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  Topic: AF Dave Questions Human-Chimp Chromo Evo, Creation/Evolution Debate< Next Oldest | Next Newest >  
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 05 2006,05:27   

Another layman question ... what's the meaning of 5' and 3' ... what do the numbers designate and what do the single quote marks indicate?

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: May 05 2006,05:48   

Dave asks:

I am wondering about what Alan Fox meant by this ...
Quote
Oooh, I think I see a problem. the codons that alternate would have to be of the same number of nucleotides or master/complement will not work.


Let me anwer by saying it was a stupid remark. Codons will, of course have the same number of bases in both strands, so the remark is not even wrong.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,05:53   

Quote
Another layman question ... what's the meaning of 5' and 3' ... what do the numbers designate and what do the single quote marks indicate?


They indicate that the person who said this--

Quote
(1) No one to my knowledge has ever proposed a stepwise solution of HOW the 2A and 2B chimp chromosomes joined.  This appears to be a HUGE obstacle.
(2) The join was 'head-to-head'.  If my understanding is true (stated below) that chromosomes are read in only one direction, then this would be a SECOND HUGE OBSTACLE.
...

The blow for Neodarwinism comes, however, with the discovery that the theoretical ‘join’ is head-to-head. Since the chromosomes are always ‘read’ in the same direction, this means that the same ‘sentence’ would be read backwards, and would make no biochemical sense!


--hasn't got so much as a freshman's understanding of biology, yet shoots his mouth off about it.

   
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: May 05 2006,05:54   

afdave

From here
Quote
Each strand has polarity, such that the 5'-hydroxyl (or 5'-phospho) group of the first nucleotide begins the strand and the 3'-hydroxyl group of the final nucleotide ends the strand; accordingly, we say that this strand runs 5' to 3' ("Five prime to three prime")

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,06:26   

Let me give you an analogy, AFDave. Imagine you were interested in the question of whether we were nearing the Peak Oil point, so you hung out on Peak Oil blogs with geologists. And one day, somebody showed up there and posted
Quote
"You're all wrong, there's infinite gasoline, we'll never ever ever run out of gasoline, just look at this link to SomeCompleteCrank.com. And by the way, what the heck is "petroleum"?


Do you see how that guy looks? Well, that's what you look like, here.

   
Glen Davidson



Posts: 1100
Joined: May 2006

(Permalink) Posted: May 05 2006,06:26   

Quote
Dave, you must learn that authority is no substitute for learning the issues involved yourself.

why don't you pick up a basic biology textbook sometime and learn these things for yourself?


I have to agree.  The problem with Dave is not that he doesn't know what 5' and 3' prime are, for example, but that he has no interest in learning for learning's sake--at least not with regard to evolution.  

And he cannot learn biology and evolution by giving him the answers.  That is superficial, and is the sort of "knowledge" that Dave already confuses with scientific learning.  It is probably not best to feed his mistaken beliefs by "filling in the gaps" of a "knowledge base" that is fundamentally predisposed against any objective analysis of the evidence.

--------------
http://tinyurl.com/mxaa3p....p

Nothing in biology makes sense except in the light of coincidence---ID philosophy

   
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 05 2006,06:50   

Quote
why don't you pick up a basic biology textbook sometime and learn these things for yourself?  


Thanks for the tip but Google's faster.

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
Glen Davidson



Posts: 1100
Joined: May 2006

(Permalink) Posted: May 05 2006,07:07   

Quote
Thanks for the tip but Google's faster.


And much less thorough.  That's the problem with you, DAve, you don't care to get an integrated education, but prefer to pick of "facts" to bolster your prejudices.

This was the point of my post, but as usual, you fail to understand even what it is that you lack.

--------------
http://tinyurl.com/mxaa3p....p

Nothing in biology makes sense except in the light of coincidence---ID philosophy

   
Carol Clouser



Posts: 29
Joined: Jan. 2006

(Permalink) Posted: May 05 2006,07:08   

See folks, as I have maintained all along, creationists CAN be reasoned with. It just takes patience and perseverance.

