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DNA could modify itself with no outside help, say biologists
Princeton University ^ | March 28, 2006 | Chad Boutin

Posted on 03/29/2006 1:47:22 PM PST by SampleMan

Spirals of DNA, once thought to be merely the passive memory banks that preserve life’s blueprints, may also actively modify themselves under certain conditions, according to Princeton University scientists.

A team of molecular biologists has found that some single strands of DNA are capable of removing a genetic building block from the spiral, a task previously thought to be impossible without the involvement of a separate catalyst such as RNA or proteins. Such removal, called depurination, occurs only at a single point within a particular genetic sequence, one that appears at least 50,000 times in the human genome. The team’s discovery that the removal occurs consistently in laboratory samples indicates that DNA is a more dynamic substance than was previously thought, and it raises the possibility that other unexpected behaviors still await discovery in this well-studied molecule.

“No one ever dreamed genomic DNA may have another function besides memory storage, but it apparently does,” said Jacques Fresco, the Damon B. Pfeiffer Professor in the Life Sciences at Princeton. “We don’t really know yet why or how it happens, but it makes us wonder what else DNA might be doing without our knowledge.”

Dr. Ann Skalka, senior vice president for basic science at the Fox Chase Cancer Center in Philadelphia, said the findings merit continued attention.

“This fascinating and unanticipated new property of DNA has the potential to cause substantial damage to our cells, leading to cancer or other diseases, unless it is controlled or exploited for some beneficial purpose,” she said. “We will stay tuned.”

Fresco’s team published its findings in the March 21 issue of the journal, Proceedings of the National Academy of Sciences. Also contributing to the research are Princeton researcher Olga A. Amosova and Richard Coulter, currently at West Chester University.

The double-stranded helical structure of DNA is a shape familiar to many, and these long, stringy molecules are in most circumstances unchanging and highly stable -- valuable characteristics for objects whose function is to preserve the master plan of the organism that carries them. Altering the sequence of a DNA strand is often necessary for innumerable bodily functions, such as growth and healing, but scientists previously thought that such alterations require other chemical catalysts or enzymes to do the clipping and rearranging.

When DNA does undergo such changes, its two strands sometimes separate from one another like a broken zipper splitting down the middle, the teeth of one side pulling away from the other. But in some cases, each side will then often bunch up so its teeth can latch on to others from the same side, forming small “loops” of a single-stranded DNA that extend out from the side of the double-stranded helix’s “stem.”

“For genes to express themselves and create change within the body, you absolutely have to get the two strands of DNA apart first, and it’s only through separation that DNA forms these stem-loops,” said Amosova, a research molecular biologist and Fresco’s long time collaborator. “Such separation occurs, for example, when genes are doing something to regulate the body.”

But the team found that if a stem-loop forms from a particular sequence of DNA, one of the genetic “teeth” will fall spontaneously from that side of the zipper, and the weakened strand will eventually break apart in that spot unless it is repaired by enzymes in the cell. Fresco said this sort of activity seems akin to self-mutilation at first glance.

“To a scientist, this kind of self-inflicted genetic damage appears unhealthy, the sort of thing that would cause undesirable mutations and could kill off the organism,” Fresco said. “Cells have evolved a complex DNA repair system to constantly repair such damage. But evolution has not, as we’d expect, put a stop to it. So we theorize it must be happening for some good reason that we have yet to uncover.”

Of the more than 3 billion DNA building blocks in the human genome, the 18-residue sequence that gives rise to the cleavage occurs in about 50,000 places -- a very significant number, Fresco said.

“We can only speculate now as to what aspects of biology this self-cleavage could influence, but the general function of stem-loops combined with the number of sites where depurination can occur does make us curious enough to look further,” Amosova said. “Such a self-depurination capability may, for example, be beneficial in sections of the genome involved in antibody production, where losing a building block from the sequence could lead to higher mutation rates in the antibody-coding genes. This, in turn, could lead to a larger variety of antibodies to protect the body more effectively.”

More generally, Amosova said, losing a building block increases the flexibility of the otherwise highly rigid DNA molecule, which in some circumstances needs to be bent.

