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1.0 An Electrical Engineers Point of View

http://www.cosmicfingerprints.com/blog/ee/
1.1 7 Biology Myths an Electrical Engineer Would Never Tolerate
As an Electrical Engineer, I am utterly appalled at the intellectual slop that passes for
science in biology. Engineers would lose their jobs in droves if they tolerated the mushy
thinking and lack of rigor that is routine in the life sciences.
Before I elaborate on this, some background.
10 years ago I couldnt have imagined I would become interested in DNA, biology, evolution
or any such thing. Biology in high school was b-o-r-i-n-g. Chemistry in college was a hard
slog.
I got my degree in Electrical Engineering. Specialized in communications and control
systems. Graduated and developed analog circuits. Worked as an acoustical engineer.
Designed the speakers in the 1994 Ford Probe, the 1995 Acura Vigor, the 1995 Jeep Cherokee
and the 1996 Honda Civic.
Left acoustics & pursued digital communications. Sold embedded networking hardware,
software and ICs in the automation and robotics industry. Fought digital networking
standards battles in manufacturing. Wrote an Ethernet book, published by the worlds #1
technical society for process control engineers.
And now here I am discussing DNA, evolution, and telling you about scientific discoveries so
new, you cant buy books about them in the bookstore. Im loving it.
As an outsider to the biology industry I bring a very particular perspective: That of an
engineer whos performed digital network design (very exact), analog circuit design (a quasi-
art form), and acoustics (extremely complex and messy).
All industries become incestuous as they age. They resist change. All professions are run by
good ol boys clubs. In every industry, innovations almost NEVER come from the inside.
Novel approaches usually come from outsiders. External innovations are opposed by the old
guard because they threaten the status quo.
Bill Gates was a complete outsider to the computer business. Larry and Sergey, founders of
Google, were complete foreigners to the search engine game. (Early on, they tried to sell their
search technology to Yahoo for $1 million but Yahoo turned them down.)
Fred Smith, founder of Federal Express, was a complete virgin in the shipping industry. Ray
Kroc of McDonalds wasnt a restaurant veteran; he was a milkshake machine salesman.
All these people had an outsiders point of view that enabled them to see what insiders were
blind to.
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Like these men, I am a total outsider in biology. Yet despite the fact that I wouldnt pass a test
on retroviruses or organic chemistry, as an EE I see certain things with crystal clarity that
biologists are blind to. One reason is, in Electrical Engineering, theory matches reality better
than it does in almost any other engineering discipline.
Examples: In metallurgy, when you predict the failure load of a steel beam, youre lucky if
your guess is within 10%. In chemical engineering, a 5-10% error factor is considered good
for many reactions. Civil engineers over-design bridges by 50% to 100% just to be safe.
But a model of an electrical circuit or computer chip is often accurate to within 1% and
sometimes 0.01%.
Because you cant see electricity and shouldnt touch it, EE is abstract and very mathematical.
Its also rigorous. I cant tell you how many times in my engineering classes, the professor
would be explaining something like, say, the behavior of a semiconductor, and he would
derive the calculus equation from scratch.
Of the appliances in your house, which ones work exactly the way theyre supposed to? Your
car doesnt. Your dishwasher doesnt. Your refrigerator needs new parts every few years. The
mechanical stuff is prone to problems.
But your TV does exactly what its supposed to, for years. So does your iPod and your
Microwave oven and your clock radio and your cell phone.
You can thank an EE for that.
For this reason, EEs have very high expectations of theoretical models because the model
has to be built and it has to work. Engineers dont have much tolerance for B.S.
Today:
7 Urban Legends Biologists Believe. but an Engineer Would Never Tolerate:

1. Random mutations are usually neutral or harmful but occasionally they confer a
benefit to an organism. Natural Selection filters out the harmful mutations, causing
species to evolve.
This is THE central dogma of neo-Darwinism and is allegedly accepted by virtually all
scientists. You will find it in literally 1,000 textbooks and 10,000 websites.
To the average biologist and to the average man on the street, it sounds perfectly plausible.
And I fully understand why people believe this.
But Im an EE. I know that the information in DNA is a signal. By definition, random
mutations are noise.
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Telling a communications engineer that adding noise to a signal sometimes create new, useful
data structures is like telling a nurse you can occasionally cure a common cold by swallowing
rat poison.
This is absurd! Youll be hard pressed to find any communications engineer who, upon
examining this claim, would agree with it. Have you ever had a data glitch on your computer
that improved your files? Ever?
There is not a one single principle or practice in engineering that would ever suggest that this
is actually true. All the Natural Selection in the world is powerless without a beneficial
mutation. And youll never get a major benefit from accidental copying errors.
The mutations that drive evolution are systematic and directed, not accidental.
2. 97% of your DNA is junk - an accumulation of evolutionary leftovers from random
mutations over millions of years.
The only reason anyone believes lie #2 is that they believe lie #1. Heres how any rational
person can quickly figure out that #2 is B.S.:
Human DNA holds 750 megabytes of data, the same as a Compact Disc. If 97% of your DNA
is junk, that means the 3% that isnt junk is 22 megabytes. In other words, theyre implying
that the entire plan for a human body only takes up 22 megabytes of storage space.
Heck, the Windows folder on my PC - the directory that contains most of the Operating
System - is 27 gigabytes. Does anyone actually think Microsoft Windows Vista is more
sophisticated than the human body? Bill Gates sure doesnt.
The fact that a plan for an entire human body can even be contained on one CD is nothing
short of a miracle of data compression.
Actual fact: DNA is not 3% efficient. Its more like 1,000% efficient. The same gene can be
used in completely different ways by a dozen different processes. The result is a level of data
density that software engineers only dream of.
Engineers see profound elegance where biologists see junk.
Which perspective is more in keeping with the aims of science?
3. You only need 3 things for evolution to occur: heredity, variation and selection.
Tufts university philosopher and prominent atheist Daniel Dennett famously said this. He
would never say this if he had an engineering degree.
If this were true, computer viruses (which have heredity, variation and selection) would
mutate all by themselves and develop resistance to anti-virus software. They dont.
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If this were true, the pirated copy of a copy of a copy of a copy of Windows XP or The
Eagles Hotel California that you can buy on the street corner for $2 in China would
occasionally be superior to the original. It never is.
If this were true, Bill Gates wouldnt have to employ 10,000 programmers in Redmond
Washington. He would just buy truckloads of computers, add random errors to a billion
copies of Windows and filter them through natural selection.
Nobody writes software that way. Nobody. Have you ever wondered why?
Most biologists think evolution just happens automatically. They say all you need is time and
a lot of raw materials and it will just happen.
So why dont computer programs ever evolve by themselves?
They dont and they never will - not unless theyre programmed to do so. Evolution is not a
given; at some level its always a design feature. Software programmers will tell you that self-
adaptive code is profoundly difficult to write. Never happens by accident.