Now, if we could only nail down their misguided reading of the Bible. That would obviate the need for Panda's Thumb and we could all go home.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: May 05 2006,07:58   

Quote
what's the meaning of 5' and 3'
This is a good illustration of the DNA backbone:

You can see from this that there is clearly a direction thats runs from the 5 prime carbon of one sugar to the 3 prime carbon of the other. The 'prime' is used to number the carbon atoms.

  
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 05 2006,08:28   

Thanks.  When is uni-directional reading important?  And when is it not?  I think I saw someone say that it is important for some things.  I'm trying to understand where exactly the AIG author went wrong. (other than the jokes about they woke up that morning, they went Creo, etc.)  :-)

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
Flint



Posts: 478
Joined: Jan. 2006

(Permalink) Posted: May 05 2006,08:43   

Quote
I'm trying to understand where exactly the AIG author went wrong.

But the jokes have a barb in them, yes? The AIG author went wrong in his initial conviction that reality simply *could not* be true, since it contradicts his convictions. And so he went searching for some example of how reality got it wrong. Ignorance of the topic is a great assistance in this search. Taking it for granted that God approves of lies intended to trick the audience into correct beliefs also helps a lot.

Now, armed with righteous ignorance backed by righteous dishonesty, the AIG person can defeat every windmill reality presents to him, at least in his own mind. The chromosome error is an entirely typical example, not exceptional in any way.

  
Rilke's Granddaughter



Posts: 311
Joined: Jan. 2005

(Permalink) Posted: May 05 2006,08:48   

Quote (Carol Clouser @ May 05 2006,12:08)
See folks, as I have maintained all along, creationists CAN be reasoned with. It just takes patience and perseverance.

Now, if we could only nail down their misguided reading of the Bible. That would obviate the need for Panda's Thumb and we could all go home.

But Carol, you exist as the perfect counter-example.

And since the Thumb has nothing to do with religion, your point is meaningless.

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: May 05 2006,08:58   

Quote (afdave @ May 05 2006,13:28)
Thanks.  When is uni-directional reading important?  And when is it not?  I think I saw someone say that it is important for some things.  I'm trying to understand where exactly the AIG author went wrong. (other than the jokes about they woke up that morning, they went Creo, etc.)  :-)

It's always important. Replication and transcrition only occurs by 'reading' the master strand from 3' to 5' (therefore, DNA and RNA are synthetised in the opposite direction 5' -> 3';).

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,09:46   

Dave, here's the problem. You're not equipped to understand biology well enough to understand why AiG's arguments are without merit. The writers at AiG are counting on their other readers having the same problem.

Unfortunately, unless you're willing to take the time and effort to at least take a few undergraduate biology classes, you're never going to be equipped to understand why these arguments are incorrect.

So what should you do? Well, you should do what the rest of us non-specialists do: you should place credence in the work of people who actually do have the competence to understand this stuff. In other words, the scientists who are doing the work. You should basically stay away from sites like AiG, because those guys most emphatically are not doing any actual research. They either honestly don't know what they're doing, and are leading you astray, or they do know what they're doing and are counting on you not knowing what they're doing, and leading you astray.

If the AiG guys really were doing any research, they'd be publishing it (and I mean in peer-reviewed scientific journals, not on some website intended for naive non-specialists).

In science, dishonest research is always eventually uncovered. The history of science is littered with examples, and there's even an annual prize awarded—the IgNobel Prize—for the most ludicrously wrong research (awarded by the Journal of Irreproducible Results).

On the other hand, bad, wrong, dishonest, deceitful claims are never retracted by groups like AiG. Dembski's another example. His work has been refuted again and again and again, and yet somehow he never issues retractions.

--------------
2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
incorygible



Posts: 374
Joined: Feb. 2006

(Permalink) Posted: May 05 2006,11:00   

Quote (afdave @ May 05 2006,13:28)
Thanks.  When is uni-directional reading important?  And when is it not?  I think I saw someone say that it is important for some things.  I'm trying to understand where exactly the AIG author went wrong. (other than the jokes about they woke up that morning, they went Creo, etc.)  :-)

Afdave,

As to where the AIG author went wrong, Flint's answer above is probably most accurate.  More superficially, however, he seems to have confused a chromosome with a single strand of DNA. DNA strands are paired in chromosomes, but only single strands are transcribed (as the AIG author notes, in one direction only).  The author's elementary mistake (a high-school student would know better) led him to the wrong conclusion about a "head-to-head" fusion being read "backwards".