“Flexibility could help with DNA packaging, which happens any time you need to stuff DNA into a tight place,” she said. “In particular, viruses typically pack a lot of DNA strands into their shells, leaving virtually no space unused. It may also play a role in the folding of DNA in chromosomes.”

Still, Fresco said, it remains too early to tell where the discovery will lead, though the team will look for some possible biological role for their finding.

“Thus far we have observed this effect under laboratory conditions that closely resemble those within the cell. Now, we would like to observe them directly in the cell nucleus,” he said. “If we have indeed found one way that DNA can change itself spontaneously, there might be others, and we plan to hunt for them.

“Additionally, I might mention that this discovery was made while we were exploring ways to repair the genetic mutation that causes sickle cell anemia,” Fresco said. “We noticed that the depurination occurs right next to the site of the mutation responsible for the disease, but we don’t yet know if there’s any relation between these two facts. We certainly hope we’ve noticed an effect that will eventually offer some new approaches to many diseases.”


TOPICS: News/Current Events
KEYWORDS: biology; dna; evolution
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To: WKB
And you know this how?

I'm assuming you don't take Luke 14:26 literally, for one. The passage has meaning for sure, but if this what Jesus meant verbatim, well that would make Him pretty crazy and contradict everything else He taught us, wouldn't it?

121 posted on 03/30/2006 9:53:53 AM PST by Quark2005 (Confidence follows from consilience.)
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To: SampleMan

I have already said my piece.


122 posted on 03/30/2006 9:58:29 AM PST by hawkaw
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To: Quark2005

I think John 6.53 would be a better example
of what you are saying. :>)


123 posted on 03/30/2006 9:58:40 AM PST by WKB (Take care not to make intellect our god; Albert Einstein)
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To: Quark2005

Looks like you are blessed with a wonderful family - best of luck & blessings to you and them.

I am.
Thanks


Do you think it is possible there is an undetermined
length of time between Gen 1.1 and Gen 1.2?


124 posted on 03/30/2006 9:59:07 AM PST by WKB (Take care not to make intellect our god; Albert Einstein)
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To: hawkaw

Good, that's a relief.


125 posted on 03/30/2006 9:59:29 AM PST by SampleMan
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To: WKB
Do you think it is possible there is an undetermined length of time between Gen 1.1 and Gen 1.2?

To be honest, I don't have any idea. I've heard this (Gap Theory, I think it's commonly called) before. I don't look at these chapters as attempt of God to explain the sequence of natural history, but rather as divinely inspired poetry that conveys a message of the strength of God's creative power. I don't really think we do a favor to either God or science when we try to get scientific information to line up with the order of the words in these chapters.

He didn't give us a description of quantum physics, genetics and plate tectonics (which wouldn't have gone over too smoothly in an age of tribal nomads who thought the earth was flat, the stars were angels in the dome of the sky and usually never left more than 50 miles from their birthplace). He only chose to give us a bold clue that there's a lot of wonder to be found in God's gift of Creation, and gave us the gift of a mind capable of beginning to unravel these wonders.

126 posted on 03/30/2006 10:24:49 AM PST by Quark2005 (Confidence follows from consilience.)
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To: Quark2005; WKB
I don't look at these chapters as attempt of God to explain the sequence of natural history, but rather as divinely inspired poetry that conveys a message of the strength of God's creative power.

A good exposition of this thesis:


127 posted on 03/30/2006 10:46:54 AM PST by Stultis (I don't worry about the war turning into "Vietnam" in Iraq; I worry about it doing so in Congress.)
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To: Quark2005
Specifically Hyers argues that Genesis 1 & 2 is principally a polemic against the surrounding polytheistic cultures. The point isn't chronology, science, etc, but rather emphasizing that stars, planets, sun, moon etc are created things; not gods or some other sort of divine, sacred entities as in the polytheistic scheme.
128 posted on 03/30/2006 10:54:55 AM PST by Stultis (I don't worry about the war turning into "Vietnam" in Iraq; I worry about it doing so in Congress.)
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To: Stultis

Looks like a good read. (Usually I glance at references made to books on FR and move on, but this actually looks fascinating to me). Do you recommend it?