4. Biology is nothing more than sophisticated physics and chemistry.
Thats like saying the Internet is nothing more than sophisticated copper wire and silicon
chips.
Im an e-commerce consultant. I practically live on the Internet. I have conversations with
people about the Internet all the time. Nobody I talk to ever describes the Internet that way.
Do you?
You talk about things like email and Google and Facebook. You tell your friend about the
Youtube video where the guy goes to every country in the world and does his little dance jig.
And the latest gaffe by Sarah Palin. All those things are INFORMATION.
90% of Electrical Engineering is concerned with controlling and processing information. Only
a small part of EE is concerned with things like motors and generators and watts and
horsepower. Even power equipment is controlled by information.
All the interesting things you do with electricity involve signals or digital codes. Temperature
measurement or text messages or a radio transmission.
The SOFTWARE is more interesting than the hardware. So it is with DNA. Chemicals are
just the hardware.
Until the biology profession accepts that the real power in biology is in the information -
the software and not the chemicals - it will continue to slam into brick walls and put
forth evolutionary theories that make wrong predictions.
It will continue to get nowhere in Origin of Life research.
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Information never improves by accident. Information evolves only through highly structured
processes.
5. Genetic Algorithms Prove Darwinian Evolution.
A Genetic Algorithm (GA) is a computer program that modifies code and then evaluates the
code against some pre-programmed goal, keeping the winners and discarding the losers. GAs
refine software programs through an evolution-like process.
GAs are not a be-all-end-all by any means, and they have limited application. But they are
useful.
Some years ago Richard Dawkins wrote a software program that took the following garbage
text:
WDLTMNLT DTJBKWIRZREZLMQCO P
After only 43 iterations, by deleting characters it didnt want, the program reached its pre-
programmed goal:
METHINKS IT IS LIKE A WEASEL
Traditional Darwinian evolution by definition has no goals, just blind natural selection.
Dawkins program has a definite goal and is programmed to reach it. This program has
nothing to do with formal Darwinian evolution. Its intelligent evolution.
Every single Genetic Algorithm Ive ever seen, no matter how simple or complicated,
only works if it has pre-programmed goals. Which requires both a program and objectives.
Ive never seen a GA that actually mirrored Darwinian Evolution. They always sneak in some
element of design.
Which only adds to the reasons why the Neo-Darwinian theory of purposeless random events
is wrong. Real world evolution is pre-programmed and has goals of some sort pre-loaded. Ive
never seen an exception. This is no different than computer programs that evolve.

6. The human eye is a pathetic design. Its got a big blind spot and the wires are
installed backwards.
There are many, many variations on this argument. Its just another version of Junk DNA.
When I was a manufacturing production manager, I had to produce an indicator lamp
assembly for a piece of equipment. The design had a light bulb and 2 identical resistors,
which I thought were stupid. I suggested that we replace the 2 resistors with one resistor of
twice the value. This would save money and space. I told the customer the design was
obviously lousy.
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The engineer got angry and almost took his business elsewhere. Then my boss spent 30
minutes lecturing me. He reminded me that my job was to put the customers product into
production, not insult him with my warped critique of his design skills.
What I didnt know was that 600 volts would arc across one resistor, but not across two. A
second, redundant resistor was an elegant way to solve that problem and it only cost 2
cents.
I learned the hard way that when you criticize a design, you may have a very incomplete
picture of the many constraints the designer has to work within.
Designs always have delicate tradeoffs. Some have amazing performance but are extremely
difficult to manufacture. Sometimes a minor change in material would make a huge
improvement but the material is unavailable. Sometimes you have to make a compromise
between 15 competing priorities. Sometimes people have no appreciation for how difficult
that maze is to navigate.
I am not saying that there are no sub-optimal designs in biology - Im sure there are lots of
sub-optimal designs. Furthermore I do believe that life followed an evolutionary process and
many designs are best guesses engineered by the organisms ancestors.
But human beings must be very careful to not proudly assert that we could obviously do
better. We dont know that. We do not understand whats involved in designing an eye
because weve never built one.
My friend, if you lose your eye, theres not a single arrogant scientist in the world who
can build you a new one. Especially not the scientists who try to tell you why the design
of the eye is pathetic.
If I were selecting an eye surgeon, Id look for one who has deep respect for the eye, not
disdain for it. How about you?
Every engineer knows that you never truly know how something works until you can build it.
Merely taking it apart is not enough. Until we can DESIGN eyes for ourselves, we must be
very cautious about what we say. The scientist must ALWAYS be humble in the face of
nature and you should be wary of anyone who is not.

