davidH

lol,
no it wasn't lost, lol.

And yet as I have said everything I have read contradicts that.
For once and for all lets get this straight.
1. What type of deletions occured?

Maybe this is where I have been going wrong - cause most of the types of mutation I have read about have the word fatal in the sentance. I posted this before showing what I had read. Yet it wasn't answered.
What type of mutations do you claim to be neutral?
Every deletion in the exon basically messes up all that comes after it to a certain point, only those in introns it would seem are neutral.

No I never meant that. I am only questioning whether most mutations are infact harmful. I'm not talking about mutations in the intron but the majority of those in the exon.
On an overall view it may seem that the mutations are infact neutral - but maybe that is because they occurred in the intron, what I'm questioning is whether or not mutations in the exon are mostly neutral.
I am not using it to demonstrate that the theory can't work - but questioning whether if infact the majority of mutations are harmful whether evolution could have occurred. I am not making the mutations being harmful a fact, I'm just questioning something that goes against everything that I have read.

No we can't use our continued presence to prove that wrong. Because mutations are rare - we covered this. Therefore in theory it would be possible that the harmful mutations wouldn't hinder the developement and race of humans. It is safe to assume that the harmful mutations don't render us extinct but not safe to assume that because this apparently contradicts the theory of evolution then the mutations musn't be harmful after all.
Unless you can show that mutations would indeed cause the human race to become extinct.
I am assuming this to be the case (that harmful mutations would cause our extinction) because you argue that our presence contradicts this.
However hypothetically if mutations were harmful and we are still here, then the finger has to be pointed at the whole theory of evolution. Maybe there is another explanation why we are here - therefore you have to be open minded - examine the evidience in the light of reality and not in the light of a theory.
Anyway enough of that.


Really? I had no idea about this. I just have the link to this topic and so I can go straight to it without going through everything else.
Could you give me the link? Thanks.

Are you really sure of this? I don't think it is chance that causes the mutation. True maybe chance mutation can cause resistance to antibiotic but I doubt that is the case with antibiotics in the body.
Why then are you to only take antibiotics if neccessary when you are sick. Why are you to keep on taking the whole lot prescribed and not stop have way through?
Why are the doctors so worried about prescribing antibiotics unless they are absolutely necessary?

Surely they would worry if it was only a chance mutation that caused the resistance and so they could do nothing about.
- Check up on that would you? I really think it is the antibiotics that cause the mutations if they are not concentrated enough to kill a bacterium and are in it's presence.

Thanks for explaining this.
One point however - you are taking this to be in the context of a mutation that occurs by chance and not in the presence of antibiotic. If in the presence of an antibiotic it would mutate and have a massive advantage over is non-resistant ones and so it would dominate.

One more thing cause I have to go here;

Is the energy required to replicate a bit more DNA really going to affect the bacterium all that much? Cause surely the amounts would be minute.

theyeti

What have you been reading, Chick tracts? And contradicts what, that most mutations are neutral or that the harmful ones get weeded out by natural selection? We have given you lots of reasons why most mutations are neutral. The most important are 1) most DNA is "junk" DNA, 2) protein sequences are very plastic and can mutate significantly without affecting function. I don't much care what you've been reading, but if you refuse to believe me then please quit asking.

Why are you caught up on deletions? They are only one kind of mutation, and probably, as far as evolution is concerned, the least significant. Duplications are probably the most important. But anyway, a deletion can be a single base pair, a whole gene, or anything in between.

Most mutations that are talked about are fatal. Obviously, these are the ones of medical significance. The neutral and beneficial ones don't get much mention because no one notices them. But this has nothing to do with the frequency of occurance.

Okay, this is it. This will be my absolute last reply to you. When I claim that most mutations are neutral, it doesn't matter what kind. I am talking about all of them together. Again, you are stuck on deletions, but point mutations are far more common, and they most often neutral. Deletions and insertions cause frameshifts only if 1) they occur within an exon (which only make up 3% of our DNA) and 2) they are not a multiple of three. Even still, there is a possibility that they won't be harmful and even a possiblity of being helpful.

Well I'm glad you clarified that. Most mutations in the exons will still be neutral. First of all, up to 1/3 of mutations will not change the amino acid sequence. Secondly, as I've said, the amino acid sequence is relatively plastic for most proteins. Of the remainer, most will be weakly harmful, and a few will be catastrophic. The goal of mutagenesis (which is a technique that I use) is to try to find the catastrophic ones, since they will tell you how it is that the protein works.

