Transcript A Protein - Grace Church

Design in Biology
Which One is Designed?
The Appearance of Design
“Biology is the study of complicated things
that give the appearance of having been
designed for a purpose.”
(Dawkins, The Blind Watchmaker)
“Biologists must constantly keep in mind that
what they see was not designed, but rather evolved.”
(Crick, What Mad Pursuit)
They believe that random mutation and natural selection is a
design substitute.
Question: Is there a design substitute, or is the design
from an intelligent source?
Beware of Definitions for Life’s Development
A. Evolution--Change over time; or a heritable change in the
characteristics within a population from one generation to the next.
B. Darwinian Evolution--The common descent of
all organisms from single celled organisms by the
mechanism of variation operated on by natural selection.
C. Neo-Darwinian Evolution--Darwinian Evolution with random
genetic mutation as the variation mechanism.
D. Micro-Evolution--Small changes in organisms due to random
mutations, genetic variability, and natural selection.
E. Macro-Evolution--Darwinian or Neo-Darwinian evolution.
F. Chemical Evolution--Chemicals forming the molecules of life
then organizing to form the first cells by random, natural processes.
A or D being true do not imply that B, C, E, or F are true.
Life’s Building Blocks
Atoms--the building blocks of matter
(hydrogen, oxygen, carbon, and others)
Molecules--combination of atoms bound together by electrical
forces (water, sugar, salt, amino acids, and many others)
Amino Acids--molecules that are the building blocks of proteins
Proteins--folded chains of amino acids that form the structural
building blocks and machinery in cells
DNA--a long, ladder-like molecule, found in a cell’s nucleus, that
stores the information (code or directions) for building and
regulating proteins (deoxyribonucleic acid)
Mutation--an error in the DNA code
Cells--the building blocks of living organisms
Design in the Cell
Cells are the Basic Building Blocks of
Living Organisms
1839, Schleiden & Schwann proposed that cells are
the smallest, most fundamental unit of life.
Until the late 19th century, cells were thought to be
simple bags of protoplasm.
In the late 19th century, scientists started discovering
that cells contain compounds which
undergo complex chemical reactions.
Today, we see a staggering complexity
that suggests design.
The Cell Has Design Characteristics
Separate compartments with unique chemical
environments and controlled access passages
between compartments
A molecular transportation network to supply
raw materials and distribute finished products
Microprocessor regulation of gene expression,
growth, repair, and response to environmental
conditions
Molecular protein machines that do cell work
Cargo haulers
Cables, ropes, pulleys
Switches
Energy conversion
Unzipping, reading, and duplicating DNA
From Unlocking the Mystery of Life
Propulsion
Manufacturing
A library containing information that specifies all the above (DNA)
See M. Behe, Darwin’s Black Box, pg 4-5.
Design in Proteins
Molecular Machines
A Protein is a String of Amino Acids
Amino acids are molecules.
There are 20 different amino acids
used in proteins.
There are hundreds to thousands of
amino acids in a protein string.
Phenylalanine
Histidine
Leucine
Glutamine
Isoleucine
Asparagine
Methionine
Lysine
Valine
Aspartic acid
Serine
Glutamic acid
Proline
Cysteine
Threonine
Tryptophan
Alanine
Arginine
Thyrosine
Glycine
Amino acids in a string, from Darwin’s Black Box
A Protein (Amino Acid String) Folds into a
Precise Three Dimensional Shape.
Proteins form the structure and
machinery of a cell.
Shape and charges on the
protein’s surface determine
interaction with other proteins
and molecules.
Many proteins have the
characteristics of a
microprocessor combined with a
functional machine.
They are sometimes called
enzymes.
DNA Polymerase
From David Keller
Molecular Machines--The Ribosome
The ribosome is a molecular
machine made of 50 proteins
that uses mRNA as a template
to assemble amino acids,
brought to it by tRNA, into
proteins.
Molecular Machines--F1F0 ATP Synthase
This machine is imbedded in
the wall of a mitochondria. H+
powers a protein motor that
drives a turbine that attaches
PO4 to ADP to make ATP for
cell energy. Or it works in
reverse to pump H+.