7. There is no such thing as purpose in nature. There is only the appearance of
purpose.
Teleology is a scientific term which is defined as purpose in nature. Atheism denies
teleology in the universe. For this reason some biologists have forbidden their students to use
purposeful language.
In 1974 Ernst Mayr illustrated it like this:
1. The Wood Thrush migrates in the fall in order to escape the inclemency of the weather
and the food shortages of the northern climates.
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2. The Wood Thrush migrates in the fall and thereby escapes the inclemency of the weather
and the food shortages of the northern climates.
Statement #1 is purposeful, statement #2 is not. Mayr does fancy footwork in order to avoid
reference to design in biology. (It also converts all of his writing to colorless passive
sentences. Any good writer will tell you passive language is a sign of mushy thinking.)
The famous biologist JBS Haldane joked, Teleology is like a mistress to a biologist: he
cannot live without her but hes unwilling to be seen with her in public.
Everything in biology is purposeful. Which is precisely why biology is fundamentally
different than chemistry. Chemicals have no purpose. Organisms do. You cannot formulate a
coherent description of life if you deny purpose.
For proof of this, look no further than the genetic code. Every codon in DNA maps to an
amino acid that it is SUPPOSED TO make - but an error is possible. It is not possible to even
talk about any code at all without acknowledging purpose. Purpose is absolutely implicit in
every strand of DNA in every organism in the world.
In his book Perceptual Control Theory, William Powers explains that the study of any goal-
directed (control feedback) system is fundamentally different than the study of rocks or
chemicals or magnetic fields or anything purely physical. The failure to acknowledge this has
wreaked all kinds of havoc in science for 150 years.
Even something as simple as a thermostat cannot be understood if you see it as only an
assembly of molecules. A thermostat is programmed to hold your room at a certain
temperature. The thermostats purpose can only be understood from a top-down point of view.
It has a goal.
In Electrical Engineering, the top-down nature of information is described by something we
call the OSI 7 Layer Model. Simplified explanation: The 7 Layer model says that in your
computer, theres an Ethernet cable that connects you to the Internet. The copper wire and the
voltage on that wire is Layer 1 - the physical layer.
Layer 2 is is the 1s and 0s that voltage represents. Layers 3, 4, 5 and 6 are the operating
system and layer 7 is your spreadsheet or email program or web browser, the application
layer.
When you send me an email, information is encoded from the top down and sent through your
Ethernet cable.
When I receive your email, information is decoded from the bottom up starting with the signal
on the cable, and I read your email on my screen.
ALL information is organized this way - in a top-down hierarchy. The wire has its purpose.
The 1s and 0s have their purpose. The operating system has a purpose, my email program
has a purpose and your message has a purpose.
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You cannot deny purpose in computers or biology without immediately contradicting yourself
2 minutes later. Even a person who denies purpose is purposefully denying it.
Everything I just told you, I absolutely know to be true as a result of my education and
experience as an engineer. Which is why Im willing to make ballsy proclamations like
Darwinism as we currently know it is going to crumble in the next 2-5 years.
Yes, I know that might sound ridiculous. Some people scoff at that.
But people scoffed at the idea that communism would fall. They were quick to remind you
that every time someone tried to cross the Berlin Wall, they got shot by the guards in the
tower.
But then one day someone made it across and nobody opened fire. Then another. Then
another. It didnt take long before that wall became rubble. The fall of communism was
surprisingly swift and thorough.
Just a few years ago, people mocked the idea that real estate prices would stop rising. But
those who had a deep understanding of the inside story of both of those industries saw the
cracks forming. (My friend Nathan, who was a mortgage broker at the time, tells me about
stacks of paper being sold, that no sane investor would touch with a 10 foot pole.)
Darwinism as we know it CANNOT stand under the weight of 21st century DNA research.
Its impossible. Because Ive read the literature. Amazon is absolutely littered with books
written from every imaginable point of view, both religious and non-religious, pointing to the
creaking, groaning edifice of Neo-Darwinism.
It is inevitable that it will fall. And its not going to be long.
It will be replaced by an algorithmic model of Evolution.
BOLD HYPOTHESIS: When Biologists accept what Electrical Engineers know about
information, a whole bunch of problems in biology will be solved:
1. The random mutation theory will be discarded. It will be replaced with Transposition,
Natural Genetic Engineering, Horizontal Gene Transfer and Genome Doubling. Suddenly
evolution will make sense because it is understood as an engineered process not random
accident.
2. Well discover that what was originally thought to be junk DNA is actually the heart of the
most sophisticated database format ever devised.
3a. Evolution will not be taken for granted but deeply appreciated as an utterly ingenious
mechanism, pre-programmed into living things. As software engineers replicate the
evolutionary algorithm in computer programs, well achieve huge breakthroughs in Artificial
Intelligence.
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3b: Evolution is orchestrated at a very high level within the organism. It is controlled by a
mechanism that is currently poorly understood. This mechanism is beautifully efficient,
elegant, fractal, and follows a very exact mathematical protocol. Bioninformatics will become
the most rigorous discipline in engineering. The code of this protocol will be cracked
because of the Human Genome Project and the public availability of DNA sequences. This
discovery will lay the foundation of an entire new branch of Computer Science in the
21st century.
4. The Physics and Chemistry paradigm of biology will be replaced with a Bioinformatics
paradigm. Evolution and the origin of life theories will make much more successful
predictions.
5. Neo-Darwinism will be discarded because biologists will recognize that biological
evolution is just like Genetic Algorithms: It employs pre-programmed goals and educated
guesses, not random chance.
6. Rather than assuming designs in biology are pathetic or stupid well discover deeper
reasons for why organisms are the way they are. And greater insights into the subtlety of
living things.
7. Everything in biology makes sense once you understand that every single one of the 5
million trillion trillion cells on earth is purposeful and intentional and the original cells were
designed to evolve and adapt.
Finally I would like to suggest that there is nothing in the world that can teach us more about
digital communications and software programming than DNA. DNA is an absolute gold mine,
a treasure trove of insights of data storage, error correction, software architecture, robust
design and fractal data compression. Every Electrical Engineer and Computer Science major
should study it intensively.
And there is much we engineers can learn from the biologists - because even the simplest
living thing is more elegant than the greatest man-made supercomputer. As Engineers and
Biologists begin to talk to each other, the 21st century will be amazing indeed.
Perry Marshall
P.S.: Innovations almost always come from outsiders. This means that those who read
widely and embrace multiple disciplines - pockets of humanity that dont normally talk to
each other - can enjoy long and prosperous careers as innovators.
The watchword of 21st century biology will be Interdisciplinary - the great mysteries will
be solved by people who bring the expertise of other fields to bear on the biggest questions in
science.
My challenge to you: Make a deliberate decision to step outside of your normal and familiar
environment and innovate. The world will reward you for it.
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2.0 The Information Challenge
By Richard Dawkins
http://www.skeptics.com.au/publications/articles/the-information-challenge/
In September 1997, I allowed an Australian film crew into my house in Oxford without
realising that their purpose was creationist propaganda. In the course of a suspiciously
amateurish interview, they issued a truculent challenge to me to give an example of a genetic
mutation or an evolutionary process which can be seen to increase the information in the
genome. It is the kind of question only a creationist would ask in that way, and it was at this
point I tumbled to the fact that I had been duped into granting an interview to creationists a
thing I normally dont do, for good reasons. In my anger I refused to discuss the question
further, and told them to stop the camera. However, I eventually withdrew my peremptory
termination of the interview as a whole. This was solely because they pleaded with me that
they had come all the way from Australia specifically in order to interview me. Even if this
was a considerable exaggeration, it seemed, on reflection, ungenerous to tear up the legal
release form and throw them out. I therefore relented.
My generosity was rewarded in a fashion that anyone familiar with fundamentalist tactics
might have predicted. When I eventually saw the film a year later
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, I found that it had been
edited to give the false impression that I was incapable of answering the question about
information content
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. In fairness, this may not have been quite as intentionally deceitful as it
sounds. You have to understand that these people really believe that their question cannot be
answered! Pathetic as it sounds, their entire journey from Australia seems to have been a
quest to film an evolutionist failing to answer it.
With hindsight given that I had been suckered into admitting them into my house in the
first place it might have been wiser simply to answer the question. But I like to be
understood whenever I open my mouth I have a horror of blinding people with science
and this was not a question that could be answered in a soundbite. First you first have to
explain the technical meaning of information. Then the relevance to evolution, too, is
complicated not really difficult but it takes time. Rather than engage now in further
recriminations and disputes about exactly what happened at the time of the interview (for, to
be fair, I should say that the Australian producers memory of events seems to differ from
mine), I shall try to redress the matter now in constructive fashion by answering the original
question, the Information Challenge, at adequate length the sort of length you can
achieve in a proper article.
2.1 Information
The technical definition of information was introduced by the American engineer Claude
Shannon in 1948. An employee of the Bell Telephone Company, Shannon was concerned to
measure information as an economic commodity. It is costly to send messages along a
telephone line. Much of what passes in a message is not information: it is redundant. You
could save money by recoding the message to remove the redundancy. Redundancy was a
second technical term introduced by Shannon, as the inverse of information. Both definitions
were mathematical, but we can convey Shannons intuitive meaning in words.
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Redundancy is any part of a message that is not informative, either because the recipient
already knows it (is not surprised by it) or because it duplicates other parts of the message. In
the sentence Rover is a poodle dog, the word dog is redundant because poodle already
tells us that Rover is a dog. An economical telegram would omit it, thereby increasing the
informative proportion of the message. Arr JFK Fri pm pls mt BA Cncrd flt carries the
same information as the much longer, but more redundant, Ill be arriving at John F Kennedy
airport on Friday evening; please meet the British Airways Concorde flight. Obviously the
brief, telegraphic message is cheaper to send (although the recipient may have to work harder
to decipher it redundancy has its virtues if we forget economics). Shannon wanted to find a
mathematical way to capture the idea that any message could be broken into the information
(which is worth paying for), the redundancy (which can, with economic advantage, be deleted
from the message because, in effect, it can be reconstructed by the recipient) and the noise
(which is just random rubbish).
It rained in Oxford every day this week carries relatively little information, because the
receiver is not surprised by it. On the other hand, It rained in the Sahara desert every day this
week would be a message with high information content, well worth paying extra to send.
Shannon wanted to capture this sense of information content as surprise value. It is related
to the other sense that which is not duplicated in other parts of the message because
repetitions lose their power to surprise. Note that Shannons definition of the quantity of
information is independent of whether it is true. The measure he came up with was ingenious
and intuitively satisfying. Lets estimate, he suggested, the receivers ignorance or uncertainty
before receiving the message, and then compare it with the receivers remaining ignorance
after receiving the message. The quantity of ignorance-reduction is the information content.
Shannons unit of information is the bit, short for binary digit. One bit is defined as the
amount of information needed to halve the receivers prior uncertainty, however great that
prior uncertainty was (mathematical readers will notice that the bit is, therefore, a logarithmic
measure).
In practice, you first have to find a way of measuring the prior uncertainty that which is
reduced by the information when it comes. For particular kinds of simple message, this is
easily done in terms of probabilities. An expectant father watches the Caesarian birth of his
child through a window into the operating theatre. He cant see any details, so a nurse has
agreed to hold up a pink card if it is a girl, blue for a boy. How much information is conveyed
when, say, the nurse flourishes the pink card to the delighted father? The answer is one bit
the prior uncertainty is halved. The father knows that a baby of some kind has been born, so
his uncertainty amounts to just two possibilities boy and girl and they are (for purposes
of this discussion) equal. The pink card halves the fathers prior uncertainty from two
possibilities to one (girl). If thered been no pink card but a doctor had walked out of the
operating theatre, shook the fathers hand and said Congratulations old chap, Im delighted
to be the first to tell you that you have a daughter, the information conveyed by the 17 word
message would still be only one bit.
2.2 Computer information
Computer information is held in a sequence of noughts and ones. There are only two
possibilities, so each 0 or 1 can hold one bit. The memory capacity of a computer, or the
storage capacity of a disc or tape, is often measured in bits, and this is the total number of 0s
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or 1s that it can hold. For some purposes, more convenient units of measurement are the byte
(8 bits), the kilobyte (1000 bytes or 8000 bits), the megabyte (a million bytes or 8 million bits)
or the gigabyte (1000 million bytes or 8000 million bits). Notice that these figures refer to the
total available capacity. This is the maximum quantity of information that the device is
capable of storing. The actual amount of information stored is something else. The capacity of
my hard disc happens to be 4.2 gigabytes. Of this, about 1.4 gigabytes are actually being used
to store data at present. But even this is not the true information content of the disc in
Shannons sense. The true information content is smaller, because the information could be
more economically stored. You can get some idea of the true information content by using
one of those ingenious compression programs like Stuffit. Stuffit looks for redundancy in
the sequence of 0s and 1s, and removes a hefty proportion of it by recoding stripping out
internal predictability. Maximum information content would be achieved (probably never in
practice) only if every 1 or 0 surprised us equally. Before data is transmitted in bulk around
the Internet, it is routinely compressed to reduce redundancy.
Thats good economics. But on the other hand it is also a good idea to keep some redundancy
in messages, to help correct errors. In a message that is totally free of redundancy, after
theres been an error there is no means of reconstructing what was intended. Computer codes
often incorporate deliberately redundant parity bits to aid in error detection. DNA, too, has
various error-correcting procedures which depend upon redundancy. When I come on to talk
of genomes, Ill return to the three-way distinction between total information capacity,
information capacity actually used, and true information content.
It was Shannons insight that information of any kind, no matter what it means, no matter
whether it is true or false, and no matter by what physical medium it is carried, can be
measured in bits, and is translatable into any other medium of information. The great biologist
J B S Haldane used Shannons theory to compute the number of bits of information conveyed
by a worker bee to her hivemates when she dances the location of a food source (about 3
bits to tell about the direction of the food and another 3 bits for the distance of the food). In
the same units, I recently calculated that Id need to set aside 120 megabits of laptop computer
memory to store the triumphal opening chords of Richard Strausss Also Sprach Zarathustra
(the 2001 theme) which I wanted to play in the middle of a lecture about evolution.
Shannons economics enable you to calculate how much modem time itll cost you to e-mail
the complete text of a book to a publisher in another land. Fifty years after Shannon, the idea
of information as a commodity, as measurable and interconvertible as money or energy, has
come into its own.
2.3 DNA information
DNA carries information in a very computer-like way, and we can measure the genomes
capacity in bits too, if we wish. DNA doesnt use a binary code, but a quaternary one.
Whereas the unit of information in the computer is a 1 or a 0, the unit in DNA can be T, A, C
or G. If I tell you that a particular location in a DNA sequence is a T, how much information
is conveyed from me to you? Begin by measuring the prior uncertainty. How many
possibilities are open before the message T arrives? Four. How many possibilities remain
after it has arrived? One. So you might think the information transferred is four bits, but
actually it is two. Heres why (assuming that the four letters are equally probable, like the four
suits in a pack of cards). Remember that Shannons metric is concerned with the most
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economical way of conveying the message. Think of it as the number of yes/no questions that
youd have to ask in order to narrow down to certainty, from an initial uncertainty of four
possibilities, assuming that you planned your questions in the most economical way. Is the
mystery letter before D in the alphabet? No. That narrows it down to T or G, and now we
need only one more question to clinch it. So, by this method of measuring, each letter of the
DNA has an information capacity of 2 bits.
Whenever prior uncertainty of recipient can be expressed as a number of equiprobable
alternatives N, the information content of a message which narrows those alternatives down to
one is log2N (the power to which 2 must be raised in order to yield the number of alternatives
N). If you pick a card, any card, from a normal pack, a statement of the identity of the card
carries log252, or 5.7 bits of information. In other words, given a large number of guessing
games, it would take 5.7 yes/no questions on average to guess the card, provided the questions
are asked in the most economical way. The first two questions might establish the suit. (Is it
red? Is it a diamond?) the remaining three or four questions would successively divide and
conquer the suit (is it a 7 or higher? etc.), finally homing in on the chosen card. When the
prior uncertainty is some mixture of alternatives that are not equiprobable, Shannons formula
becomes a slightly more elaborate weighted average, but it is essentially similar. By the way,
Shannons weighted average is the same formula as physicists have used, since the nineteenth
century, for entropy. The point has interesting implications but I shall not pursue them here.
2.4 Information and evolution
Thats enough background on information theory. It is a theory which has long held a
fascination for me, and I have used it in several of my research papers over the years. Lets
now think how we might use it to ask whether the information content of genomes increases
in evolution. First, recall the three way distinction between total information capacity, the
capacity that is actually used, and the true information content when stored in the most
economical way possible. The total information capacity of the human genome is measured in
gigabits. That of the common gut bacterium Escherichia coli is measured in megabits. We,
like all other animals, are descended from an ancestor which, were it available for our study
today, wed classify as a bacterium. So perhaps, during the billions of years of evolution since
that ancestor lived, the information capacity of our genome has gone up about three orders of
magnitude (powers of ten) about a thousandfold. This is satisfyingly plausible and
comforting to human dignity. Should human dignity feel wounded, then, by the fact that the
crested newt, Triturus cristatus, has a genome capacity estimated at 40 gigabits, an order of
magnitude larger than the human genome? No, because, in any case, most of the capacity of
the genome of any animal is not used to store useful information. There are many
nonfunctional pseudogenes (see below) and lots of repetitive nonsense, useful for forensic
detectives but not translated into protein in the living cells. The crested newt has a bigger
hard disc than we have, but since the great bulk of both our hard discs is unused, we neednt
feel insulted. Related species of newt have much smaller genomes. Why the Creator should
have played fast and loose with the genome sizes of newts in such a capricious way is a
problem that creationists might like to ponder. From an evolutionary point of view the
explanation is simple (see The Selfish Gene pp 44 45 and p 275 in the Second Edition).
14