Let's work it out so you can see for yourself.

Our simplistic AIG author (erroneously) imagined two single strands of DNA, say, ACGCTA and GGAACT, and realized that if these two strands were fused "head-to-head" vs. "head-to-tail", ACGCTAGGAACT would transribe a different product than ACGCTATCAAGG.

Of course, this simplification was completely wrong, as any high-school biology student could point out: chromosomes are paired strands of DNA that only 'fit together' in 5' to 3' backbones.

Here is the correct situation.

Suppose we start with two simplified "chromosomes" of 6 base-pairs each, with each of those 6 base units coding for a protein product (1-4):

Chromosome a:
3' ACTGAG 5' (Protein 1)
5' TGACTC 3' (Protein 2)

Chromosome b:
3' CGCAGT 5' (Protein 3)
5' GCGTCA 3' (Protein 4)

So our four 'proteins' are 'read' (3' - 5' remember) from the sequences ACTGAG (1), CTCAGT (2), CGCAGT (3), and ACTGCG (4).

Note that the DNA backbone fits together 5' - 3' (see the above diagram), so if these two chromosomes were to fuse, it would be by matching a 5' end with a 3' end.

Here's where the AIG author goes wrong -- he notices that our new fused chromosome has two potential forms (assuming it fuses in the order a - b, otherwise it's four, but I'll stick to two because it makes no difference). I've noted the point of fusion with a dash.

By matching 5' to 3', chromosome ab could look like:

3' ACTGAG-CGCAGT 5'
5' TGACTC-GCGTCA 3'

OR the "inverted" (note this term has no real meaning, nor does "head-to-head" in the AIG Author's sense)

3' ACTGAG-ACTGCG 5'
5' TGACTC-TGACGC 3'

Looking at the proteins transcribed by each of the potential fused chromosomes, you'll see that they would result in identical gene products (read the sequences from 3' to 5', and substitute our protein numbers above):

3' 1-3 5'
5' 2-4 3'

vs.

3' 1-4 5'
5' 2-3 3'

So you can see, all the 'genes' are read correctly and transcribed for the chromosome as a whole, and our AIG author didn't think too hard (at all?) about the windmill he was tilting at.

Of course, this is all very simplistic (I've kinda skipped the whole RNA thing, etc.).  If you want a more accurate picture, sketch out 'chromosomes' that are more than one 'protein' long.  Or better yet, as you've been advised before, open a biology textbook and really learn how this stuff works (knowing more than an AIG author doesn't cut it).  You'll also figure out all kinds of interesting things, like why chromosomal recombination (mixing up heads and tails happens relatively frequently during sex ;) ) can be severe if it occurs in the middle of a coding region (as opposed to outside it).  Open the book, sketch it out, and see for yourself.  (Hint: how would the result be different if 1, 2, 3 and 4 weren't independent genes/gene-products, but parts of the same gene/product? What would that mean for the 1-3 vs. 1-4 chromosomal arrangements shown above?)

(Edited a few times to make it as clear as possible.)

  
ltracey



Posts: 4
Joined: May 2006

(Permalink) Posted: May 05 2006,14:29   

Quote (afdave @ May 05 2006,11:50)
Quote
why don't you pick up a basic biology textbook sometime and learn these things for yourself?  


Thanks for the tip but Google's faster.

Google may be faster but it's only helpful if you:
a) know what sources are reliable vs. those that aren't trustworthy
b) have a basic understanding of the topic you're looking to find more about
c) Are willing to wade through some chaff to get to the wheat.

It may be faster, but it's like feeding your brain Mickey D's too much.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,14:46   

Quote


Google may be faster but it's only helpful if you:
a) know what sources are reliable vs. those that aren't trustworthy
Quoting AiG pretty much means the quoter can't tell science from jargon-heavy babbling.

   
Tom Ames



Posts: 238
Joined: Dec. 2002

(Permalink) Posted: May 05 2006,15:29   

Quote (afdave @ May 05 2006,08:27)
Another layman question ... what's the meaning of 5' and 3' ... what do the numbers designate and what do the single quote marks indicate?

