43 (168295) 12-14-2004 11:00 PM Reply to: Message 8 by CreepingTerror12-14-2004 4:13 PM

CreepingTerror writes:

quote:
So can we give a rough estimate to the improbability of evolution?

Given that we can see evolution happen right in front of our eyes, the probability of evolution is exactly 1.

Are you trying to compute the probability that any given, specific organism coming about by evolution? Let me try to show you the difference between those two questions:

Supposed I have a standard deck of 52 cards and I draw one.

What is the probability of me drawing the Ace of Spades?
What is the probability of me drawing an Ace?
What is the probability of me drawing a Spade?
What is the probability of me drawing a black card?
What is the probability of me drawing a card?

See how each of those possibilities becomes more and more probable? i start from the worst case scenario (1 in 52) to a guaranteed result (1 in 1).

Life reproduces chemically. No chemical reaction is ever perfect. Therefore, we will necessarily have changes in the genetic structure from one generation to the next when dealing with the entire population.

Evolution simply has to happen. Unless you are willing to claim that there is perfect replication, then there is no other alternative but evolution.

But in the end, be very careful not to confuse the probability of a specific outcome with the probability of any outcome.

Rrhain
WWJD? JWRTFM!

 This message is a reply to: Message 8 by CreepingTerror, posted 12-14-2004 4:13 PM CreepingTerror has taken no action

Rrhain
Member (Idle past 1145 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003

 Message 19 of 43 (168325) 12-14-2004 11:59 PM Reply to: Message 11 by CreepingTerror12-14-2004 4:38 PM

Re: improbablity of what
CreepingTerror writes:

quote:
Well, my point is that if the entire evo process took Approx 3.5 billion years, and the earth has been around for what 4-4.5 billion years then the universe must be rolling it's dice really well.

Yep, you're confusing the probability of getting a specific outcome with the probability of getting any outcome. You're also combining this with a variant of the logical error of the Anthropic Principle. We should not be surprised to find that a process that can create the conditions we see actually created it.

Here's another exercise in probability:

Suppose you have 10 darts, each of which has a 1-in-10 chance of hitting the target. I throw all 10. What is the probability of me hitting the target at least once? The quick way to determine this is not to try and come up with a list of all possible results where the target was hit at least once but rather to notice that that situation is complementary to the question of finding the probability that the target never gets hit...which can only happen one way.

Thus, the result is (9/10)10: Each dart has a 9-in-10 chance of missing and there are 10 darts, each of which is independent of the others.

Note that this result is about 35%...which means that the complementary probability of hitting the target at least once is about 65%.

And the point? The universe is a huge place. Even if the probability of an event occurring is very low, we have a huge number of chances to get a hit at least once.

There also seems to be a problem of you trying to force a calculation of going from the first life immediately to the current form. Instead, we need to calculate the probability of going from the previous state to the current one. That is, if we are trying to get five 6s on a set of dice, the probability of getting that from a roll of all five dice is very low (two-thousandths of a percent)...but the probability of getting that from a roll of one die given that you've already hit four 6s on the other dice is now 1-in-6.

And that doesn't even consider the chemical specifics that might favor certain reactions over others. If I take two moles of hydrogen gas and a mole of oxygen gas, mix them at standard temperature and pressure, and then spark the mixture, I get water. Yes, there will be some unreacted gas left over and some hydrogen peroxide, but the primary reaction is water. You cannot simply make a calculation of probability based upon an assumption of independence of all variables and that all outcomes are equally likely. It may very well be that the resulting outcome is much more likely than you care to admit.

And I also get the feeling that you're also trying to sneak in abiogenesis into this request of yours. Remember, evolution does not depend upon how life came into existence. Evolution is solely about how life diversified after it came into existence. Life could have arisen chemically through abiogenesis, supernaturally through god zap-poofing it into existence, extraterrestrially through panspermia or alien seeding, interdimensionally through a rift in space-time, or any other method you care to name. So long as that life did not replicate perfectly from generation to generation, then evolution is satisfied.

quote:
and heck, who knows if the planet was favorable for the rise of Evo during that whole time.