2.5 Gene duplication
Evidently the total information capacity of genomes is very variable across the living
kingdoms, and it must have changed greatly in evolution, presumably in both directions.
Losses of genetic material are called deletions. New genes arise through various kinds of
duplication. This is well illustrated by haemoglobin, the complex protein molecule that
transports oxygen in the blood.
Human adult haemoglobin is actually a composite of four protein chains called globins,
knotted around each other. Their detailed sequences show that the four globin chains are
closely related to each other, but they are not identical. Two of them are called alpha globins
(each a chain of 141 amino acids), and two are beta globins (each a chain of 146 amino acids).
The genes coding for the alpha globins are on chromosome 11; those coding for the beta
globins are on chromosome 16. On each of these chromosomes, there is a cluster of globin
genes in a row, interspersed with some junk DNA. The alpha cluster, on Chromosome 11,
contains seven globin genes. Four of these are pseudogenes, versions of alpha disabled by
faults in their sequence and not translated into proteins. Two are true alpha globins, used in
the adult. The final one is called zeta and is used only in embryos. Similarly the beta cluster,
on chromosome 16, has six genes, some of which are disabled, and one of which is used only
in the embryo. Adult haemoglobin, as weve seen contains two alpha and two beta chains.
Never mind all this complexity. Heres the fascinating point. Careful letter-by-letter analysis
shows that these different kinds of globin genes are literally cousins of each other, literally
members of a family. But these distant cousins still coexist inside our own genome, and that
of all vertebrates. On a the scale of whole organism, the vertebrates are our cousins too. The
tree of vertebrate evolution is the family tree we are all familiar with, its branch-points
representing speciation events the splitting of species into pairs of daughter species. But
there is another family tree occupying the same timescale, whose branches represent not
speciation events but gene duplication events within genomes.
The dozen or so different globins inside you are descended from an ancient globin gene
which, in a remote ancestor who lived about half a billion years ago, duplicated, after which
both copies stayed in the genome. There were then two copies of it, in different parts of the
genome of all descendant animals. One copy was destined to give rise to the alpha cluster (on
what would eventually become Chromosome 11 in our genome), the other to the beta cluster
(on Chromosome 16). As the aeons passed, there were further duplications (and doubtless
some deletions as well). Around 400 million years ago the ancestral alpha gene duplicated
again, but this time the two copies remained near neighbours of each other, in a cluster on the
same chromosome. One of them was destined to become the zeta of our embryos, the other
became the alpha globin genes of adult humans (other branches gave rise to the nonfunctional
pseudogenes I mentioned). It was a similar story along the beta branch of the family, but with
duplications at other moments in geological history.
Now heres an equally fascinating point. Given that the split between the alpha cluster and the
beta cluster took place 500 million years ago, it will of course not be just our human genomes
that show the split possess alpha genes in a different part of the genome from beta genes.
We should see the same within-genome split if we look at any other mammals, at birds,
reptiles, amphibians and bony fish, for our common ancestor with all of them lived less than
15