129 posted on 03/30/2006 10:56:59 AM PST by Quark2005 (Confidence follows from consilience.)
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To: AntiGuv
It's tough to debate the meaning of life, the universe, and everything without getting a bit worked up sometimes..

Which is why we have the Restaurant At The End Of The Universe...

130 posted on 03/30/2006 11:03:01 AM PST by LibertarianSchmoe
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To: Stultis
The point isn't chronology, science, etc, but rather emphasizing that stars, planets, sun, moon etc are created things; not gods or some other sort of divine, sacred entities as in the polytheistic scheme.

Interesting. I guess getting people to think of stars, lightning, the moon, etc. as part of God's handiwork rather than gods themselves was quite an impressively accomplishment for a work in that era, and quite a revolutionary concept - actually a step in getting people to break away from superstition rather than embrace it.

131 posted on 03/30/2006 11:12:20 AM PST by Quark2005 (Confidence follows from consilience.)
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To: mlc9852

"What would be an example of "randomness"?"

In the quantum world.


132 posted on 03/30/2006 11:27:46 AM PST by sagar
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To: sagar

Well, that isn't very specific but thanks anyway.


133 posted on 03/30/2006 11:28:40 AM PST by mlc9852
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To: SampleMan

If this is a fundamental discovery, the removal of all the so-called carcinogens would not eliminate cancer.

Looks the program is terminal.


134 posted on 03/30/2006 11:35:50 AM PST by Old Professer (The critic writes with rapier pen, dips it twice, and writes again.)
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To: Quark2005
Yeah. It was some years ago, but I remember it is a good and worthwhile read.

It's in a reading list I created many years ago for an evangelical freind who was trying to work out science and faith issues. Kinda dated by now, but some good books in there:

                    READING LIST ON CHRISTIANITY, SCIENCE
                            AND "CREATION SCIENCE"



       Barbour, Ian.  ISSUES IN SCIENCE AND RELIGION.  Harper, 1966.
            -Classic work covering a lot of ground.

       Bube, Richard H.  THE HUMAN QUEST:  A NEW LOOK AT SCIENCE AND THE
         CHRISTIAN FAITH.  Word, 1971.
            -By a well known evangelical apologist.
            
       Burke, Derek; ed.  CREATION AND EVOLUTION.  InterVarsity, 1985.
            -Debate format between proponents of "creation science"
            and scientifically trained Evangelical opponents of
            same.  (A title in the series "When Christians
            Disagree.")

       Frye, Ronald M.; ed.  IS GOD A CREATIONIST?:  THE RELIGIOUS CASE
         AGAINST CREATION SCIENCE.  Scribner's, 1983.
            -Essays by various Christians collectively critiquing
            the "creation science" approach to science and biblical
            interpretation.

       Gilkey, Langdon.  MAKER OF HEAVEN AND EARTH:  THE CHRISTIAN
         DOCTRINE OF CREATION IN THE LIGHT OF MODERN KNOWLEDGE.
         Doubleday, 1959.
            -A thorough study of the doctrine of creation.

       -----.  CREATIONISM ON TRIAL:  EVOLUTION AND GOD AT LITTLE ROCK.
         Winston Press, 1985.
            -A participating theologian's account of the trial of
            the Arkansas "balanced treatment" for "creation science"
            law.  Includes valuable ruminations throughout, and in
            concluding chapters, on science and religion in modern
            society.

       Gillispie, Charles Coulston.  GENESIS AND GEOLOGY:  A STUDY IN THE
         RELATIONS OF SCIENTIFIC THOUGHT, NATURAL THEOLOGY, AND SOCIAL
         OPINION IN GREAT BRITAIN, 1790-1850.  Harper, 1959.
            -A valuable standard work.  See also, Porter '77.

       Godfrey, Laurie R.; ed.  SCIENTISTS CONFRONT CREATIONISTS.
         Norton, 1983.
            -An excellent scientific critique of "creation science"
            in an anthology format.