See what I mean? The conditions of the earth before life arose are immaterial when it comes to the probability of evolution. Evolution is not abiogenesis nor is it dependent upon abiogenesis. Are you claiming god cannot create life that evolves?

quote:
I mean, evolution is still theory.

So is gravity, quantum mechanics, light, and the idea that germs cause disease. You are confusing the vernacular definition of "theory" as "an educated guess" with the scientific definition of "theory" as "analysis of a set of facts to explain the facts." You cannot have a theory without a fact to base it upon.

When I drop a ball from my hand, it falls to the ground. Since we use words to communicate, we have a word for the force that pulls the ball down and it just happens to be "gravity." That's a fact.

But what is "gravity"? How does it work? It is only through experimentation that we discover universal gravitation of F = Gm1m2/r2 and even that appears to be incomplete. The Pioneer space probes are currently leaving the solar system and their motion cannot be completely explained by our current understanding of gravity.

That's the gravitational theory. The fact that we don't understand everything about gravity (we don't even know what it is...is it a force on particles or a warpage of space-time or something else?) doesn't change the fact that when I drop a ball from my hand, it falls to the ground under the force of gravity. As the cliche goes, when Newton was working on the physics that would change our understanding of gravity, falling apples did not suspend themselves in midair waiting for the outcome.

Evolution is the same way. When we observe populations of organisms over time, they change. Since we use words to communicate, we have a word for the process that causes the change and it just happens to be "evolution." That's a fact.

But what is "evolution"? How does it work? Do characteristics acquired after an organism is born contribute to the characteristics of the next generation (Lamarck)? Or is there something fundamental about the organism that doesn't change except during the reproduction process (Darwin)? It is only through experimentation that we find things like chromosomes and genes and can see how they mutate from generation to generation, how selective pressures actively change the population (and thus determine what set of characteristics we have to work with for the next set of mutations).

That's the evolutionary theory. The fact that we don't understand everything about evolution (is this particular organism a transition between these two or these other two?) doesn't change the fact that when we observe populations of organisms over time, they change.

And notice that we have much more solid evidence for explaining evolution than we do for gravity. We have an actual mechanism for evolution (mutation and selection). We can manipulate that mechanism directly (introduction of mutagens, genetic engineering, artificial selection). We still don't really know what the mechanism of gravity is let alone have a means to manipulate it.

And yet here you are picking on evolution as if it were some unwanted stepchild of science. "Still theory"? That's the best thing there is in science. Theories are what we use to explain facts. There can be no theory without a fact. We cannot have evolutionary "theory" without there being evolutionary "fact."

quote:
We're not completely sure.

Yes, we are.

Here's an experiment you can do in the privacy of your own bio lab. It isn't very expensive and doesn't require very many materials.

Take a single E. coli bacterium of K-type. This means the bacterium is susceptible to T4 phage. Let this bacterium reproduce until it forms a lawn. Then, infect the lawn with T4 phage.

What do we expect to happen? That's right, plaques should start to form and, eventually, the entire lawn will die. After all, every single bacterium in the lawn is descended from a single ancestor, so if the ancestor is susceptible, then all the offspring should be susceptible, too.

But what we actually see is that some colonies of bacteria in the lawn are not affected by the phage.

How can this be? Again, the entire lawn is descended from a single ancestor. They should all behave identically. If one is susceptible, then they're all susceptible. If one is immune, then they're all immune. This can't be an example of "adaptation" because if one could do it, they all could do it.

But since there is a discrepancy, we are left with only one conclusion: The bacteria evolved. There must be a genetic difference between the bacteria that are surviving and those that died.

Indeed, we call the new bacteria K-4 because they are immune to T4 phage.

But we're not done. Take a single K-4 bacterium and repeat the process: Let it reproduce to form a lawn and then infect the lawn with T4 phage.