500 million years ago. Wherever it has been investigated, this expectation has proved correct.
Our greatest hope of finding a vertebrate that does not share with us the ancient alpha/beta
split would be a jawless fish like a lamprey, for they are our most remote cousins among
surviving vertebrates; they are the only surviving vertebrates whose common ancestor with
the rest of the vertebrates is sufficiently ancient that it could have predated the alpha/beta
split. Sure enough, these jawless fishes are the only known vertebrates that lack the
alpha/beta divide.
Gene duplication, within the genome, has a similar historic impact to species duplication
(speciation) in phylogeny. It is responsible for gene diversity, in the same way as speciation
is responsible for phyletic diversity. Beginning with a single universal ancestor, the
magnificent diversity of life has come about through a series of branchings of new species,
which eventually gave rise to the major branches of the living kingdoms and the hundreds of
millions of separate species that have graced the earth. A similar series of branchings, but this
time within genomes gene duplications has spawned the large and diverse population of
clusters of genes that constitutes the modern genome.
The story of the globins is just one among many. Gene duplications and deletions have
occurred from time to time throughout genomes. It is by these, and similar means, that
genome sizes can increase in evolution. But remember the distinction between the total
capacity of the whole genome, and the capacity of the portion that is actually used. Recall that
not all the globin genes are actually used. Some of them, like theta in the alpha cluster of
globin genes, are pseudogenes, recognizably kin to functional genes in the same genomes, but
never actually translated into the action language of protein. What is true of globins is true of
most other genes. Genomes are littered with nonfunctional pseudogenes, faulty duplicates of
functional genes that do nothing, while their functional cousins (the word doesnt even need
scare quotes) get on with their business in a different part of the same genome. And theres
lots more DNA that doesnt even deserve the name pseudogene. It, too, is derived by
duplication, but not duplication of functional genes. It consists of multiple copies of junk,
tandem repeats, and other nonsense which may be useful for forensic detectives but which
doesnt seem to be used in the body itself.
Once again, creationists might spend some earnest time speculating on why the Creator
should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.
2.6 Information in the genome
Can we measure the information capacity of that portion of the genome which is actually
used? We can at least estimate it. In the case of the human genome it is about 2%
considerably less than the proportion of my hard disc that I have ever used since I bought it.
Presumably the equivalent figure for the crested newt is even smaller, but I dont know if it
has been measured. In any case, we mustnt run away with a chaunvinistic idea that the
human genome somehow ought to have the largest DNA database because we are so
wonderful. The great evolutionary biologist George C Williams has pointed out that animals
with complicated life cycles need to code for the development of all stages in the life cycle,
but they only have one genome with which to do so. A butterflys genome has to hold the
complete information needed for building a caterpillar as well as a butterfly. A sheep liver
fluke has six distinct stages in its life cycle, each specialised for a different way of life. We
16

shouldnt feel too insulted if liver flukes turned out to have bigger genomes than we have
(actually they dont).
Remember, too, that even the total capacity of genome that is actually used is still not the
same thing as the true information content in Shannons sense. The true information content is
whats left when the redundancy has been compressed out of the message, by the theoretical
equivalent of Stuffit. There are even some viruses which seem to use a kind of Stuffit-like
compression. They make use of the fact that the RNA (not DNA in these viruses, as it
happens, but the principle is the same) code is read in triplets. There is a frame which
moves along the RNA sequence, reading off three letters at a time. Obviously, under normal
conditions, if the frame starts reading in the wrong place (as in a so-called frame-shift
mutation), it makes total nonsense: the triplets that it reads are out of step with the
meaningful ones. But these splendid viruses actually exploit frame-shifted reading. They get
two messages for the price of one, by having a completely different message embedded in the
very same series of letters when read frame-shifted. In principle you could even get three
messages for the price of one, but I dont know whether there are any examples.
2.7 Information in the body
It is one thing to estimate the total information capacity of a genome, and the amount of the
genome that is actually used, but its harder to estimate its true information content in the
Shannon sense. The best we can do is probably to forget about the genome itself and look at
its product, the phenotype, the working body of the animal or plant itself. In 1951, J W S
Pringle, who later became my Professor at Oxford, suggested using a Shannon-type
information measure to estimate complexity. Pringle wanted to express complexity
mathematically in bits, but I have long found the following verbal form helpful in explaining
his idea to students.
We have an intuitive sense that a lobster, say, is more complex (more advanced, some
might even say more highly evolved) than another animal, perhaps a millipede. Can we
measure something in order to confirm or deny our intuition? Without literally turning it into
bits, we can make an approximate estimation of the information contents of the two bodies as
follows. Imagine writing a book describing the lobster. Now write another book describing
the millipede down to the same level of detail. Divide the word-count in one book by the
word-count in the other, and you have an approximate estimate of the relative information
content of lobster and millipede. It is important to specify that both books describe their
respective animals down to the same level of detail. Obviously if we describe the millipede
down to cellular detail, but stick to gross anatomical features in the case of the lobster, the
millipede would come out ahead.
But if we do the test fairly, Ill bet the lobster book would come out longer than the millipede
book. Its a simple plausibility argument, as follows. Both animals are made up of
segments modules of bodily architecture that are fundamentally similar to each other,
arranged fore-and-aft like the trucks of a train. The millipedes segments are mostly identical
to each other. The lobsters segments, though following the same basic plan (each with a
nervous ganglion, a pair of appendages, and so on) are mostly different from each other. The
millipede book would consist of one chapter describing a typical segment, followed by the
phrase Repeat N times where N is the number of segments. The lobster book would need a
17