Molecular Machines--Bacterial Flagellum
From Behe; Darwin’s Black Box, p 71. Originally fromVoet and Voet
Design in DNA
DNA is a Molecule that Folds and Twists
Into a Chromosome
Chromosome
Chromosome pairs
(One from Mother, one from Father)
humans 23
apes 24
dogs 39
flowering plants >100
Our 46 chromosomes are made of
3 billion base pairs.
base pair
molecules
sugar &
phosphate
molecules
DNA
Harris; DDD-V; September 2004
DNA Has a Ladder-like Structure
Phosphate
Base
Sugar
A
Sugar and phosphate
molecules form the sides.
Base
T
Base molecules form the rungs.
C
G
G
C
T
A
There are 4 types of base molecules:
Adenine--Thiamine
Cytosine--Guanine
A & T always go together.
C & G always go together.
2% of DNA Consists of Base-Pair Sequences That
Are Codes for Building Proteins
Instead of a sequence of letters that form words and ideas, DNA
uses a sequence of molecules (bases) as a code that gives
directions for protein assembly and regulation.
Three bases in a row (a codon) specifies an amino acid.
Sequences of codons specify the sequence of amino
acids to be used in assembling a protein.
DNA
GCT = Alanine
AAA= Lysine
TCT = Serine
TTT = Phenylalanine
(The other 98% of DNA is highly organized
software that regulates cell and protein functions.)
Base
Pairs
How the DNA-Protein Process Works 1
(Greatly Simplified)
A protein machine, RNA
polymerase, reads the bases in a
DNA gene.
It copies the base sequence to
make a messenger RNA (mRNA)
Molecule.
RNA Polymerase
The structure of RNA has a
single strand, sugar-phosphate
backbone with bases attached.
The bases are the same as for
DNA except uracil is substituted
for thiamine.
mRNA From Unlocking the Mystery of Life
How the DNA-Protein Process Works 2
(Greatly Simplified)
The mRNA is transported out of the
nucleus to a protein manufacturing
machine called a ribosome.
Amino acids are brought to the
ribosome by transfer RNA (tRNA).
The ribosome uses the mRNA as a
template to assemble amino acids into
a string.
Robosome
The string of amino acids folds, with
help from another machine, into a
functioning protein.
Protein assembly From Unlocking the Mystery of Life
Journey Inside the Cell Video
DNA is a Code
The entire DNA code contains roughly the same quantity of
information as 300 encyclopedia volumes.
The information in DNA is highly organized with efficient data
retrieval, cross references, and a sophisticated hierarchical
structure.
All known codes have an intelligent cause:
Computer codes
Written language
Morse code
Numbers
Construction plans
Both Proteins and DNA are Required for Reproduction
The information from DNA is read by molecular reading machines
and transferred to molecular manufacturing machines.
Molecular manufacturing machines use the information from DNA to
assemble amino acids into proteins.
Proteins form the molecular machines that replicate DNA during cell
reproduction.
Evolution requires reproduction.
Reproduction requires the interdependent
system of DNA and molecular machines.
This interdependent system is evidence
for design.
Unzipping from Unlocking the Mystery of Life Video
Can Chemical
Evolution
Design the
First Cell?
The Chemical Evolution Hypothesis
1. Chemicals in the early Earth atmosphere formed the basic molecules
necessary for life, which settled into oceans and ponds;
2. The basic molecules assembled into proteins and DNA;
3. Proteins, DNA, and other molecules assembled into the first living
cells; and
4. All of the above were done by natural, chemical processes.
Water
Hydrogen
Methane
Carbon
monoxide
Carbon dioxide
Ammonia
Nitrogen
No Oxygen
Fatty acids
Amino Acids
Sugars
Purines
Pyrimidines
Membranes
Proteins
Protocells
Cells
RNA & DNA
All in about
170 M Years
Life’s Basic Molecules Have Been Formed,
But Chemical Evolution Stops There
The Miller-Urey experiment in 1953 (and others) synthesized
amino acids (the building blocks of proteins), and
heterocyclic bases (the building blocks of DNA)
from the gases assumed to compose the “early atmosphere.”