What do we expect to happen? That's right: Absolutely nothing. All of the bacteria are descended from a single ancestor that is immune to T4 phage. Therefore, they all should survive and we shouldn't see any plaques form.

But we do. Plaques do, indeed start to form. How can this be? Again, all the bacteria in the lawn are descended from a single ancestor that was immune to T4 phage, so they shold all behave identically. If one is immune, then all are immune. There must be something else going on.

Something evolved, but the question is what. What evolved? Could it be the bacteria experiencing a reversion mutation back to K-type? No, that can't be it. Suppose any given bacteria did revert back to wild. It is surrounded by K-4 type who are immune to T4 phage. As soon as the lawn is infected, those few bacteria will die and immediately be replaced by the offspring of the immune K-4 bacteria. We would never see any plaques forming because the immune bacteria keep filling in any holes that appear.

So if it isn't the bacteria that evolved, it must be the phage. And, indeed, we call the new phage T4h as it has evolved a new host specificity.

There is a similar experiment where you take bacteria that have had their lactose operons removed and they evolve to be able to digest lactose again.

You might want to look up the information regarding the development of bacteria capable of digesting nylon oligimers. It's the result of a single frame-shift mutation.

This is evolution. And please don't be disingenuous and claim that it's still a bacterium. Of course it's a bacterium. Evolution doesn't go from bacterium to ostrich in one step. If you could show that happening, you would completely overthrow our understanding of how life diversified and would probably win a Nobel Prize and could write your own ticket for the rest of your life. I am simply pointing out the proof of concept: Life changes from generation to generation.

If 1 + 1 = 2, why can't 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 = 10? We've seen speciation happen both in the lab and in the wild, but those experiments require more equipment and are much more sophisticated.

quote:
Jump me if you want, but that's how I see it.

I'm going to be blunt here: Who cares about how you see it? Reality is not a popularity contest. It does not care about your opinion.

quote:
Fine there's a lot of evidence, but we're not completely sure.

Incorrect. It is because we have a lot of evidence that we are sure. Could we be wrong? Of course...show us a replicatable experiment that takes a single bacterium and produces an ostrich in a single generation and I will be the first to admit we really screwed up. Find a fully formed rabbit fossil in Pre-Cambrian rock strata and I will eat so much crow they will become an endangered species.

But we never see that. We have looked and looked and looked and have never found anything that even hints at contradiction of the basic premise: Populations of organisms change over time. While we are cognizant of the possibility that we are wrong, it would be disingenuous in the extreme to deny all the evidence that seems to indicate that we are right simply to satisfy a personal distaste for what it might mean.

quote:
If you can convince me otherwise

Another blunt question:

Just what experience do you have in biology in general and evolutionary biology in particular that leads you to think that you have an informed opinion to begin with? When was the last time you were in a biology lab? When was the last time you took an actual biology class and spent more than a week discussing evolutionary processes? When was the last time you read a journal article regarding evolution?

Can you really say that you have what it takes to make a reasoned judgement about the fundamental concept of all biology if you haven't actually done any serious work in the subject?

By all means, question those who advocate for evolution. Make them explain themselves. If you don't understand something, don't just accept it. But realize that there is a difference between coming to a subject knowing that you don't know very much about it and coming to it thinking that you are capable of denying what literally thousands of other people have spent every working moment of their lives studying when all you have is the most nebulous of investigation of the field. You just might be able to find out where they went wrong, but you need to know what they did first before you can discover their error.

Rrhain
WWJD? JWRTFM!

 This message is a reply to: Message 11 by CreepingTerror, posted 12-14-2004 4:38 PM CreepingTerror has replied

 Replies to this message: Message 20 by crashfrog, posted 12-15-2004 12:08 AM Rrhain has taken no action Message 22 by CreepingTerror, posted 12-15-2004 12:29 AM Rrhain has replied

Rrhain
Member (Idle past 1145 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003

 Message 21 of 43 (168336) 12-15-2004 12:21 AM Reply to: Message 15 by CreepingTerror12-14-2004 10:35 PM

Re: improbablity of what
CreepingTerror writes:

quote:
But that doesn't change the fact that the chances of a mutation having a beneficial effect are extremely low.