       Hooykaas, R.  RELIGION AND THE RISE OF MODERN SCIENCE.  Eerdmans,
         1972.
            -Argues that religion (esp. creation doctrine) provided
            an impetus to the scientific revolution.  For a critique
            see Rolf Gruner, "Science, Nature and Christianity,"
            JOURNAL OF THEOLOGICAL STUDIES, 26:55-81, 1975.

       Hyers, Conrad.  THE MEANING OF CREATION:  GENESIS AND MODERN
         SCIENCE.  John Knox, 1984.
            -Theology and cosmology of Genesis.  Argues that any
            attempt to evaluate the "scientific merit" of the Bible
            (whether the purpose is to praise or denigrate) is a
            concession of scripture to science.  Genesis should be
            interpreted in terms of issues and concepts current and
            crucial to its authors, not those developed during the
            scientific revolution.  Criticizes "progressive
            creationism" (Ramm '54 and Young '77) as well as "strict
            creationism."

       Jeeves, Malcolm A.  THE SCIENTIFIC ENTERPRISE AND CHRISTIAN FAITH.
         InterVarsity, 1969.
            -The compatibility of science and Christianity.  Based
            on the 1965 International Conference of Science and
            Faith.

       Kitcher, Philip.  ABUSING SCIENCE:  THE CASE AGAINST CREATIONISM.
         MIT Press, 1982.
            -Critique of "creation science" focusing especially on
            the philosophical issues (eg. evolution & ethics pp.
            194-202).

       Lindberg, David C. & Ronald L. Numbers; eds.  GOD AND NATURE:
         HISTORICAL ESSAYS ON THE ENCOUNTER BETWEEN CHRISTIANITY AND
         SCIENCE.  Univ. of Calif., 1986.
            -A superb and well organized collection of essays by
            highly competent scholars.  Numbers' essay on "The
            Creationists" outlines the development of 20th century
            anti-evolutionism.  (A book length history by Numbers is
            reportedly in progress.)

       Livingstone, David N.  DARWIN'S FORGOTTEN DEFENDERS:  THE
         ENCOUNTER BETWEEN EVANGELICAL THEOLOGY AND EVOLUTIONARY THOUGHT.
         Eerdmans, 1987.
            -Shorter work covering some of the same ground as Moore
            '79.

       Moore, James R.  THE POST DARWINIAN CONTROVERSIES:  A STUDY OF THE
         PROTESTANT STRUGGLE TO COME TO TERMS WITH DARWIN IN GREAT
         BRITAIN AND AMERICA 1870-1900.  Cambridge, 1979.
            -A very important work with the surprising thesis "that
            Darwin's theory was accepted in substance by those whose
            theology was distinctly orthodox, and was not embraced
            by liberal Christians."  This book has a great
            bibliography (which is expanded in the 1981 edition).

       Peacocke, Arthur A.  CREATION AND THE WORLD OF SCIENCE.  Clarendon
         Press, 1979.
            -Going beyond issues of accommodation and relation, with
            which most of the works here listed are concerned,
            Peacocke attempts to fully incorporate modern science
            into theology.

       Porter, Roy.  THE MAKING OF GEOLOGY:  EARTH SCIENCE IN BRITAIN
         1660-1815.  Cambridge, 1977.
            -This standard history is included due to a common, if
            tacit, assumption that "creation science" is merely
            anti-evolutionary.  In truth, its most distinctive
            elements -- "flood geology," a young earth, and so on --
            were falsified and abandoned by the scientific community
            long before Darwin.  (See also:  Gillispie '59, and
            Young '88 chapters 1-5.)  Porter's work also shows that
            pre-Darwinian geologists had little difficulty
            reconciling their findings with their religious beliefs.

       Ramm, Bernard.  THE CHRISTIAN VIEW OF SCIENCE AND SCRIPTURE.
         Eerdmans, 1954.
            -This attempt to avoid the straitjacket of "hyper-
            orthodoxy" was very influential among evangelicals
            (though not so much, apparently, as the revival of
            Ramm's "hyper-orthodoxy" in the guise of "scientific
            creationism").  Ramm's defense of "progressive
            creationism" is criticized in Hyers pp. 80-92.