Now it's possible that some are beneficial. But here's the rub. If a protein can be improved upon significantly, we expect that that mutation would have occured already. With known mutation rates, there is more than enough time for ancient proteins to have had all of their amino acids substituted with every other one. So we therefore expect natural selection to have optimized the protein such that there are few if any remaining beneficial mutations left. The exceptions to this are when 1) an organism finds itself in a unique environment such that a given protein is no longer optimized and 2) a novel new protein has been formed that performs a function only very weakly. In both of these cases the chances of a beneficial mutation are much, much greater. So you simply can't look at the chances for a beneficial mutation in a well adapted protein and assume that it's always been like that. This is the main flaw in your reasoning, and I have already tried to explain this at length.

We have covered this, and you're wrong. Mutations are not rare. They have been provided for you in earlier posts, and there have been other threads on this.

Which I never assumed. I did not mention evolution. I merely pointed out that given the known mutation rate (all of us have at least several), if the majority of them were seriously harmful, then each of us would suffer severe deformities and die. This was after bending over backwards to explain to you that most mutations were not seriously harmful, and then you refusing to acknowlede that.

*sigh* The theory of evolution incorporates what we know about mutation, but what we know about mutation is not dependent on the theory of evolution. But what we know about mutation is determined empirically. If all mutations were seriously harmful, then the ammount that we experience would certainly render us extinct. Since we are not extict then either 1) most mutations are not seriously harmful or 2) the empirically derived mutation rate is way, way off. There's no reason to suspect #2 but there is every reason to suspect #1. Why you can't seem to understand this simple logic is beyond me.

Great, go bug Oolon for awhile. Incidentally, you are doing yourself a great disservice by not reading the other threads here, at least if you're interested in learning about evolution in terms of both theory and evidence. The thread in question is <a href="http://iidb.org/cgi-bin/ultimatebb.cgi?ubb=get_topic&f=58&t=000197" target="_blank">davidH: Fossils, Floods and the Age of the Earth</a>. But you can find all threads just by going to the forum main page <a href="http://iidb.org/cgi-bin/ultimatebb.cgi?ubb=forum&f=58" target="_blank">here</a>.

Yes.

Huh?

Because it encourages the spread of antibiotic bacteria by killing off the non-resistant ones. If you stop taking antibiotics halfway through, only the most resistant bacteria will be left, and they will quickly multiply so that now all of them are resistant. Then when you get more antibiotics, they won't work. If you finish your 'scrip, you should kill them all off unless some are fully resistant, in which case you need to switch antibiotics. It is because of Darwinian evolution that doctors must do what they do.

It won't affect it that much, but it doesn't have to. Bacteria replicate very fast, and they are in enormous competition with one another. Any slight advantage one has in terms of metabolic efficiency will mean that its clones will come to dominate. Don't underestimate the power of the force...I mean natural selection.

theyeti

[ February 11, 2002: Message edited by: theyeti ]</p>

Dr Rick

Below is a simpe explanation of antibiotic therapy and resistance.

The mechanisms that cause antibiotic resistance are the same ones that underlie all of evolution: random mutations and natural selection. These processes occur in your body and anywhere else bacteria grow. Antibiotics place selective pressure on bacteria; those that succumb to antibiotics die and do not reproduce their genes while those that survive can pass their genes on to other generations. If a particular gene confers antibiotic resistance then that gene is passed to future generations. Bacteria multiply very frequently, and so resistant organisms can quickly become dominant during the course of therapy as an antibiotic kills the sensitive ones.

Bacterial infections kill by overwhelming a person's body and immune system; antibiotics help the immune system wipe out an infection by killing most of the organisms so that if there are a few remaining resistant bacteria, they are small enough in number that they do not overwhelm the body's defenses.

If a course of antibiotic therapy is stopped prematurely, the remaining numbers of bacteria may be too great for the immune system and the infection may recur or flare back-up. If this happens, the remaining bacterial population will have experienced the selective pressure of prior antibiotic exposure and so will have greater resistance the second time.

Antibiotics should be used only when necessary because repeated usage of antibiotics is associated with increased antibiotic resistance. Generally speaking, the more an antibiotic is used, the greater its environmental presence and effects on natural selection which favors survival of resistant organisms. Also, antibiotics may cause serious and rarely even lethal side-effects in some patients, so their use is an unneccessary risk in patients that aren't sick or likely to become sick without them.