Irrelevant. The vast majority of mutations are neutral and we never notice them. You, specifically, are likely to have 3 to 6 of them compared to your parents. Does that make you defective?

Since the deleterious mutations are selected against, the neutral mutations are neither selected for nor against, and the beneificial mutations are selected for, what do you think is going to happen over time? You seem to be stuck on a single organism, single event mode of thinking. You need to start thinking much more broadly. Evolution doesn't happen to an individual. It happens to a population.

And note that it is difficult to determine if a mutation is beneficial or deleterious until you actually run it through the environment in which it exists. Is having a short, squat body that retains body fat a good thing or a bad thing? What about having a long, lean body that doesn't amass body fat? Wouldn't that depend upon the environment in which you live?

And if the environment changes, mutations that would be considered of one kind might suddenly shift to another. Take the sickle-cell anemia trait. If you're homozygous for it, you'll have trouble but if you're heterozygous for it, you may never know you have it if you aren't in certain types of environments. But one thing that the sickle-cell trait provides is some protection against malaria. And is it really any surprise to find that populations that are likely to have sickle-cell trait in the population are more concentrated in areas that are likely to have malaria as a probable infection? Take someone living on a high mountain with a sickle-cell allele who is having trouble with the thin air and stick him in a hot jungle. What was once a hindrance is now a benefit.

Things are much more complicated than you are making them out to be.

quote:
And as just as unlikely (I'll admit some ignorance on both of these topics) is the perfect combination of molecules to give rise to life.

As I suspected. You are confusing evolution with abiogenesis. The two have nothing to do with each other. Evolution can happen no matter how life arose. Are you seriously claiming god cannot create life that evolves?

That said, you're most likely confusing the probability of going from a completely random set of molecules directly to a living organism rather than dealing with the probability of doing it step-by-step. Getting five 6s on a single roll of five dice is very unlikely. But getting five 6s when you've already rolled four of them is much more possible.

quote:
Have scientists been able to replicate this process (molecules to amino acids to life)to any extent.

You're going to have to define what you mean by "life." We have been able to create, from non-living reagents, self-replicating, homochiral, auto catalysing molecues that evolve. Is that life? If it isn't, it's really close.

But again, that question is irrelevant with regard to evolution. Evolution is something that happens to life after it exists. It does not explain how life came to be in the first place.

quote:
What other scientifically viable theories are there that contradict Evo.

None. That's the thing. People have been trying and trying to find ways to stick it to evolution and they have all failed. That doesn't mean that current evolutionary theory is absolutely, positively correct with no possibility for error. It simply means that you're going to have to do a lot of work in order to overturn it.

And if you are successful, you will be considered a hero. There is no conspiracy against such work. If you could overturn the dominant paradigm of any field, you would become the most celebrated person in that field. There's a reason we remember people like Newton and Einstein and Godel. They completely changed the way we thought about everything.

Rrhain
WWJD? JWRTFM!

 This message is a reply to: Message 15 by CreepingTerror, posted 12-14-2004 10:35 PM CreepingTerror has taken no action

Rrhain
Member (Idle past 1145 days)
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003

 Message 39 of 43 (168402) 12-15-2004 4:14 AM Reply to: Message 22 by CreepingTerror12-15-2004 12:29 AM

Re: improbablity of what
CreepingTerror responds to me:

quote:
Good post, except for the part where you told me to shut up because I'm not as smart as you.

No, I was not saying you're not as smart as me. I was saying that it seems you may not be as experienced. Just because people are brilliant doesn't mean they are capable. Stephen Hawking is a genius, no doubt, but I would doubt if he understood the deep complexities of open heart surgery. While a good grounding in investigative pursuits can help a person figure out how one might go about solving a problem, it doesn't really help in the actual solving. Experience and familiarity with a subject count for something and when we're dealing with fields that are as wide-reaching and all-encompassing as evolution, it requires a tremendous amount of work and effort to effectively discuss it.

