Nat

"I have to admire your forbearance with Vanderzyden here, but I can't help but wondering why someone who is so eager to take on the knowledgeable students/doctor/scientists in this forum doesn't want to take the trouble to learn the most rudimentary basics (i.e. definition of a "point mutation") first. "

It certainly concerns me, but if he stays civil, I'll indulge him.

Vanderzyden

lpetrich

Please tell us more, and provide a good web resource if you are aware of one.


Thanks,

John

Jesus Tap-Dancin' Christ

This is high-school genetics. I went through it in 9th grade.

DNFTT

ps418

Support for my claim that mutations are not universally harmful, but also neutral and sometimes beneficial? It would make more sense to provide that information on this thread. Regarding neutral mutations, this is simply basic genetics. For instance, to take once example, most codons can tolerate point-mutations in the third base position, and still code for the same amino acid, and thus the mutations would be neutral. Regarding beneficial mutations, you can read find information about some examples on the internet.

<a href="http://www.gate.net/~rwms/EvoMutations.html" target="_blank">Examples of Beneficial Mutations and Natural Selection </a>

<a href="http://www.talkorigins.org/faqs/mutations.html" target="_blank">Are Mutations Harmful?</a>

<a href="http://www.nmsr.org/nylon.htm" target="_blank">NMSR - The Nylon Bug</a>

<a href="http://iidb.org/ubb/ultimatebb.php?ubb=get_topic&f=58&t=000070" target="_blank">Topic: Another Beneficial Mutation In Humans </a>

<a href="http://www.cs.colorado.edu/~lindsay/creation/dup_favorable.html" target="_blank">Can A Duplication Mutation Be Beneficial? </a>

Regarding my statement that even AiG acknowledges the existence of beneficial mutations, see the article: <a href="http://www.answersingenesis.org/Home/Area/faq/dont_use.asp" target="_blank">Arguments we think creationists should NOT use. </a>

Patrick

scigirl

I'll try to explain the difference between a point mutation and a frameshift mutation:

Here is a very short DNA sequence:

ATG CAC CAA TGG

The corresponding mRNA sequence for this gene would be then:

AUG CAC CAA UGG

Here's the protein sequence:

M H Q W

(these letteres represent the amino acids methionine, histidine, glutamine, and tryptophan).

Note that the code is non-overlapping. That's a very important concept to know. Also, it takes three bases to make one amino acid.

Now let's give our gene a point mutation (I'll just show the RNA sequence):

AUG CAC CAA UGA

A point mutation is a change in one base which only affects one amino acid. You can think of it as one base turning into another base. There is still the same number of bases in the gene. Note that if the code was overlapping, point mutations would usually affect more than one amino acid. But - it isn't, and they don't.

Here's our new protein:

M H Q

What happened to tryptophan? Well the ribosome was reading along, and it read "UGA." In this case, instead of recruiting an amino acid, it stopped and let go of the mRNA. This is what a stop codon does - it stops translation. Note we still have most of our protein though.

This is an example of a "nonsense mutation" - a codon that used to code for something turned into a codon that coded for nothing (nonsense). Other point mutations could turn a codon for one amino acid into a codon for another amino acid, and this is called a missense mutation. Here's an example of that:

AUG CAC CAA GGG

would give us M H Q G (G now stands for glycine, not guanidine of course!)

Some point mutations are devastating to the protein, and others are harmeless. Still others "improve" the protein's function. The distinction between a 'variation' and a 'mutation' in the genetic code is not an easy one to make.

Anyway, let's move on.

Now we are going to make a frameshift mutation.

I am going to delete the first base.

AUG CAC CAA UGG ----&gt;

UG CAC CAA UGG

But remember ribosomes read in threes, and only read in one direction. So here's the new sequence, as viewed from a ribosome's point of view (I love anthropomorphism!)

UGC ACC AAU GG

Our new protein:

C T N

(Don't be thrown off by the fact that some amino acid letter codes are C and G - they are not referring to the mRNA anymore! C = cysteine, T = threonine, N = asparagine)

The GG can't code for anything cuz it's only 2 bases.

Note that our protein is completely different. Before it was either shorter (with the nonsense point mutation) or had a different base at the end (the missense point mutation).

The frameshift mutation not only made our protein shorter, but it changed the entire sequence downstream of where the deletion occured! In other words, it affected more than one base.

You can see that a lot of these mutations are drastic - and it probably doesn't seem like they can contribute much to evolution. Well nonsense and frameshift mutations probably don't (unless you are talking about viruses.) However, you can also see that simple missense point mutations could change the sequence of a protein ever so slightly to give it a new function.