[ February 11, 2002: Message edited by: rbochnermd ]</p>

Quetzal

Re: Nuclear plant disaster in former USSR.

[Morpho raises hand from back of room. "Oooh, ooh, pick me, pick me! I know the answer to this one!"] First, a quibble: the 1986 accident took place in Ukraine at the Chernobyl Nuclear Power Plant (ChNPP), not Russia and not Belarus (I’m currently sitting about 90 km from the heart of the plant). The accident caused atmospheric release of substantial quantities of volatile radionuclides, including Sr-90, Pu-239/240 (an interesting development, since it had not been predicted that Pu could be wind transported), Cs-134/137, and I-131. Very high concentrations of other heavy radionuclides (including U-234/235, rare earth isotopes, etc) were deposited nearer the plant. In all, over 125,000 km2 of the territories of Ukraine, Belarus and Russia were heavily contaminated. The most heavily effected large population center was Gomel, in Belarus (ChNPP is almost on the border with Belarus, and Gomel had the bad luck to be down wind), with Minsk (Belarus), as well as several smaller towns in Russia, being effected. Obviously, the most intensive contamination occurred in the immediate vicinity of the plant, causing the abandonment of numerous small towns and villages, notably Pripyat, and the creation of a 45 km radius exclusion zone around the plant. One of the main foci of my current contract is working with the inhabitants of Slavutych, Ukraine (the town created for the survivors of ChNPP disaster).
Health effects: 31 people died immediately from radiation exposure (including plant workers, firefighters, and military), while 237 were treated for acute radiation sickness. However, as can be imagined, the most problematic health issues are long term, stochastic problems. As you can see from the accompanying chart, there has been a significant (by a factor of 20) increase in thyroid cancer in the effected areas, mostly among children.



There has not been a concurrent statistical increase in birth defects or miscarriage – indicating the radiation did not effect gametes. This is borne out by numerous published studies (I can track at least a few down if anyone’s interested) showing there were no statistically significant increases in either Belarus or Ukraine in chromosome abnormalities and no consistent evidence of a detrimental physical effect of the Chernobyl accident on congenital abnormalities or pregnancy outcomes. In addition, no reliable data have shown any significant association between adverse pregnancy outcome or birth anomalies even in the most contaminated regions. I tracked down one study that seemed to indicate an increase in germline mutations was found among children of exposed workers at the plant (including rescue, firefighter, and cleanup personnel) <a href="http://www.ippnw.ch/content/pdf/Verschiedene_PDF/rs_genetische_folgen_chernobyl.pdf" target="_blank"> here </a> but the article appears to indicate that the mutations are at worst neutral.

These may seem somewhat counterintuitive, until you realize that there is substantial difference between what would be expected from whole-body irradiation and environmental uptake. Increase in thyroid cancers are attributable to ingestion of contaminated milk, food, and water. Chromosome damage, immune system suppression, etc are deterministic results of high-dosage whole body contamination, and therefore would not likely be present except in the cases of people in the immediate vicinity of the plant.

Environmental effects: There were some severe immediate environmental effects in the area surrounding the plant. One example is the so-called “Red Forest” (about 700 m from the plant itself) where over 375 ha (for the metrically challenged, that’s about 900 acres) of pine forest was exposed to incredibly high concentrations of radionuclides (primarily fuel, contaminated control rods, etc) and died to a tree.



There is also anecdotal evidence (no verified statistics that I can find) relating to increased birth defects among domestic cattle (although 15,000 head were destroyed by the government immediately).

However, one of the most fascinating aspects of the disaster is that there appears to be a net increase in biodiversity within the exclusion zone. Obviously, this relates to the absence of humans rather than the presence of beneficial mutations . A 1999 survey by scientists from Texas Tech and the Savannah River Ecology Laboratory, in conjunction with the Slavutych International Radioecology Laboratory, showed the presence of breeding populations of very rare or endangered species in the highly contaminated exclusion zone. As far as radiation effects on the ecosystem around the plant, the only information I’ve got relates to a study conducted in 1997 on barn swallows. The study showed a higher incidence of albinism among swallows. The author believes this is a negative mutational effect – although not fatal. The frequency of albinism among these swallows is substantially higher around Chernobyl than in other populations. There is also correlation on decrease in population density (although it is difficult to determine the causative relationships if any, and there may be confounding variables involved – i.e., albinism as a marker for more severe deleterious mutations). The full citation for this article is: Ellegren H, Lindgren G, Primmer CR, Moller AP. 1997. Fitness losss and germline mutations in barn swallows breeding in Chernobyl. Nature 389:593-596. If your French is any good, you can read a synopsis of the key findings in <a href="http://www.multimania.com/mat66/hirondelle.html" target="_blank"> Les hirondelles de Tchernobyl </a>.

