DNA Technology

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2 Corinthians 131-3 1 This will be my third
visit to you. Every matter must be established
by the testimony of two or three witnesses. 2
I already gave you a warning when I was with you
the second time. I now repeat it while absent On
my return I will not spare those who sinned
earlier or any of the others, 3 since you are
demanding proof that Christ is speaking through
me. He is not weak in dealing with you, but is
powerful among you.
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Repetition and Organization of DNA Sequences

• Timothy G. Standish, Ph. D.

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Abstract

• When Darwinism and intelligent design make the
  same prediction and this prediction goes against
  interpretation of data, proponents of Darwinism
  may step back from the predictions arising from
  their worldview, then attempt to say that data
  interpreted to go against both intelligent design
  and Darwinism disproves ID while ignoring the
  fact that if, the interpretation of the data is
  true, it also calls into question Darwinism.
• Junk DNA provides an interesting case history of
  this phenomenon.

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Background

• During the late 1960s papers began to appear that
  showed eukaryotic DNA contained large amounts of
  repetitive DNA that did not appear to code for
  proteins (i.e., Britten and Kohne, 1968).
• By the early 1970s, the term Junk DNA had been
  coined to refer to this non-coding DNA (i.e.,
  Ohno, 1972).

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Evidence

• Conservation of protein (and DNA) sequences is
  commonly interpreted to indicate functionality
• Significant variation in non-coding DNA is
  evident between relatively closely related
  species and even within species (i.e., Zeyl and
  Green, 1992).
• Mutation of some non-coding DNA does not produce
  significant changes in phenotype (Nei, 1987).

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What is Junk DNA?

• Junk DNA is DNA that does not code for
  proteins this is the definition that we will
  use.
• The meaning of junk DNA has become restricted
  significantly in recent years as the
  functionality of much of what was once considered
  junk has become obvious. Most modern genetics
  texts avoid the term. Even when junk DNA is
  mentioned, it may be given significantly
  different definitions. For example, Lodish et
  al. (1995) called it Extra DNA for which no
  function has been found.

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Types of Junk DNA

• Nine different types of DNA were listed as junk
  DNA by Nowak (1994)
• These nine types can be grouped into three larger
  groups
• Repetitive DNA sequences
• Untranslated parts of RNA transcripts (pre-mRNA)
• Other non-coding sequences

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Repetitive DNA

• Repeated sequences seem too short to code for
  proteins and are not known to be transcribed.
• Five major classes of repetitive DNA
• Satellites - Up to 105 tandem repeated short DNA
  sequences, concentrated in heterochromatin at the
  ends (Telomeres) and centers (Kinetochore) of
  chromosomes.
• Minisatellites - Similar to satellites, but found
  in clusters of fewer repeats, scattered
  throughout the genome
• Microsatellites - Shorter still than
  minisatellites.
• 4 and 5 Short (300 bp) and Long (up to 7,000 bp)
  Interspersed Elements (SINEs and LINEs) - Units
  of DNA found distributed throughout the genome

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Untranslated Parts of mRNA

• Not all of the pre-mRNA transcribed from DNA
  actually codes for the protein. These non-coding
  parts are never translated.
• Three non-coding parts of eukaryotic mRNA
• 5' untranslated region
• Introns - Segments of DNA that are transcribed
  into RNA, but are removed from the RNA transcript
  before the RNA leaves the nucleus as mRNA
• 3' untranslated region

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A Simple Eukaryotic Gene
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Other Non-coding Sequences

• Pseudogenes - DNA that resembles functional
  genes, but is not known to produce functional
  proteins. Two types
• Unprocessed pseudogenes
• Processed pseudogenes
• Heterogeneous Nuclear RNA - A mixture of RNAs of
  varying lengths found in the nucleus.
  Approximately 25 of the hnRNA is pre-mRNA that
  is being processed, the source and role of the
  remainder is unknown.

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Problems With Junk DNA

• Junk DNA makes up a significant portion of total
  genomic DNA in many eukaryotes.
• 97 of human DNA is junk
• If this DNA is functionless, this phenomenon
  presents interpretation problems for both
  naturalism and intelligent design.

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The Problem for ID

• It is hard to imagine a designer creating so
  elegantly and efficiently at higher levels, but
  leaving a lot of junk at the DNA level.
• This calls into question the intelligent-design
  argument that organisms are so complex and
  efficient that they must be the result of design
  rather than the result of random events.
• Darwinists have eagerly proclaimed junk DNA to be
  molecular debris left behind in the genome as
  organisms have changed over time - The potsherds
  of evolution.