But there are serious problems:
1. Oxygen in the early atmosphere.
2. Contaminants.
3. Chirality: left and right “handedness.”
4. The building blocks have never been
seen to assemble naturally into
proteins and DNA outside the cell.
Thaxton, Bradley, Olsen; The Mystery of Life’s Origin; Philosophical Library, NY, 1984.
Wells; Icons of Evolution; Regnery, 2000.
Assembling a Protein from Amino Acids Without
Design is Extremely Improbable
A reproducing cell requires at least 100 proteins with a median length of
400 amino acids.
If a “right handed” amino acid is included in the amino acid chain, the
chain cannot function as a protein.
Randomly synthesizing a chain of 400 left-handed amino acids
with 1080 tries (number of atoms in the universe)
every micro-second since the beginning of time
is less likely than 1 in 10 billion.
There are not enough atoms and time in the universe to randomly
assemble 400 exclusively left-handed amino acids into a chain.
In addition, the right type of bond between amino acids is required.
Even with proper bonds and chirality, very few amino acid strings will
fold into functioning proteins.
And, there is no known natural means of assembling amino acids into
strings outside the cell.
Crick (co-discovered DNA structure
in 1953), Life Itself, 1988: “An honest
man, armed with all the knowledge
available to us now, could only state
that in some sense, the origin of life
appears at the moment to be almost a
miracle, so many are the conditions
which would have had to have been
satisfied to get it going.”
Can NeoDarwinian
Evolution be a
Design
Substitute?
Random Mutation and Natural Selection are
the Basis for Neo-Darwinian Theory
Charles Darwin believed that observed small changes in
organisms (micro-evolution) were due to variation acted upon by
natural selection.
Micro
Evolution
He reasoned that if small changes occur over a short time, change
in basic form (macro-evolution), due to accumulated small steps
are possible over a long time.
Macro
Evolution
Can Random Mutation and Natural Selection
Explain Innovations?
Evolution From a Single Cell to Modern
Organisms Requires Thousands of Innovations:
Sight
Nervous systems
Respiratory systems
Circulatory systems
Skeletal systems
Immune systems
Molecular machines
These innovations require thousands of new proteins and new interprotein interactions.
Proteins work in multi-protein complexes, usually 6 or more.
The Bacterial Flagellum is an Innovation
Requiring Interaction Among 40 Proteins
For a simple bacterium to develop a flagellum would require roughly
40 new interacting proteins produced by mutations.
The flagellum, like other innovations, is irreducibly complex, which
means the flagellum is useless unless all proteins are present.*
Useless protein interactions and associated mutations do not spread
in a population because of their energy cost.
All 40 interacting proteins would have to be present at the same time
to give an advantage.
*combination lock analogy
Interactions Among More than Three Proteins are
Out of Reach for Neo-Darwinian Processes
According to Michael Behe:
No new “advantageous” inter-protein interactions have been seen in
1020 malaria, 1020 HIV, and 1013 E. Coli cells.
We would not expect to see two coordinated interactions among three
proteins in 1040 cells.*
Only 1040 bacterial cells have lived since life began; therefore,
interactions among more than three proteins are out of reach.
Intelligent design, with a goal in mind, is a much better
explanation than a neo-Darwinian process.
*combination lock analogy
Michael Behe; The Edge of Evolution; Free Press, 2007.
What About The Fossil Record?
The fossil record shows a progression from single celled
organisms to complex multi-celled organisms over time.
Organism
Asserted Age
Blue-green algae and bacteria
Single celled animals
Cambrian Explosion
Higher plants on land
Fish, amphibians, forests, insects
Reptiles
Dinosaurs, flowering plants
Mammals, birds
Man
3.5 billion
1 billion
550 million
425-400 million
400-345 million
345-280 million
225-65 million
65 million
1 million?
It also shows major animal classes and phyla appearing abruptly,
fully formed, and living unchanged for millions of years. During
the Cambrian Explosion, most phyla (main groups) appeared
without intermediate forms over a few million years.
