NCBI needs help

David Kristofferson kristoff at genbank.bio.net
Thu Jul 2 21:51:44 EST 1992

frist at ccu.umanitoba.ca writes:

>Be careful- if you start producing your own freeware tools and (shudder)
>give them away (you commies!), it might be considered economic terrorism!

Let's "get real," folks.  None of the NCBI controversy extends to
academic developers and the public domain software produced by them.
You may have forgotten this by now, but the first major public domain
software source (the BIONET lending library) and all of these freely
accessible newsgroups came from the BIONET National Computer Resource
for Molecular Biology under a grant to a **commercial company.** If I
remember correctly, you, Brian, were a donor to the lending library.
The kind of exaggeration provided above simply obscures the issues.
Let's look at some of these now.

>In the case of NCBI, it's not just Entrez or Blast but the whole
>developer's toolkit that they provide. In principle, this should save a 
>great amount of reinvention of the wheel. The whole point here is that
>you could NEVER get something like that from a commercial firm, because
>it is not in their best interests to release source code. What they 
>want to do is create more and more products. 
>However, there is only  a very limited amount of money to pay for those
>products. In my opinion, the availability of tools such as those from NCBI
>is potentially a great boon to science, as well as a very economical
>step. It costs the taxpayer a lot less if an agency like NCBI produces
>tools that everyone can use. Shouldn't that be a consideration?

I believe that Steve Smith at Harvard (and possibly others out there)
have been working on user interfaces that are freely distributable and
include source code.  That is perfectly within Steve's right to do so.

My understanding of *federal* regulations, however, is that the
*government* is not allowed to compete against private industry.  NCBI
and the commercial developers (which have been in this field for quite
a few years) have tried to work out ways in which they can cooperate
instead of compete, but this requires a careful delineation of
responsibilities which I understand has been worked out at least in
part.  Obviously NCBI plays an important role in database production
and has also produced some very nice database searching software which
we use on GOS (BLAST and IRX).  Just how broad of a mandate that they
have, however, is one subject of controversy.  As a hypothetical
example, it would obviously be direct competition with the private
sector if they were to distribute a comprehensive sequence analysis
package because many of these have been available from a variety of
sources for many years.

Let me address by **analogy** the general philosophical issues raised
by Brian above; the following is definitely *NOT* a detailed
description of the NCBI/Software Association controversy, but does
cast some light on some of the general concerns that may have been
raised in the debate.

Centrifuges and rotors cost scientists a **lot** of money, much more
than a measly molbio software package, and we all know that resources
are tight these days.  Why not, for "the good of science," create a
federal agency that makes centrifuges and rotors and gives them away
for free to all of the researchers in the country or charges at most a
nominal fee???  This would save taxpayers money, right??  Why not do
the same for DNA sequenators which cost in the $100,000 range???  Why
should there be companies such as Beckman, Dupont, and ABI out there
duplicating each other's efforts when we could attract all of the *best*
instrument people to Washington and stop all of this waste and
reinventing of the wheel???

Of course, Beckman, Dupont, and ABI are fairly good-sized companies,
and, if this hypothetical situation were to occur, they might be a lot
harder to persuade that the above course of action is reasonable.
They might even object a little.  However, "Joe's Rotor Emporium"
which employs 20-30 people in a small business might be more inclined
to accept the wisdom of the government.  Heck, what would you do if
you were Joe and the scientific community was sending in FAXes to
their Congressman/woman complaining about the potential loss of their
free instruments?

Consider this question too.  Can we cite "the good of science" and
simply ignore Joe or force him out of business AND add his people to
the unemployment lines just because his company is small, i.e., not a
Beckman or a Dupont??  Is Joe greedy or unethical if he expresses his
concerns for his business to his Congressman?  Should he, instead,
just stand aside and say, 

  "I am concerned that what is being done in Washington might possibly
   lead to the demise of my business in which I have invested many years
   and dollars.  However, for the good of science, I am going to close up
   shop and go away quietly."

Unfortunately for Joe, this kind of unselfishness would not even yield
him a Boy Scout merit badge 8-).

The "good of science" can obviously do wonders for humanity, but let's
be careful that we do not start letting the ends justify the means

I think that better solutions are possible.

I'll let you answer these questions for yourself, Brian.  You're
obviously a smart guy.  Please just note that there are no attacks on
academic developers here.  I'd like to see a little less emotion and a
little more reason on this issue.

Finally, I realize that, for those who absolutely despise commercial
companies (I too was subject to a lot of negative comments towards
them during my academic career), the above explanations may not sway
their opinions one way or another.

I do have a message for the younger, less-established members of the
community however.  Academic jobs in biology have been tight.  When I
joined IntelliGenetics in 1986 after an academic job search (only one
offer which I decided against), the average age of the people here was
29.  We have probably earned a few gray hairs over the last six years
given all that we have been through, but this is definitely not an
organization of greedy, cigar-chomping fat cats, nor would this
describe the people at the other companies with which I am familiar in
this field.

I think that, if many of you desire to remain in science after
investing much effort into your graduate education, you should
strongly consider **supporting** the establishment of biotech
industries because it is more likely than not that jobs will be
created in this area rather than in academics.  One doesn't have to be
a conservative Republican to see the wisdom in this.


				David Kristofferson, Ph.D.

				GenBank Manager

                                AND a proud employee of
                                IntelliGenetics, Inc.

				kristoff at genbank.bio.net

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