There is an ongoing international effort to monitor and evaluate both the health effects and environmental effects of the Chernobyl explosion. It’s basically too soon to tell…

hammegk

Interesting thread! A few thoughts:
How do ya'all respond to the 'tricky god' hypothesis?
Do the rules needed to guide stochastic processes in a computer (or elsewhere) provide the ID criteria?
Could you comment on John Cairn's work that implied a 'look-ahead' component in bacterial mutation?

theyeti

You're probably referring to the subsequent work of Barry Hall and "adaptive" mutations, which he has also referred to as "Cairnsian" mutations after John Cairns. It was later discovered that the phenomenon ocurrs when some bacteria that are under stress enter into a hyper-mutation phase in which the correct beneficial muation is more likely to come about. There's no "looking ahead" involved, though it did cause quite a stir when it was first discovered. You may want to read recent papers by Patricia Foster.

theyeti

davidH

Sorry for being away so long! But I'm back again.

Just a note to say that I had written quite a bit of stuff (offline) and I pressed something by mistake and everything has been deleted and I can't get it back!! Annoying!

So it did seem to be selective pressure rather than chance. The way I always understood it was that when you stopped taking the antibiotics before the course was finished, the conc. of the antibiotic dropped to a level where it didn't kill the bacteria but applied selective pressure that was enough to cause a mutation in the bacterium rendering it immune to the antibiotic.
Hence the reason why you had to take the full dose - so that most bacteria where destroyed.


Thanks Morpho for the info. I got my information from a national geographic on the disaster so I'll try and get you the details - but maybe you'll find it just as fast yourself.

Yo theyeti, do you believe that mutations and natural selection formed us, or do you know that it did?

Cause this is a point where I have been critised before. I'm told that I believe in a God, yet he can't be seen, felt, "sensed" in anyway, and so my belief is ungrounded.
Yet isn't it the same with evolution? What if the areas that are currently under research find something that completely refutes evolution (hypothetically) and yet you have said that you know that it is true?
You see I think that belief is involved in both.Since belief is involved faith is also involved;
because faith is being....and certain of what we do not see (Heb 11v1)

And yet I have sensed God, hence the reason why I am here.

I can't spend any longer here, but I'll be back soon.

tronvillain

davidH:
Selective pressure does not cause mutations. Go repeat that to yourself a few time. Some antibiotics are mutagens, but that is not the important factor in antibiotic resistance (bacteria become resistant to antiobiotics that are not mutagenic). If you stop taking the antibiotics before you are supposed to, and there is variation in resistance to the antibiotic that has a genetic basis, then you will have selected for antibiotic resistance by killing of the more suceptible bacteria but not the more resistant bacteria. When the population recovers, it will have a much higher frequency of resistant bacteria.

Oolon Colluphid

1. It is irrefutable: he's there to create stuff, except when he isn't, at which point he's still there but just covering his tracks. It amounts to 'because that's how god wanted it', which is a useless explanation (see my post in <a href="http://iidb.org/cgi-bin/ultimatebb.cgi?ubb=get_topic&f=58&t=000250&p=5" target="_blank">this thread</a>).
[Edited to add thread. Doh!]

2. It makes god a liar, and I thought the bible mentioned something about lying not being a good thing. Or is it 'do what I say not what I do'?

3. It is very unparsimonious. It posits not only a completely un-evidenced creator, but then gives him a character which means he looks like he's not there. Except where his promoters think he's needed. See point 1.

Reason enough to discount him from investigations, I'd have thought.

Oolon

[ March 01, 2002: Message edited by: Oolon Colluphid ]</p>

davidH

I don't think that that hypothesis is correct. Because the God of the Bible isn't like that.

Oolon, he is there to be found - if you look for him with all your heart. Those that don't want to find God will always find things to turn to and will find things that they embrace as the truth and try and convince themselves that there is no God. Others shut the fact of God out and convince themselves that they don't care less.