If you want to explore evolution, you need to learn about gene duplications and THEN point mutations and other stuff. The gene gets duplicated - so the cell has one good copy, and one to play around with. That's how hemoglobins evolved.

scigirl

scigirl

Once again I urge you to check out this <a href="http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html" target="_blank">on-line biology book</a>.

It has great explanations, and it also explains how we know that, say, the code is non-overlapping.

Here's the code translator, which might be helpful to you:



Here's how to read amino acid language:

<a href="http://www.mun.ca/biochem/courses/3107/aasymbols.html" target="_blank">http://www.mun.ca/biochem/courses/3107/aasymbols.html</a>

A Ala alanine
C Cys cysteine
D Asp aspartic acid
E Glu glutamic acid
F Phe phenylalanine
G Gly glycine
H His histidine
I Ile isoleucine
K Lys lysine
L Leu leucine
M Met methionine
N Asn asparagine
P Pro proline
Q Gln glutamine
R Arg arginine
S Ser serine
T Thr threonine
V Val valine
W Trp tryptophan
Y Tyr tyrosine

scigirl

scigirl

I think in all this frameshift/point mutation fray, the fundamental question posed in the first thread is being lost.

Let's list the facts as we know them:

1. Humans have in their DNA a sequence that correlates to the following protein sequence:

Human Urate Oxidase Pseudogene translated:

Met A H Y H N N Y K K N D E V E F V R T G Y G K E Met V K V L H I Q Stop D G K Y H S I K E V A T S V Q L T L S S K K D Y L H G D N S D I I P T D T I K N T V H V L A K F K E I K S I E A F G V N I C E H F L S S F N H V I R A Q V Y Met E E I P W K H L G K N G V K H V H A F I H T P T G T H F C E V E Q L R S G P Q V I H S G I K D L K V L K T T Q S G F E G F I K D Q F T T L P E V K D Stop C F A T Q V Y C K W R Y H Q C R D V D F K A T W D T I R D L V Met E K S A G P Y D K G E Y L T S V Q K T L C D I Q V L S L S R V P A I E D Met E I S L P N I H Y F N I D Met S K Met G L I N K E E V L L P L D N P Y G K I T G T V K R K L S S R L Stop

2. The sequence, without the stop codons, is found to make a fully functional protein - the urate oxidase protein - in other animals.

3. In humans, and in chimps, and in gorillas, this same sequence exists, WITH the stop codons. However, due to the stop codons, it is non-functional. This DNA sequence does not make protein.

4. Scientists have observed point mutations occuring in nature, and have discovered several natural causes of them.

Vanderzyden - do you dispute any of those facts?

Whether or not there might be a survival advantage to not making the protein, let's just examine these facts. If a creator didn't want humans to make the urate oxidase gene at all, than why even bother giving us nearly the entire sequence, and giving chimps the same sequence with the same mutation? The gene isn't doing anything - why go through the effort of preserving lots of the gene, but throwing in a couple stop codons for fun? Why not just leave it out?

And why is this similarity seen in chimps and bonobos if we are not really related?

I just don't get intelligent design. I fail to see how the logic works.

Evolution not only explains why, it explains how. We have the gene sequence in our DNA because at one point, our ancestors actually made this protein. Then it was mutated at some point, and this gene - mutations and all - was passed on throughout generations.

Then you find out that the lack of this gene may have given us a survival advantage - and boom - even more support for evolution. Our DNA is mutating and changing around all the time - and occasionally it gives us some new quirk that helps us survive better in a certain environment and gets passed on.

scigirl

Ha and i forgot to posit the fundamental question that I thought was getting lost. Here it is:

And yes, Vanderzyden, you need to answer the question 'why.' Well maybe you don't, but the theory of intelligent design DOES need to answer it, because right now all they are doing is, "Well evolution does have an explanation as to why and how this happened, but we just know they are wrong, and that God did it for . . some reason we just don't know." They can believe that if they want, but it isn't a scientific statement in any form or fashion.

[ October 26, 2002: Message edited by: scigirl ]</p>

pz

No, it is not. Your definition is false.
Good grief. This guy has the gall to argue with biologists, and he doesn't know the answer to those questions? That's trivial stuff that you learn in high school biology!

Why are we wasting our time with this [expletive][redacted noun]?

RufusAtticus

It really worries me that Vander is so quick to poopoo evolution and when he doesn't even know the basics of Genetics.

It's like me poopooing engineering without understanding welding.

Nat

"It's like me poopooing engineering without understanding welding."

Hey - I did my undergrad in engineering (electrical) and I sure as hell wouldn't trust myself with an arc welder!