I am not a biologist. I'm a mathematician. However, in the process of getting my math degree I took a fair amount of biology (population bio is very math-centric). I wouldn't dream of claiming I understand it all, but I do have some experience. I've read the books, done the homework, and spent some time in the lab.

Now, I don't want to get into a fight over credentialing. That's the logical fallacy of the argument from authority. People aren't right because they're important or have sheepskins out the wazoo. They're right because they have the evidence and analysis to back up their claims. But in order to get the evidence and do the analysis, you have to get your hands a little bit dirty. The wonderful thing about science is that anybody can do it.

Take astronomy, for example. It doesn't take a lot of equipment to become an amateur stargazer and if you're willing to spend hours in the cold, dark night far away from civilization in order to get away from the light pollution, you can do an amazing amount of work. Many new celestial objects are discovered by amateur astronomers. The sky is so big and events happen so quickly that no one person or group can possibly see all of it. The professional astronomers find the amateur ones quite helpful because they are looking where the professionals aren't. While you won't be able to get data as detailed or far reaching as the Hubble, every comet and asteroid we find is more information about how the solar system came to be and how it functions. By all means, go out and look up.

My comment was a challenge, though. Consider the possibility that maybe, just maybe, you're wrong. If (and mind you, I said, "if") that were the case, what would you do to find out how things really functioned? You'd have to go out and look at things, fiddle with them, ask others for their experiences, share your results, and try to replicate theirs, right?

My question was asked to find out just how much of that you have done. It isn't a crime not to have done much. Nobody can be an expert on everything. And even the experts weren't always so and had to start somewhere. Everybody has ideas about how things ought to be, but hopefully you will approach this subject with the open mind you said and I hope you have.

quote:
What are some examples of speciation in a laboratory, not saying it can't happen mind you, just I'd like to know what they are.

Here are a few...and even some at higher levels of taxa:

Ishikawa M, Ishizaki S, Yamamoto Y, Yamasato K.
Paraliobacillus ryukyuensis gen. nov., sp. nov., a new Gram-positive, slightly halophilic, extremely halotolerant, facultative anaerobe isolated from a decomposing marine alga.
J Gen Appl Microbiol. 2002 Oct;48(5):269-79.
PMID: 12501437 [PubMed - in process]

Kanamori T, Rashid N, Morikawa M, Atomi H, Imanaka T.
Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the alpha-Proteobacteria.
FEMS Microbiol Lett. 2002 Dec 17;217(2):255-261.
PMID: 12480113 [PubMed - as supplied by publisher]

Fudou R, Jojima Y, Iizuka T, Yamanaka S.
Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: Novel moderately halophilic myxobacteria isolated from coastal saline environments.
J Gen Appl Microbiol. 2002 Apr;48(2):109-16.
PMID: 12469307 [PubMed - in process]

Golyshin PN, Chernikova TN, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM.
Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.
Int J Syst Evol Microbiol. 2002 May;52(Pt 3):901-11.
PMID: 12054256 [PubMed - in process]

Ivanova EP, Mikhailov VV.
[A new family of Alteromonadaceae fam. nov., including the marine proteobacteria species Alteromonas, Pseudoalteromonas, Idiomarina i Colwellia.]
Mikrobiologiia. 2001 Jan-Feb;70(1):15-23. Review. Russian.
PMID: 11338830 [PubMed - indexed for MEDLINE]

Stackebrandt E, Schumann P.
Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae.
Int J Syst Evol Microbiol. 2000 May;50 Pt 3:1279-85.
PMID: 10843073 [PubMed - indexed for MEDLINE]

Rrhain
WWJD? JWRTFM!

 This message is a reply to: Message 22 by CreepingTerror, posted 12-15-2004 12:29 AM CreepingTerror has taken no action

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