Famous “Intermediates”
The fossil record contains few if any intermediate links, and all are
controversial. Are they intermediate or independent with intermediate
characteristics?
Archaeopteryx— “Paleontologists now agree that
Archaeopteryx is not the ancestor of modern birds1.”
Whales—A 2001 National Geographic article cited
evidence that Hippos are the closest land dwelling relatives of whales.
A 2007 Nature article cited evidence that Indohyus, a small, deerlike
animal is the whale’s closest land relative.
Tiktaalik—A 2006 article in Nature calls this fish with limb-like
front fins the intermediate between fish and amphibians. A 2010
Nature article tells of finding tetrapod footprints,
with toes, dated at 20 million years before Tiktaalik.
1. Wells, Icons of Evolution
Picture from Icons of Evolution
Problems With Neo-Darwinian Evolution
Organization and Information Content of DNA—The information
in DNA is highly organized with efficient data retrieval, cross
references, and a sophisticated hierarchical structure.* It does not fit
a random mutation scenario.
Necessity of New Protein Interactions—Random mutation and
natural selection cannot explain the new proteins and inter-protein
interactions necessary for biological innovations.
Common Descent—New body plans appearing suddenly and
questionable intermediates make common descent doubtful.
Epigenetic information and body plans—DNA (and mutation) may
have little to do with body plan. New research is showing that
something in the egg besides DNA determines body plan*.
Common Descent by the mechanism of random mutation and
natural selection is not a credible design substitute.
*See the Epilogue of Stephen Myer’s Signature in the Cell.
According to the Evidence, They are Both
Designed.
How Can We Explain Design In Biology?
Genesis 1: In the beginning, God
created the heavens and the earth and
every living thing according to its kind.
John 1: In the beginning was the
Word, and the Word was with God, and
the Word was God. Through Him all
things were made.
Rom 1:20 For since the creation of the
world, God's invisible qualities-his
eternal power and divine nature-have
been clearly seen, being understood
from what has been made, so that men
are without excuse.
Reading
The Mystery of Life’s Origin; Thaxton, Bradley, Olson, 1984
Evolution: A Theory in Crisis; Michael Denton, 1986
Darwin on Trial; Phillip Johnson, 1993
Darwin’s Black Box; Michael Behe, 1996
Nature’s Destiny; Michael Denton, 1998
Intelligent Design; William Dembski, 1999
Icons of Evolution; Jonathan Wells, 2000
The Edge of Evolution; Michael Behe, 2007
Signature in the Cell; Stephen C. Meyer, 2009
The Myth of Junk DNA; Jonathan Wells; 2011
Internet
Discovery.org
IntelligentDesignNetwork.org
NMIDnet.org
ARN.org
Probability of Randomly Assembling a Protein
Consider an average protein that is 400 amino acids long.
19 of 20 amino acids are naturally produced in both left and right
handed molecules
Assume amino acids are randomly attached into a string (polymer).
The probability of getting a polymer made of all “left handed” amino
acids is 1/2380 = 4 x 10-115.
Assume that we get 1080 tries (very generous) at building this protein
every micro-second since the beginning of time (very generous).
1080 is roughly the number of atoms in the universe.
The number of micro-seconds since the beginning of time is:
15x109 yr x 8760 hr/yr x 3600 sec/hr x 106 micro-sec/sec
= 4.7 x 1023 micro-seconds
We get 1080 x 4.7 x 1023 = 4.7 x 10103 tries.
Probability of Randomly Assembling a Protein
The probability of getting one success over all these tries is,
4.7 x 10103 x 4 x 10-115 = 1.9 x 10-11
which is less than 1 in 10 billion.
This is almost impossible odds, and we have been very generous.
A reproducing cell requires at least 100 proteins.
The probability of getting the right bond is ½ for each amino acid.
Other kinds of amino acids will poison the process.
Very few left-handed amino acid polymers will fold into functional
proteins. An estimate is 1 in 1074 for 150 amino acids.
There is no known natural mechanism for assembling amino acids
into polymers outside the cell.