I don't feel that it's appropriate to pile on afdave, but something needs to be pointed out. This quote of his ought to be contrasted with an earlier quote:

Quote
I can see that the Flank and Davidson have read the book ‘How to Win Friends and Influence People’ … I have an idea for a simple, fun exercise. I’m an Electrical Engineer and business man and I used to fly AF jets. I like simple, uncomplicated arguments and I like people to cut to the chase … fast. Let’s say I was undecided about where life on earth came from or how it began. I hear the YECs and the ID people saying it came from an Intelligent Agent/God or whatever. I hear the Darwinists saying it happened by chance evolution. And everybody quotes all these long-winded academic sources. I would love to hear from each of you, everybody in YOUR OWN WORDS, not referring to a single outside source what YOUR theory is and WHY you believe it in 5 simple statements, i.e. the top 5 reasons for your belief. Take me from when and how it all began to where you think its going and why … very short and simple so my pea brain can understand it … try explaining it nicely and politely.


The point being that complicated technical subjects cannot be transmitted to uneducated listeners in "5 simple statements".

Someone who's never come across the 5'->3' convention for DNA strand direction is simply not equipped to understand the molecular arguments for evolution. There's no shame in this: it is, after all, a specialized and technical body of knowledge. But I would not presume to say to afdave "I've never understood why airplanes don't need to flap their wings. Could you teach me how to fly a jet next week?"

The DI and AiG's pseudoscientific truthiness encourages people to expect that the principles of molecular evolution are within the grasp of everyday uninformed intuition.

But intelligent readers ought to be able to appreciate why this is not so. If they want to become informed they'll start by assuming the humility of the novice. If they simply want to continue pushing a partisan or sectarian agenda, they'll not let ignorance be a barrier to expressing their opinion.

--------------
-Tom Ames

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,15:36   

Tom Ames said:
Quote
blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah


Tom, I like to cut to the chase. Please explain what that post means in three words. And no outside sources.

And then I'll tell you why I don't believe you.

   
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 05 2006,18:18   

Quote
"I've never understood why airplanes don't need to flap their wings. Could you teach me how to fly a jet next week?"
I'm not asking anyone to teach me to BE a molecular biologist.  I'm just trying to find the truth about certain biological realities by relying on supposed experts on both sides of the controversy.  I think people on both sides are necessarily a little biased toward their own viewpoint, but I trust that each strives for the truth as best they know how.  I enjoy hearing from you guys, and up until this little incident, I have found AIG to be reliable.  One would think a medical doctor at AIG would be a reliable source, and in all fairness to him, he may be reliable in many areas.  And I'm not ready to call him a liar until I hear his side of the story.  We have seen that Dr. LeJeune was mistaken about Down's syndrome as well--it happens.

Thanks 'incorygible' for the detailed explanation.  I would be interested to hear Alan Fox and Jeannot's comments on incorygible's explanation and also would like to know what your specialties are.

Thanks!

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: May 05 2006,19:04   

Quote (afdave @ May 05 2006,23:18)
I'm not asking anyone to teach me to BE a molecular biologist.  I'm just trying to find the truth about certain biological realities by relying on supposed experts on both sides of the controversy.


But therein lies the rub, Dave. In order to evaluate the evidence in favor of evolution, if you're not going to take the word of the scientists doing the research, you need to be a molecular biologist.

Or, you could do some research into the backgrounds of the people making the claims. If you're looking at, e.g., DNA evidence connecting humans and chimps, you're going to want to read stuff written by people who work in the relevant field. Especially people who have left a long paper trail of peer-reviewed articles in their field of expertise. One thing you'll quickly find is that the people with AiG and the Discovery Institute have not left such a paper trail, at least not in the relevant fields. A prime example would be William Dembski. Demski has a graduate degree in mathematics (which is the only remotely relevant field; his other degrees are in philosophy and religion), but he's published virtually no peer-reviewed articles in mathematics, and none in the field in which he is supposedly an expert: information theory. Dembski has absolutely no formal training in biology, which is why little he says about the field has much credibility.

Granted, there's more to science than credentials. But when you have one person, e.g., Michael Behe, who has published virtually nothing of note in peer-reviewed articles on the topic of "irreducible complexity" contradicted by people who publish a dozen or more papers a year in the relevant fields, it should be obvious who has more credibility.