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Straw Gods

• This argument is based on assumptions about the
  way the designer/God must be
• God is God and He can create in any way He wants.
  If He wants to create organisms with lots of
  unnecessary DNA, then He can do that if He wants
• In other words, God cant be defined, then, based
  on a faulty definition, argued against on the
  basis of that definition

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Darwinists Jumped on the Data

• Dawkins (1993) and Orgel and Crick proposed that
  successful genes are selfish in that they care
  only about perpetuation of their own sequence.
  Thus repetitive DNA represents successful selfish
  genes.
• Brosius and Gould (1992) suggested nomenclature
  assuming junk DNA was once functional DNA,
  currently functionless, and is raw material for
  future functional genes.
• Walter Gilbert and others (Gilbert and Glynias,
  1993 Dorit and Gilbert, 1991 Dorit et al.,
  1990) suggested exons are the nuts and bolts of
  evolution while introns are the space between
  them. Thus, to make a functional protein,
  standard parts can be used, just as we use
  standard nuts, bolts and other parts to make a
  bridge or bicycle

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The Problem for Darwinists

• Darwinism predicts at least some degree of
  efficiency as natural selection should select
  against less fit or efficient members of a
  population.
• Only the most efficient organisms would be
  expected to survive in a selective environment.
  The large amount of junk DNA in some eukaryotes
  genomes seems very inefficient.
• One would think that a trend would be evident in
  organisms going from less to more efficient use
  of DNA. In fact, if junk DNA really is junk, then
  the trend is almost the opposite with the most
  primitive organisms having the least junk DNA.

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Changes in the Quantity of DNA

• The amount of non-coding DNA can vary
  significantly between closely related organisms
  (i.e., salamanders) indicating that changes in
  non-coding DNA is an easy evolutionary step.
• If change is easy, why are those with more than
  the average not less fit?
• If DNA is junk, it would be an added burden, but
  the burden might not be significant, thus change
  would be neutral in terms of fitness

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Do Changes in Junk DNA Quantity Impact Fitness?

• Making DNA requires significant input of energy
  as dNTPs, along with production of enzymes to
  produce and maintain the DNA. Factor all that
  into the human average of 75 trillion cells 6 x
  109 bp/nucleus and the cost seems significant.
• Unneeded DNA presents a danger to the cell.
• Mutations could result in the production of junk
  RNA wasting resources and potentially interfering
  with production of needed RNAs and consequently
  proteins.
• Junk proteins could be made that would waste cell
  resources at best, or, at worst, may alter the
  activity of other proteins

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Non-coding DNA has a Significant Impact

• Sessions and Larson (1987) showed that in
  salamanders larger amounts of genomic DNA
  correlates with slower development
• Meagher and Costich (1996) showed significant
  negative correlation between junk DNA content and
  calyx diameter in S. latifolia
• Petrov and Hartl (1998) have shown that, at least
  in Drosophila species, functionless DNA is
  rapidly lost

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Evidence for Functionality in Non-coding DNA

• As early as 1981 (Shulman et al., 1981)
  statistical methods were published for obtaining
  coding sequences out of the morass of noncoding
  DNA.
• More recently neural networks have been used to
  locate protein coding regions (Uberbacher and
  Mural, 1991).
• Searls (1992, 1997) suggested that DNA exhibits
  all the characteristics of a language, including
  a grammar.
• Mantegna et al. (1994) applied a method for
  studying languages (Zipf approach) to DNA
  sequences and suggested noncoding regions of DNA
  may carry biological information. (This has not
  gone unchallenged see Konopka and Martindale,
  1995.)

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Roles of Non-coding DNA Expressed as RNA

• Introns - May contain genes expressed
  independently of the exons they fall between.
• Many introns code for small nuclear RNAs
  (snoRNAs). These accumulate in the nucleolus,
  and may play a role in ribosome assembly. Thus
  the introns cut out of pre-mRNA may play a role
  in producing, or regulating production of
  machinery to translate the mRNAs code
• 3' Untranslated Regions - Play an important role
  in regulating some genes (Wickens and Takayama,
  1994).
• Heterogeneous nuclear RNA - Only speculation is
  possible, but with the discovery of ribozymes and
  RNAi it is possible these RNAs are playing an
  important role