different chapter for each segment. This isnt quite fair on the millipede, whose front and rear
end segments are a bit different from the rest. But Id still bet that, if anyone bothered to do
the experiment, the estimate of lobster information content would come out substantially
greater than the estimate of millipede information content.
Its not of direct evolutionary interest to compare a lobster with a millipede in this way,
because nobody thinks lobsters evolved from millipedes. Obviously no modern animal
evolved from any other modern animal. Instead, any pair of modern animals had a last
common ancestor which lived at some (in principle) discoverable moment in geological
history. Almost all of evolution happened way back in the past, which makes it hard to study
details. But we can use the length of book thought-experiment to agree upon what it would
mean to ask the question whether information content increases over evolution, if only we had
ancestral animals to look at.
The answer in practice is complicated and controversial, all bound up with a vigorous debate
over whether evolution is, in general, progressive. I am one of those associated with a limited
form of yes answer. My colleague Stephen Jay Gould tends towards a no answer. I dont think
anybody would deny that, by any method of measuring whether bodily information
content, total information capacity of genome, capacity of genome actually used, or true
(Stuffit compressed) information content of genome there has been a broad overall trend
towards increased information content during the course of human evolution from our remote
bacterial ancestors. People might disagree, however, over two important questions: first,
whether such a trend is to be found in all, or a majority of evolutionary lineages (for example
parasite evolution often shows a trend towards decreasing bodily complexity, because
parasites are better off being simple); second, whether, even in lineages where there is a clear
overall trend over the very long term, it is bucked by so many reversals and re-reversals in the
shorter term as to undermine the very idea of progress. This is not the place to resolve this
interesting controversy. There are distinguished biologists with good arguments on both sides.
Supporters of intelligent design guiding evolution, by the way, should be deeply committed
to the view that information content increases during evolution. Even if the information
comes from God, perhaps especially if it does, it should surely increase, and the increase
should presumably show itself in the genome. Unless, of course for anything goes in such
addle-brained theorising God works his evolutionary miracles by nongenetic means.
Perhaps the main lesson we should learn from Pringle is that the information content of a
biological system is another name for its complexity. Therefore the creationist challenge with
which we began is tantamount to the standard challenge to explain how biological complexity
can evolve from simpler antecedents, one that I have devoted three books to answering (The
Blind Watchmaker, River Out of Eden, Climbing Mount Improbable) and I do not propose to
repeat their contents here. The information challenge turns out to be none other than our old
friend: How could something as complex as an eye evolve? It is just dressed up in fancy
mathematical language perhaps in an attempt to bamboozle. Or perhaps those who ask it
have already bamboozled themselves, and dont realise that it is the same old and
thoroughly answered question.
18

2.8 The Genetic Book of the Dead
Let me turn, finally, to another way of looking at whether the information content of genomes
increases in evolution. We now switch from the broad sweep of evolutionary history to the
minutiae of natural selection. Natural selection itself, when you think about it, is a narrowing
down from a wide initial field of possible alternatives, to the narrower field of the alternatives
actually chosen. Random genetic error (mutation), sexual recombination and migratory
mixing, all provide a wide field of genetic variation: the available alternatives. Mutation is not
an increase in true information content, rather the reverse, for mutation, in the Shannon
analogy, contributes to increasing the prior uncertainty. But now we come to natural selection,
which reduces the prior uncertainty and therefore, in Shannons sense, contributes
information to the gene pool. In every generation, natural selection removes the less
successful genes from the gene pool, so the remaining gene pool is a narrower subset. The
narrowing is nonrandom, in the direction of improvement, where improvement is defined, in
the Darwinian way, as improvement in fitness to survive and reproduce. Of course the total
range of variation is topped up again in every generation by new mutation and other kinds of
variation. But it still remains true that natural selection is a narrowing down from an initially
wider field of possibilities, including mostly unsuccessful ones, to a narrower field of
successful ones. This is analogous to the definition of information with which we began:
information is what enables the narrowing down from prior uncertainty (the initial range of
possibilities) to later certainty (the successful choice among the prior probabilities).
According to this analogy, natural selection is by definition a process whereby information is
fed into the gene pool of the next generation.
If natural selection feeds information into gene pools, what is the information about? It is
about how to survive. Strictly it is about how to survive and reproduce, in the conditions that
prevailed when previous generations were alive. To the extent that present day conditions are
different from ancestral conditions, the ancestral genetic advice will be wrong. In extreme
cases, the species may then go extinct. To the extent that conditions for the present generation
are not too different from conditions for past generations, the information fed into present-day
genomes from past generations is helpful information. Information from the ancestral past can
be seen as a manual for surviving in the present: a family bible of ancestral advice on how
to survive today. We need only a little poetic licence to say that the information fed into
modern genomes by natural selection is actually information about ancient environments in
which ancestors survived.
This idea of information fed from ancestral generations into descendant gene pools is one of
the themes of my new book, Unweaving the Rainbow. It takes a whole chapter, The Genetic
Book of the Dead, to develop the notion, so I wont repeat it here except to say two things.
First, it is the whole gene pool of the species as a whole, not the genome of any particular
individual, which is best seen as the recipient of the ancestral information about how to
survive. The genomes of particular individuals are random samples of the current gene pool,
randomised by sexual recombination. Second, we are privileged to intercept the information
if we wish, and read an animals body, or even its genes, as a coded description of ancestral
worlds. To quote from Unweaving the Rainbow: And isnt it an arresting thought? We are
digital archives of the African Pliocene, even of Devonian seas; walking repositories of
wisdom out of the old days. You could spend a lifetime reading in this ancient library and die
unsated by the wonder of it.
19

1 The producers never deigned to send me a copy: I completely forgot about it until an
American colleague called it to my attention.
2 See Barry Williams (1998): Creationist Deception Exposed, The Skeptic 18, 3, pp 7 10,
for an account of how my long pause (trying to decide whether to throw them out) was made
to look like hesitant inability to answer the question, followed by an apparently evasive
answer to a completely different question.


20


A Response to Dr. Dawkins' "The Information Challenge"
By: Casey Luskin
Evolution News & Views
October 4, 2007

In September, 2007, I posted a link to a YouTube video where Richard Dawkins was asked to
explain the origin of genetic information, according to Darwinism. I also posted a link to
Dawkins' rebuttal to the video, where he purports to explain the origin of genetic information
according to Darwinian evolution. The question posed to Dawkins was, "Can you give an
example of a genetic mutation or evolutionary process that can be seen to increase the
information in the genome?" Dawkins famously commented that the question was "the kind
of question only a creationist would ask . . ." Dawkins writes, "In my anger I refused to
discuss the question further, and told them to stop the camera." Dawkins' highly emotional
response calls into question whether he is capable of addressing this issue objectively. This
will be a response assessing Dawkins' answer to "The Information Challenge."

Part 1: Specified Complexity I s the Measure of Biological Complexity.
Dawkins writes, "First you first have to explain the technical meaning of 'information'." While
that sounds reasonable, Dawkins pulls a bait-and-switch and defines information as "Shannon
information"a formulation of "information" that applies to signal transmission and does not
account for the type of specified complexity found in biology.

It is common for Darwinists to define information as "Shannon information," which is related
to calculating the mere unlikelihood of a sequence of events. Under their definition, a
functionless stretch of genetic junk might have the same amount "information" as a fully
functional gene of the same sequence-length. ID-proponents don't see this as a useful way of
measuring biological information. ID-proponents define information as complex and specified
informationDNA which is finely-tuned to do something. Stephen C. Meyer writes that ID-
theorists use "(CSI) as a synonym for "specified complexity" to help distinguish functional
biological information from mere Shannon informationthat is, specified complexity from
mere complexity." As the ISCID encyclopedia explains, "Unlike specified complexity,
Shannon information is solely concerned with the improbability or complexity of a string of
characters rather than its patterning or significance."
The I nconvenient Truth for Dawkins: The difference between the Darwinist and ID
definitions of information is equivalent to the difference between getting 10 consecutive losing
hands in a poker game versus getting 10 consecutive royal flushes. One implicates design,
while the other does not.

It is important to note ID proponents did not invent the notion of "specified complexity," nor
were they the first to observe that "specified complexity" is the best way to describe
biological information. My first knowledge of the term being used comes from leading origin
of life theorist Leslie Orgel, who used it in 1973 in a fashion that closely resembles the
modern usage by ID proponents:
21

[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken
as the prototypes of simple, well-specified structures, because they consist of a very large
number of identical molecules packed together in a uniform way. Lumps of granite or random
mixtures of polymers are examples of structures which are complex but not specified. The
crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to
qualify because they lack specificity.

(Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection," pg.189 (Chapman &
Hall: London, 1973).)
Orgel thus captures the fact that specified complexity requires both order and a specific
arrangement of parts or symbols. This matches the definition given by Dembski, where he
defines specified complexity as an unlikely event that conforms to an independent pattern.
This establishes that specified complexity is the appropriate measure of biological
complexity.

Additionally, Richard Dawkins' article admits that "DNA carries information in a very
computer-like way, and we can measure the genome's capacity in bits too, if we wish." That's
an interesting analogy, reminiscent of the design overtones of Dawkins concession elsewhere
that "[t]he machine code of the genes is uncannily computer-like. Apart from differences in
jargon, the pages of a molecular biology journal might be interchanged with those of a
computer engineering journal." (Richard Dawkins, River Out of Eden: A Darwinian View of
Life, pg. 17 (New York: Basic Books, 1995).) Of course, Dawkins believes that the processes
of random mutation and unguided selection ultimately built "[t]he machine code of the genes"
and made it "uncannily computer-like." But I do not think a scientist is unjustified in
reasoning that in our experience, machine codes and computers only derive from intelligence.

Part 2: Does Gene Duplication Increase Information Content?
In this section, I will show why merely citing gene duplication does not help one understand
how Darwinian evolution can produce new genetic information. Dawkins' main point in his
"The Information Challenge" article is that "[n]ew genes arise through various kinds of
duplication." So his answer to the creationist question that so upset him is gene duplication.
Yet during the actual gene-duplication process, a pre-existing gene is merely copied, and
nothing truly new is generated. As Michael Egnor said in response to PZ Myers: "[G]ene
duplication is, presumably, not to be taken too seriously. If you count copies as new
information, you must have a hard time with plagiarism in your classes. All that the miscreant
students would have to say is 'It's just like gene duplication. Plagiarism is new information-
you said so on your blog!'"

Duplicating Genes Doesn't Increase Biological Information in Any Important Sense
I now have 2 questions to ask of Darwinists who claim that the mechanism of gene
duplication explains how Darwinian evolutionary processes can increase the information
content in the genome:
(1) Does gene duplication increase the information content?

(2) Does gene duplication increase the information content?
22

Asking the question twice obviously does not double the meaningful information conveyed by
the question. How many times would the question have to be duplicated before the
meaningful information conveyed by the list of duplicated questions is twice that of the
original question? The answer is that the mere duplication of a sentence does NOT increase
the complex and specified information content in any meaningful way. Imagine that a builder
of houses has a blueprint to build a new house, but the blueprint does not contain enough
information to build the house to the specifications that the builder desires. Could the builder
obtain the needed additional information merely by photocopying the original blueprint? Of
course not.

Darwinists Must Give Detailed Accounts of how a Duplicated Gene Acquires its New
Function
The Darwinist would probably reply to my objection by saying, "Well, it isn't just gene
duplication that increases the genetic information such information is increased when gene
duplication is coupled with the subsequent evolution of one of the new copies of the gene."
Aye, there's the rub.

Darwinists laud the mechanism of gene duplication because they claim it shows how one
copy of a gene can perform the original function, freeing up the other copy to mutate, evolve,
and acquire a new function. But the new genetic information must somehow be generated
during that subsequent evolution of the gene. To explain how Darwinian processes can
generate new and meaningful genetic information, Darwinists must provide a detailed
account of how a duplicate copy of a gene can evolve into an entirely new gene. But ask
Darwinists for details as to how the duplicate copy then starts to perform some new
function, and you probably won't get any. At least, Dawkins didn't given us any details
(as I explain below) about this in his "The Information Challenge" article, which I am
rebutting here.

A recent study in Nature admitted, "Gene duplication and loss is a powerful source of
functional innovation. However, the general principles that govern this process are still
largely unknown." (Ilan Wapinski, Avi Pfeffer, Nir Friedman & Aviv Regev, "Natural history
and evolutionary principles of gene duplication in fungi," Nature, Vol. 449:54-61 (September
6, 2007).) Yet the crucial question that must be answered by the gene duplication mechanism
is, exactly how does the duplicate copy acquire an entirely new function? Stephen Meyer
explains in Proceedings of the Biological Society of Washington that it is difficult to imagine
how duplicated genes acquire new functions since they must successfully undergo "neutral
evolution" and traverse a random walk in order to acquire a new function:
[N]eo-Darwinists envision new genetic information arising from those sections of the genetic
text that can presumably vary freely without consequence to the organism. According to this
scenario, non-coding sections of the genome, or duplicated sections of coding regions, can
experience a protracted period of "neutral evolution" (Kimura 1983) during which alterations
in nucleotide sequences have no discernible effect on the function of the organism.
Eventually, however, a new gene sequence will arise that can code for a novel protein. At that
point, natural selection can favor the new gene and its functional protein product, thus
securing the preservation and heritability of both.

This scenario has the advantage of allowing the genome to vary through many generations, as
23

mutations "search" space of possible base sequences. The scenario has an overriding problem,
however: the size of the combinatorial space (i.e., the number of possible amino acid
sequences) and the extreme rarity and isolation of the functional sequences within that space
of possibilities. Since natural selection can do nothing to help generate new functional
sequences, but rather can only preserve such sequences once they have arisen, chance alone
random variationmust do the work of information generationthat is, of finding the
exceedingly rare functional sequences within the set of combinatorial possibilities. Yet the
probability of randomly assembling (or "finding," in the previous sense) a functional sequence
is extremely small.

(Stephen C. Meyer, "The origin of biological information and the higher taxonomic
categories," Proceedings for the Biological Society of Washington, Vol. 117(2):213-239
(2004).)
The I nconvenient Truth for Dawkins: At best, the mechanism of gene duplication shows how
a hiker can get to the foot of a hiking trail, but never explains how the hiker finds the peak of
the mountain, while doing a random, blindfolded walk. We don't need to know that genes can
make copies of themselves; we need to know how the duplicate gene evolves, step-by-step,
into an entirely new gene.

Mistaking Similarity as Evidence for Common Descent, and then Mistaking Common
Descent as Evidence for Darwinian Evolution
Rather than giving a step-by-step mutational account of how a duplicated gene acquires a new
function, Dawkins' article substitutes bland evidence of sequence identity between different
genes as evidence for Darwinian evolution by gene duplication. Dawkins gives the example
of the evolution of various globin genes that he claims arose via gene duplication. His
evidence is that "[c]areful letter-by-letter analysis shows that these different kinds of globin
genes are literally cousins of each other, literally members of a family." Of course the
"[c]areful letter-by-letter analysis" simply means finding amino acid sequences that are
similar or identical between two different proteins. David Swift explains that such claims of
relationship "are inferred solely on the basis of assuming a common ancestry and then
deriving a route of polypeptide evolution, typically the most parsimonious one, to fit the
known present day amino acid sequences and consistent with the observed pattern of
conserved amino acids." (David Swift, Evolution Under the Microscope, pg. 165 (Leighton
Academic Press, 2002), emphasis in original.) At best, such sequence identity demonstrates
common ancestry (if one ignores the possibility of common design), but it does not
demonstrate Darwinian evolution. Michael Behe easily rebutted the over-extrapolation from
sequence-similarity to Darwinian evolution in both Darwin's Black Box and The Edge of
Evolution:
"Although useful for determining lines of descent ... comparing sequences cannot show how a
complex biochemical system achieved its functionthe question that most concerns us in this
book. By way of analogy, the instruction manuals for two different models of computer put
out by the same company might have many identical words, sentences, and even paragraphs,
suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing
the sequences of letters in the instruction manuals will never tell us if a computer can be
produced step-by-step starting from a typewriter....Like the sequence analysts, I believe the
evidence strongly supports common descent. But the root question remains unanswered: What
24

has caused complex systems to form?" (Michael Behe, Darwin's Black Box, pgs. 175-176.)