Quote
 I think people on both sides are necessarily a little biased toward their own viewpoint, but I trust that each strives for the truth as best they know how.


I doubt it. Members of the DI and AiG have been caught again and again in flagrant misrepresentations of the research of others, while at the same time performing virtually no research of their own. You can't simply do a "he said, she said" balance between the statements of evolutionary biologists and ID/Creationists.

--------------
2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
incorygible



Posts: 374
Joined: Feb. 2006

(Permalink) Posted: May 06 2006,00:18   

Quote (afdave @ May 05 2006,23:18)
'm not asking anyone to teach me to BE a molecular biologist.  I'm just trying to find the truth about certain biological realities by relying on supposed experts on both sides of the controversy.  I think people on both sides are necessarily a little biased toward their own viewpoint, but I trust that each strives for the truth as best they know how.  I enjoy hearing from you guys, and up until this little incident, I have found AIG to be reliable.  One would think a medical doctor at AIG would be a reliable source, and in all fairness to him, he may be reliable in many areas.  And I'm not ready to call him a liar until I hear his side of the story.  We have seen that Dr. LeJeune was mistaken about Down's syndrome as well--it happens.

Thanks 'incorygible' for the detailed explanation.  I would be interested to hear Alan Fox and Jeannot's comments on incorygible's explanation and also would like to know what your specialties are.

Thanks!

*sigh* You recognize your question is one of "biological realities", and yet still insist on investigating "both sides of the controversy". You don't need expert opinion or punditry here, afdave; you need education. I (and others) tried to point you in the right direction, showing you why the source of your argument was woefully in error when it came to the absolute basics. That direction was to a biology textbook for the mechanics of DNA transcription, etc. Your question isn't about origins, ID, or evolution; it's about basic microbiology (sorry...I think AiG would term it "operational science" as opposed to "historical science", right?). If, after all this, you insist on playing "he said, she said" with a biology text and an AiG screed, well, best of luck. If it's credentials you're after, I'm sure AiG has a few touted PhDs in something or other that will put my lowly and damning MSc in evolutionary ecology to shame and justify your ignorance.

  
sir_toejam



Posts: 846
Joined: April 2005

(Permalink) Posted: May 06 2006,15:04   

Quote
justify your ignorance


bingo.

that's the only reason dave and tdiddy are here.

they want us to justify their ignorance for them, so they can feel better about themselves.

they don't want us to tear down their irrational defenses, they want us to reinforce them.

Now, only the truly desperate will stick it out here week after week, when again and again they are given nothing to prop their defenses up with.

Rather than answering their moronic questions, you all should be directing them to seek treatment from a mental health care professional.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: May 06 2006,15:41   

SHHHHHHH! The Ghost of Paley who's getting therapy isn't the Ghost of Paley who will make me laugh with a childish geocentricity model. Hush you. I want him to put forth a model so I can get all a = g + T/m - 2w x v* on his a55.



*: equation of motion for Foucault's pendulum, in a rotating reference frame, neglecting the x' and y' terms.

   
normdoering



Posts: 287
Joined: July 2005

(Permalink) Posted: May 06 2006,16:58   

Quote (afdave @ May 05 2006,23:18)
... up until this little incident, I have found AIG to be reliable.

That's almost funny.

What you mean is that you know so little of the subjects they discuss that you haven't figured out how unreliable they are yet.

But I had to check them out to see. First article I  find on their site today is this:
http://www.answersingenesis.org/docs2006/0506comet.asp

The tale of a comet
by Mark Looy

Astronomers found a comet, called Schwassmann-Wachmann 3, breaking apart. AiG claims this is evidence that our solar system is young because the comet goes around the sun every 5.4 years, “it could not have lasted billions of years. It would have shed so much material at each pass around the sun that it could not last for millions—not to mention billions—of years."

But who said it was grazing the sun in its orbit every 5.4 years for a billion years? Comets don't have stable orbits like the planets. Crazy and highly unwarranted assumption they make there.

They even noted that Hubble has shown other comets (such as Shoemaker-Levy 9) breaking up. Of course they don't tell you that Shoemaker-Levy broke up because it got caught in Jupiter's gravity well and then crashed into Jupiter.

They also link an article that attacks "Oort cloud theory."