       Ratzsch, Del.  PHILOSOPHY OF SCIENCE:  THE NATURAL SCIENCES IN
         CHRISTIAN PERSPECTIVE.  InterVarsity, 1986.
            -By a philosophy professor from Calvin College.  A
            volume in the "Contours of Christian Philosophy" series.
            (Aside from its religious thrust, this work is a useful
            introduction to the philosophy of science.)

       Russel, Colin A.  CROSS-CURRENTS:  INTERACTIONS BETWEEN SCIENCE
         AND FAITH.  Eerdmans, 1985.
            -A very readable history of science and religion
            emphasizing compatibility.

       Strahler, Arthur N.  SCIENCE AND EARTH HISTORY:  THE EVOLUTION/
         CREATION CONTROVERSY.  Prometheus, 1987.
            -A monographic examination, in textbook format, of the
            scientific issues in the Creation/Evolution controversy.

       Van Till, Howard J.  THE FOURTH DAY:  WHAT THE BIBLE AND THE
         HEAVENS ARE TELLING US ABOUT THE CREATION.  Eerdmans, 1986.
            -"Taking both the Bible and the Cosmos Seriously," Van
            Till argues that the discoveries of modern science and
            the Bible are compatible.  Focus is on his specialty of
            Astronomy.  The creation/evolution controversy is
            discussed incidently throughout, and in a separate
            chapter, as generating "more heat than light."  Brief
            annotated bibliography.

       -----; Davis Young & Clarence Menninga.  SCIENCE HELD HOSTAGE:
         WHAT'S WRONG WITH CREATION SCIENCE *AND* EVOLUTIONISM.
         InterVarsity, 1987.
            -By scientists from Calvin College.  "Creation science"
            is charged with violating the "values of science":
            professional competence, ethical standards in dealing
            with data, and principles of sound judgement in
            evaluating theories.  "Evolutionary Naturalism" is
            accused, in popularizations of science such as Sagan's
            "Cosmos," of violating the "domain of science" by
            fallaciously using science to justify its philosophical
            conclusions.

       Wonderly, D. E.  GOD'S TIME-RECORDS IN ANCIENT SEDIMENTS.  Crystal
         Press, 1977.
            -I have not seen this book, but it is frequently cited
            as a good refutation of young earth creationism and
            flood geology.

       Wright, Richard T.  BIOLOGY THROUGH THE EYES OF FAITH.  Harper &
         Row, 1989.
            -Work in a series cosponsored by the Christian College
            Coalition.

       Young, Davis A.  CREATION AND THE FLOOD.  Baker, 1977.
            -An evangelical geologist reconciles Genesis and geology
            in a "progressive creation" framework.  (Discussed in
            Hyers '84 pp. 80-92.)

       -----.  CHRISTIANITY AND THE AGE OF THE EARTH.  Zondervan, 1982.
            -A geologist shows that the claims of "young earth"
            creationism and flood geology are falsified by the
            relevant data.  (This book is out of print with
            Zondervan.  Now available from Artisan Sales; P.O. Box
            2497; Thousand Oaks, CA 91360.  $8.50 postpaid per copy;
            ten or more, $4.50 ea.)


       ALSO:


       Issues of the JOURNAL OF THE AMERICAN SCIENTIFIC AFFILIATION, now
       retitled PERSPECTIVES ON SCIENCE AND CHRISTIAN FAITH.
            -The ASA is an organization of Evangelical Christians
            with scientific training.  Membership includes both
            progressive creationists and theistic evolutionists of
            various sorts.  Proponents of orthodox "creation
            science" seem to be a distinct minority.  ASA; P.O. Box
            668; Ipswich, MA 01938.

       Beck, Stanely D.  "Natural Science and Creationist Theology,"
         BIOSCIENCE, 32:732-42, 1982.

       Hyers, Conrad.  "The Fall and Rise of Creationism," THE CHRISTIAN
         CENTURY, April 24, 1985.

