Subject: Re: Are introns just junk?

From: [email-masked]
Date: 31 Oct 93 21:01:57 -0400

In article <[email-masked]>, John Logsdon <[email-masked]> writes:
> 
> In article <[email-masked]> Arthur Kania,
> [email-masked] also writes:
>>There is probably lots of other stuff that I didn't mention; you should
> read some
>>chapters from Molecular Cell Biology (Darnell, Lodish and Baltimore) or
> another
>>basic cell bio textbook.
> 
> Well, don't take too much faith in what the major texts tell you since
> they are highly biased (i.e.: Darnell was one of the early architects of
> IE). 

Here, here!  Its been known for about 10 years that there is not a general
1:1 correspondence between exons and domains (see Blake, 1983, Nature 306:
p. 535), but this canard is repeated _ad nauseam_ in reviews and textbooks, 
such as Watson, et al. (_Molecular Biology of the Gene_) which has the 
sententious section heading "Exons Correspond to Functional Domains of 
Proteins" (p. 1146).  This textbook also informs us of "The Great 
Antiquity of mRNA Introns" (p. 1145) and that "Protein-coding Genes 
were Assembled by Exon Shuffling" (p. 1146), as though these were 
matters of established fact, which they emphatically are not.

>      Also, (donning my jeweled turbin) I predict many of these
> evolutionary conclusions about introns will be changed in the coming
> years.
> 
> John

Gosh, John, is this prediction based on some top-secret discovery by Team
Palmer, or did it come to you in a vision?  Please fill us in!

Arlin

Dr. Arlin Stoltzfus
Department of Biochemistry
Dalhousie University
Halifax, Nova Scotia
B3H 4H7 CANADA
internet: [email-masked]

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From: John Logsdon <[email-masked]>
Date: Mon, 1 Nov 1993 15:22:12 GMT

In article <[email-masked]> , [email-masked] writes:
[stuff about some crap in textbooks]

>Palmer, or did it come to you in a vision?  Please fill us in!

You make my (tongue in turbin, er... cheek) point exactly!! The textbooks
are wrong.  (It really does not take a vision or anything top-secret to
know that ;-} ) This ia particularly regarding the exon/domain thing, but
also their general heavy leaning toward Introns-Early, both which have
very little empirical support.  

___________________________________________________________
John Logsdon         Department of Biology
                     Indiana University
                     Bloomington, IN  47405
                     (812) 855-2549
                     (812) 855-6705 fax

[email-masked]
____________________________________________________________

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From: [email-masked] (David Konerding)
Date: 1 Nov 1993 18:49:39 GMT

[email-masked] wrote:
: In article <[email-masked]>, John Logsdon <[email-masked]> writes:

: Here, here!  Its been known for about 10 years that there is not a general
: 1:1 correspondence between exons and domains (see Blake, 1983, Nature 306:
: p. 535), but this canard is repeated _ad nauseam_ in reviews and textbooks, 
: such as Watson, et al. (_Molecular Biology of the Gene_) which has the 
: sententious section heading "Exons Correspond to Functional Domains of 
: Proteins" (p. 1146).  This textbook also informs us of "The Great 
: Antiquity of mRNA Introns" (p. 1145) and that "Protein-coding Genes 
: were Assembled by Exon Shuffling" (p. 1146), as though these were 
: matters of established fact, which they emphatically are not.

It saddens me somewhat, as an undergraduate studying to be a molecular
biologist, to know that Watson's text is filled with speculations
presented as fact.  I'd expect (after paying about $50 for the book,
and about $10,000 for an education) a little more.

: Arlin

: Dr. Arlin Stoltzfus
: Department of Biochemistry
: Dalhousie University
: Halifax, Nova Scotia
: B3H 4H7 CANADA
: internet: [email-masked]

--
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David Konerding						   [email-masked]
University of California, Santa Cruz			   [email-masked]

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From: [email-masked] (Michael Gilman)
Date: 3 Nov 1993 19:22:15 GMT

In article <[email-masked]>, [email-masked] wrote:

> In article <[email-masked]>, [email-masked] (David Konerding) writes:
> > [email-masked] wrote:
> stuff deleted
> Please allow me to add a little qualification to my previous statements: 
> writers of textbooks sometimes cannot present all sides in a debate, and
> so they pick the side they feel is most likely to correct.  Sometimes
> the relationship of data to theory gets over-simplified in an effort to
> persuade, or just to make a complex question more comprehensible.  
> 
> But this type of modification/simplification/distortion (call it what you 
> will) is not limited to textbooks.  Its also found in the primary literature.  
> Its also found on UseNet.  Its also found in newspapers.  Its also in our 
> very thoughts-- perhaps I'm doing it right now!  As students of science,
> we always have to be critical and skeptical, whether evaluating arguments
> in a textbook, an author's conclusions in a research article, *one's own*
> conclusions-- even one's own observations (i.e., do I see what I think I see?) 
> If it sounds too good to be true, it probably isn't.  
> 
> Arlin

Having been involved in writing a textbook, I wish to second Arlin's point.
And I'd like to add that, although every rule has exceptions, it is usually
the rules and not the exceptions that are the important things to
communicate to a student in a textbook. Students who are motivated to learn
more can be pointed to the relevant literature, so that they can explore
these exceptions and decide for themselves, heaven forbid, whether these
exceptions are significant and enlightening.

mg

-- 
Michael Gilman
Cold Spring Harbor Laboratory             email: [email-masked]
P.O. Box 100                              tel: 516-367-8406
Cold Spring Harbor, NY 11724              fax: 516-367-8454

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From: [email-masked]
Date: Thu, 4 Nov 1993 18:05:55 GMT

In article <[email-masked]>, <[email-masked]> writes:
> Xref: riscsm bionet.cellbiol:119 b

> will) is not limited to textbooks.  
[   ]
> If it sounds too good to be true, it probably isn't.  

Arlin makes a good point here.  When trying to explain a complex point, 
any instructor or textbook auther must make a coherent presentation out 
of what are usually conflicting data sets.  I used to say of one of my 
professors in grad school that he presents a beautiful picture of the 
cell--considerably more beautiful than the facts can support.
I think the best one can hope is to make one's bias clear so that the 
student has some basis for criticism.

Quoting from the Preface of "Molecular Biology of the Cell" (Alberts et 
al.)  "But these unsolved problems provide much of the excitment...
Thus, rather than simply present disjointed facts in areas that are 
poorly understood, we have often ventured hypotheses for the reader to 
consider and, we hope, to criticize."

Having said that, there does seem to be some crony-ism in the way the 
hypotheses are selected for any particular unresolved area.
And, perhaps for those who don't read the preface, it should be made 
more clear in text where the areas of confusion are. 
I would suggest that people should not be so surprised that there are 
statements in textbooks that are biased, or just plain wrong.

-tony

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