I think some more astronomically astute people here could tear that article up even more.

  
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: May 06 2006,22:49   

In a (possibly vain) attempt to prove I am not quite as stupid as my few earlier posts might indicate:

My main error was to confuse codon (which I did know - but forgot when posting - refers to a triplet of nucleotides coding for a particular amino-acid) with gene (meaning that  to indicate a nucleotide sequence staring with a promoter, containing exons and introns, finishing with a stopcode, that is transcribed by mRNA polymerase to produce mRNA,, which, after any necessary snipping out of introns, becomes the template for the translation of the encoded sequence into a particular protein.)

Very simplistically, then, could one imagine genes as extension leads with a 5' plug and 3' socket. Imagine  two leads of identical length laid out so each plug is next to each socket and twist  together, and pairs of leads can then be joined to extend the line infinitely, plug connecting to socket, socket to plug. The process can be carried on infinitely. Take one pair of leads, unplug both pairs of  leads, reverse (flip over end to end) the pair of leads by swapping the ends over and reconnect, no problem. Imagine one lead of the pair is blue and the other red, blue represents the coding or master strand of DNA and red the complement. Flipping one pair of leads means instead of a continuum of red and blue leads there will be a section where red plug connects to blue socket etc and the two runs of connected leads will have one section of lead of the opposite colour. When the particular gene is unwound to be transcribed the mRNA polymerase will attach as indicated by the promoter so will automatically find the coding strand and read off in the right direction. So in a chromosome, is the coding strand continuous or can it alternate from one individual gene to individual gene?

Tom Ames' link  seems to indicate this is so for yeast at least.

(Ducks head under parapet hoping not to appear even more stupid!;)

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: May 06 2006,23:48   

Quote (Alan Fox @ May 07 2006,03:49)
In a (possibly vain) attempt to prove I am not quite as stupid as my few earlier posts might indicate:

My main error was to confuse codon (which I did know - but forgot when posting - refers to a triplet of nucleotides coding for a particular amino-acid) with gene (meaning that  to indicate a nucleotide sequence staring with a promoter, containing exons and introns, finishing with a stopcode, that is transcribed by mRNA polymerase to produce mRNA,, which, after any necessary snipping out of introns, becomes the template for the translation of the encoded sequence into a particular protein.)

Very simplistically, then, could one imagine genes as extension leads with a 5' plug and 3' socket. Imagine  two leads of identical length laid out so each plug is next to each socket and twist  together, and pairs of leads can then be joined to extend the line infinitely, plug connecting to socket, socket to plug. The process can be carried on infinitely. Take one pair of leads, unplug both pairs of  leads, reverse (flip over end to end) the pair of leads by swapping the ends over and reconnect, no problem. Imagine one lead of the pair is blue and the other red, blue represents the coding or master strand of DNA and red the complement. Flipping one pair of leads means instead of a continuum of red and blue leads there will be a section where red plug connects to blue socket etc and the two runs of connected leads will have one section of lead of the opposite colour. When the particular gene is unwound to be transcribed the mRNA polymerase will attach as indicated by the promoter so will automatically find the coding strand and read off in the right direction. So in a chromosome, is the coding strand continuous or can it alternate from one individual gene to individual gene?

Tom Ames' link  seems to indicate this is so for yeast at least.

(Ducks head under parapet hoping not to appear even more stupid!;)

Ok, I didn't get what you meant by the RNA poly using different strands between two codons.

But you're not reading. ;)
I said (page 2 of this thread):
Quote
Of course, in a chromatid, different genes can have different master strands (that is they are read in different directions).


There is no reason preventing a strand to be either master or coding for different genes. The RNA poly just detects a promoter and starts the job.

  
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 07 2006,01:52   

Thanks to Alan Fox, Jeannot, Tom Ames and Incorygible for enlightening me on this truly fascinating subject.  I do sincerely appreciate the effort you have put forth.

Apparently, we have +1 for the "Evos " and -1 for the "Yecs."  So for all of you that like to keep score, you have my hearty congratulations!  I'm looking forward to having that hard conversation with Dr. Carl Wieland from AIG about why he is a medical doctor and yet made such an elementary mistake.  I will post that result here for you all to see, as I believe in rewarding everyone fairly for honest victories, whether they agree with my worldview or not.