135 posted on 03/30/2006 12:02:57 PM PST by Stultis (I don't worry about the war turning into "Vietnam" in Iraq; I worry about it doing so in Congress.)
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To: WKB
Just pointing how few if any definitive statements there are in this article. Evo articles are ALWAYS full of if, could have, might have, may have, might possibly be, etc etc etc.

You will find that scienctific writings are often filled with tentative language. This is because no field in science is considered conclusively proven. Evolution is no different than the rest of scientific study in this regard.

One of the main reason I stay with
"Thus says The LORD"


I do not understand how this is a logical alternative.
136 posted on 03/30/2006 12:22:14 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: WKB
No you don't. The LORD sayeth nothing whatever about computers and computer networks, for instance, but here you are.

Curious. Stultis made a number of good points regarding why your relation of the article to a lack of acceptance of evolution was unjustified and illogical, yet you chose to completely ignore his explanation. Why is that?
137 posted on 03/30/2006 12:25:55 PM PST by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: WKB; SampleMan
SampleMan said:
Apparently not all the scientists at Princeton are drinking the "everything there is to know about evolution is already known" Kool-Aid.

WKB said:
Evo articles are ALWAYS full of if, could have, might have, may have, might possibly be, etc etc etc.

For some reason we scientists either know EVERYTHING or know NOTHING. Make up your minds.

Part of good science is in defining not just what we know but also the boundaries on that knowledge. EVERY measurement made in a laboratory or in some kind of observation of the universe has some kind of error associated with it. You acknowledge that uncertainty and judge how accurate or precise your measurement happens to be (the two are not exactly the same) and therefor how much confidence you can have in your results. This is how science works.
138 posted on 03/30/2006 12:38:14 PM PST by gomaaa (We love Green Functions!!!!)
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To: gomaaa
Hey, I said, "not all the scientists". What more do you want?

Frankly I've seen more humility in fighter pilots than I see on these threads concerning the likelihood that something could be unknown.

But keep screaming, you might convince me that you're on the reasonable list.
139 posted on 03/30/2006 12:53:30 PM PST by SampleMan
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To: Dimensio
Curious. Stultis made a number of good points regarding why your relation of the article to a lack of acceptance of evolution was unjustified and illogical, yet you chose to completely ignore his explanation. Why is that?

Becasue I like definitive::

Why are these few words SO difficult for your great minds?
Could it be my tag line comes into play?

“Gen. 1:1 In the beginning God created“

Here is another reason I choose the Bible over your so called facts that are constantly on the move.

NO ifs, no could haves,no might haves,no may haves, no might possibly bes, etc etc etc and no theories.

John 6:35 Then Jesus declared,“I am the bread of life. He who comes to me will never go hungry, and he who believes in me will never be thirsty.

John 8:12 When Jesus spoke again to the people, he said, “I am the light of the world. Whoever follows me will never walk in darkness, but will have the light of life.”

John 8:24 I told you that you would die in your sins; if you do not believe that I am the one I claim to be, you will indeed die in your sins.”

John 10:7 Therefore Jesus said again, “I tell you the truth, I am the gate for the sheep. John 10:8 All who ever came before me were thieves and robbers, but the sheep did not listen to them. John 10:9 I am the gate; whoever enters through me will be saved. John 10:14“I am the good shepherd; I know my sheep and my sheep know me—

John 11:25 Jesus said to her, “I am the resurrection and the life. He who believes in me will live, even though he dies; John 11:26 and whoever lives and believes in me will never die. Do you believe this?”

John 14:2 In my Father's house are many mansions; if it were not so, I would have told you. I am going there to prepare a place for you. John 14:3 3And if I go and prepare a place for you, I will come back and take you to be with me that you also may be where I am.”

John 15:5 “I am the vine; you are the branches. If a man remains in me and I in him, he will bear much fruit; apart from me you can do nothing.

John 14:6 Jesus answered, “I am the way and the truth and the life. No one comes to the Father except through me.

140 posted on 03/30/2006 1:49:06 PM PST by WKB (Take care not to make intellect our god; Albert Einstein)
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