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Roles of Non-coding DNA

• Satellite DNA
• Attachment sites of spindle fibers during cell
  division
• Telomeres protect the ends of chromosomes
• Mini and Microsatellites - Defects are associated
  with some types of cancer, Huntingtons disease
  and fragile-X disease
• May serve as sites for homologous recombination
  with the Alu SINE
• A and T boxes resembling A-rich microsatellites
  are found associated with the nuclear scaffold
• The AGAT minisatellite has a demonstrated
  function in regulation

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Conclusions

• Less and less non-coding DNA looks like junk
• Some classes of non-coding DNA remain
  problematic, particularly Pseudogenes
• Discovery of important functions for non-coding
  DNA calls into question any support the idea of
  junk DNA provides Darwinism
• Proponents of ID must be cautious in accepting
  the interpretation put on data by Darwinists
• Darwinists need to consider the predictions made
  by their own theory before interpreting data to
  discredit ID when the interpretation is equally
  problematic in the context of natural selection

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The Globin Gene Family

• Globin genes code for the protein portion of
  hemoglobin
• In adults, hemoglobin is made up of an iron
  containing heme molecule surrounded by 4 globin
  proteins 2 a globins and 2 b globins

• During development, different globin genes are
  expressed which alter the oxygen affinity of
  embryonic and fetal hemoglobin

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Model For Evolution Of The Globin Gene Family
Pseudo genes (y) resemble genes, but may lack
introns and, along with other differences
typically have stop codons that come soon after
the start codons.
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Eukaryotic mRNA
3 Untranslated Region
5 Untranslated Region
3
5
G
AAAAA
Exon 2
Exon 3
Exon 1
Protein Coding Region
3 Poly A Tail
5 Cap

• RNA processing achieves three things
• Removal of introns
• Addition of a 5 cap
• Addition of a 3 tail
• This signals the mRNA is ready to move out of the
  nucleus and may control its lifespan in the
  cytoplasm

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Junk DNA

• It is common for only a small portion of a
  eukaryotic cells DNA to code for proteins
• In humans, only about 3 of DNA actually codes
  for the about 100,000 proteins produced by human
  cells
• Non-coding DNA was once called junk DNA as it
  was thought to be the molecular debris left over
  from the process of evolution
• We now know that much non-coding DNA is involved
  in important functions like regulating expression
  and maintaining the integrity of chromosomes

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Eukaryotes Have Large Complex Genomes

• The human genome is about 3 x 109 base pairs or
  1 m of DNA
• Thats a lot more than a typical bacterial genome
• E. coli has 4.3 x 106 bases in its genome
• Because humans are diploid, each nucleus contains
  6 x 109 base pairs or 2 m of DNA
• That is a lot to pack into a little nucleus!

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Only a Subset of Genes is Expressed at any Given
Time

• It takes lots of energy to express genes
• Thus it would be wasteful to express all genes
  all the time
• By differential expression of genes, cells can
  respond to changes in the environment
• Differential expression, allows cells to
  specialize in multicelled organisms.
• Differential expression also allows organisms to
  develop over time.

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Eukaryotic DNA Must be Packaged

• Eukaryotic DNA exhibits many levels of packaging
• The fundamental unit is the nucleosome, DNA wound
  around histone proteins
• Nucleosomes arrange themselves together to form
  higher and higher levels of packaging.

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Highly Packaged DNA Cannot be Expressed

• The most highly packaged form of DNA is
  heterochromatin
• Heterochromatin cannot be transcribed, therefore
  expression of genes is prevented
• Chromosome puffs on some insect chomosomes
  illustrate where active gene expression is going
  on

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Logical Expression Control Points

• DNA packaging
• Transcription
• RNA processing
• mRNA export
• mRNA masking/unmasking and/or modification
• mRNA degradation
• Translation
• Protein modification
• Protein transport
• Protein degradation

The logical place to control expression is before
the gene is transcribed
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A Simple Eukaryotic Gene
Transcription Start Site
3 Untranslated Region
5 Untranslated Region
Introns
3
5
Int. 2
Int. 1
Exon 2
Exon 3
Exon 1
Terminator Sequence
Promoter/ Control Region
Exons
RNA Transcript
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Enhancers
Many bases
TF
TF
TF
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Eukaryotic mRNA
3 Untranslated Region
5 Untranslated Region
3
5
G
AAAAA
Exon 2
Exon 3
Exon 1
Protein Coding Region
3 Poly A Tail
5 Cap

• RNA processing achieves three things
• Removal of introns
• Addition of a 5 cap
• Addition of a 3 tail
• This signals the mRNA is ready to move out of the
  nucleus and may control its lifespan in the
  cytoplasm