I do appreciate all the suggestions to "go out and get a biology book," but the fact is, I do not wish to become a biologist, or a genetic research scientist, or anything similar.  We have plenty of those, and thanks to the internet, much information is a few mouse clicks away.  Some have said that this gets you incomplete information and you should still go read a book.  

Well certainly, in some cases, you should go read a book ... all of Behe's and Denton's work, Dan Brown's novels (albeit with a shaker of salt), and David Barton  and Henry Morris titles have certainly been favorites of mine. (here come the rotten tomatoes)

But reading books don't work for everything and I will throw this advice out there for those wise enough to grab it and learn ...

All of my success in life can be traced to what you might call "Highly Focused, Targeted Learning.  Let's call it HFTL for short."

While many of my friends got MBA's and now have very stressful jobs working for someone else, I took the alternative approach and applied "HFTL" to the world of business, and as a result, retired last year at age 42.  I applied this same strategy to Marriage, Family and Parenting, which I knew nothing about when I got married, and I can tell you that today, after almost 17 years of marriage, it is hard to describe the happiness that my wife and my children bring into my life.  I have 5 natural children and they are so much fun that we are adopting a sixth. (we're stopping there though ... I do have limits).  

Now I am applying the HFTL strategy to the Creation/Evolution debate (I know ... some of you think there IS NO debate), but I think there is and I intend to sort the fact from the fiction on both sides in short order.  I understand it will take some time, but I am not about to subject myself to the laborious and inefficient process of getting an advanced degree in Genetics or such.  I think this kind of thing would serve you well if you are trying to teach or get published or get government research grants or other goals, but these are not my goals.

So I say all this to say "thanks, but no thanks" to those of you here who want to give me direction in life.  I truly believe it is the Creator God of the Christian Bible (maybe you will prove me wrong .. we'll see) who has guided my footsteps so far and I trust that He will continue to do so.   I do know what I am doing and I have clear goals.  I think if you stay with me, it will become clear to you what my goals are (actually, they are no secret ... stated clearly on my other thread).  It is also no embarrassment to me to lack knowledge in a particular area.  For those of you trying to embarrass me or demean me, you are wasting your time.  I have very thick skin earned in Air Force barrooms and the harsh realities of the business world.  I am very single-minded, passionate, and hard driving toward my goals and no amount of silly comments will deter me from what I am trying to accomplish.

What you WILL accomplish with silly comments is discrediting yourself.  I think everyone here wants to be viewed as fair-minded, balanced, rational scientists working hard for the good of humanity.  May I submit to you that if the Neo-Darwinist view of Origins is to prevail in Western Civilization and beyond, hurling stupid insults will not help it prevail.  You can hurl them if you like.  No one will stop you.  And selfishly, I could say "Go ahead and hurl insults" because it actually HELPS my cause.  But I want to give you a fair chance at promoting your view, and as a minority viewpoint holder on this forum, I can tell you that this approach does NOT help your cause.  And any of you that HAVE discredited yourself already by hurling insults, you can easily repair the damage, simply by stopping.  I don't plan on embarrassing you back or singling you out and I am happy to hear what you have to say, especially if it is substantive and sounds intelligent.

In any case, my investigations into the ape/human questions have only just begun.  Stay tuned for more on Monday!

And in the mean time, I invite you all to hop on over to my "AF Dave's Creator-God Hypothesis" thread and join the fun!  It's an interesting (for me anyway) mix of Science, Philosophy, Theology and soon Biblical Studies and who really knows where it will end up!

I'm headed for church, so I'll see you all on Monday!  May the God who you may not believe in bless you anyway!

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
afdave



Posts: 1621
Joined: April 2006

(Permalink) Posted: May 07 2006,02:34   

Oh ... an afterthought ... another reason to not hurl insults at me ... WE'RE CLOSELY RELATED ... don't we share something like 98.5% of our genetic info, you and I?

(OK, OK, I know ... I realize that could be spun both ways)

--------------
A DILEMMA FOR THE COMMITTED NATURALIST
A Hi-tech alien spaceship lands on earth ... DESIGNED.
A Hi-tech alien rotary motor found in a cell ... NOT DESIGNED.
http://afdave.wordpress.com/....ess.com

  
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