"[M]odern Darwinists point to evidence of common descent and erroneously assume it to be
evidence of the power of random mutation." (Michael Behe, The Edge of Evolution, pg. 95.)
Darwinists like Dawkins continue to make the mistake cited by Behe and Swift. (In fact, if
you read the aforementioned "Natural history and evolutionary principles of gene duplication
in fungi" article, you'll find it gives only anecdotal or circumstantial evidence of evolution by
gene duplication, not directly observed evidence, and there certainly aren't any detailed step-
by-step models for how the genes evolved.)

The Dangerous Road Faced by Duplicated Genes
If a duplicated gene cannot successfully traverse its random walk, it may die. As Lynch and
Conery found, "the vast majority of gene duplicates are silenced within a few million years."
(Lynch & Conery, "The Evolutionary Fate and Consequence of Duplicate Genes," Science
Vol. 290:1151-1155 (Nov 10, 2000).) Does Richard Dawkins give a step-by-step mutational
account of how globin genes evolved from one another while remaining functional at all
times, such that the duplicate copies were never "silenced," terminating their evolution? Of
course not. Dawkins has not demonstrated how Darwinian evolution can take a duplicated
gene and evolve it into a new gene. The problem for Dawkins is that duplicating a gene may
increase your amount of Shannon information, but it does not increase the amount of specified
complexity in any non-trivial sense. To explain how one gene can turn into another, Dawkins
must explain how new specified and complex information can enter the genome, and give a
step-by-step mutational account of the origin of some gene via gene duplication. Dawkins has
provided none of this.

To understand this point, consider the following sentence (with spaces removed):
METHINKSDAWKINSDOTHPROTESTTOOMUCH
If we merely consider the Shannon information of the 33 letters (not counting spaces) in the
sentence, then it has about 155 bits of Shannon Information. Now we duplicate it, like what
happens in a gene duplication event:
METHINKSDAWKINSDOTHPROTESTTOOMUCHMETHINKSDAWKINSDOTHPROT
ESTTOOMUCH
The amount of Shannon information has now doubled (~310 bits), but we have seen no non-
trivial increase in the amount of specified complexity. Still, Dawkins thinks gene duplication
is the answer, and that "[i]t is by these, and similar means, that genome sizes can increase in
evolution."

The Shannon information in the doubled-string is twice the Shannon information in the
shorter string if the shorter string does nothing to predict the sequence of the doubled-string.
By granting this assumption, we are able to increase the Shannon information in the genome,
even though this is a trivial informational increase that does not provide a meaningful increase
in the specified complexity. The key questions are (a) what process is generating the new
sequence, and (b) to what extent does that process predict the new sequence? In this sense,
25

duplicating a gene would predict that the duplicate gene would be an identical copy of the
original gene. From this standpoint, gene duplication actually does NOTHING to increase the
Shannon information in the genome because you can predict the sequence of the new stretch
of the DNA with a Probability of 1 (where Log (1) = 0), leading to an increase in the
Shannon information of 0 bits. In this sense, the Shannon information in the doubled-string
is not increased at all from the original, shorter string, as it remains 155 bits. Keep in mind
that it is Dawkins who raised the issue of increasing Shannon information in the genome via
gene duplication. Viewed in this fashion, Dawkins' claim that gene duplication can increase
the Shannon information is even more dubious: if gene duplication predicts that you will have
an identical copy of the original gene, then gene duplication not only fails to increase the
specified and complex information, it also fails to increase the Shannon information in the
genome.

But we aren't trying to simply change the "genome siz[e]," and thereby change the Shannon
information. We're trying to construct something functionally new. Thus, imagine that one
duplicate copy of the original sentence evolves into a new sentence of the same length:
BUTIMSUREDAWKINSBELIEVESHEISRIGHT
A Darwinian theorist would find that both sentences contain the word "Dawkins," and thus
share a 21% sequence identity. They would then infer that both sentences evolved from that
common ancestor via Darwinian evolution. They would conclude that a duplicated version of
the sentence "METHINKSDAWKINSDOTHPROTESTTOOMUCH" has evolved into
"BUTIMSUREDAWKINSBELIEVESHEISRIGHT."

David Swift explains that finding such similarities is not enough to justify the claim that
Darwinian evolution has produced the observed pattern: "[F]or family trees to be credible,
most if not all of the putative ancestral sequences must be functional; but this presents a major
stumbling block in the production by divergence of proteins with different functions. To get
from one set of conserved amino acids to another is either an unlikely big jump, or the
intermediates must have biological activity; but the latter seems unlikely because it
contradicts what we know about conserved amino acids." (Pg. 166). Thus, in order for
Darwinists to convince me that Darwinian evolution can produce new information, at
minimum I need to see a step-by-step mutational account of how they can take the sentence:
"METHINKSDAWKINSDOTHPROTESTTOOMUCH"
and evolve it into:
"BUTIMSUREDAWKINSBELIEVESHEISRIGHT"
by changing the first sentence one letter at a time, and having it always retain some
comprehensible English meaning along each small step of its evolution. Telling me that you
can duplicate the sentence does NOT answer the question posed in the video, "Can you give
an example of a genetic mutation or evolutionary process that can be seen to increase the
information in the genome?" As Michael Behe requested over ten years ago in Darwin's Black
Box, what is required is a "detailed, scientific [explanation of] how mutation and natural
selection could build" the sentence. (Behe, Darwin's Black Box, pg. 176.)
26


Don't Blame Natural Selection: It's Just Acting upon What Mutations Provide
It's worth noting that Dawkins finally claims that it is natural selection that "feeds information
into gene pools" by selecting for mutations that help organisms survive. Thus, Dawkins would
argue that the information in the environment is transferred into the genome of the organism.
Fair enough. But Dawkins isn't telling the most important part of this story. We all know that
mutations must provide the raw fuel upon which natural selection can act. As Gilbert, Opitz,
and Raff write:
The Modern Synthesis is a remarkable achievement. However, starting in the 1970s, many
biologists began questioning its adequacy in explaining evolution. Genetics might be adequate
for explaining microevolution, but microevolutionary changes in gene frequency were not
seen as able to turn a reptile into a mammal or to convert a fish into an amphibian.
Microevolution looks at adaptations that concern only the survival of the fittest, not the arrival
of the fittest. As Goodwin (1995) points out, "the origin of speciesDarwin's problem
remains unsolved.

(Scott Gilbert, John Opitz, and Rudolf Raff (1996) "Resynthesizing Evolutionary and
Developmental Biology," Developmental Biology 173, 1996, pg. 361.)
Natural selection can (given the right population circumstances, etc.) preserve traits that
confer a survival advantage, and it is very effective at weeding out traits that are
disadvantageous. But natural selection can only act upon what mutations provide. Thus, we
can't account for the survival of particular mutations until we account for the arrival of
particular mutations. We cannot account for the increase in information content of genomes
until we consider how random mutations produce the raw fuel that natural selection can
preserve.

My Information Challenge Reiterated:
So here is my "Information Challenge": For the sake of the argument, I will grant that every
stage of the evolutionary pathway I requested above will survive, and thus I'll give natural
selection every possible benefit of the doubt. What I need is a step-by-step mutation account
of how one sentence evolved into the other wherein the sentence remains functional i.e., it
has comprehensible English meaning at all stages of its evolution. In short, I request to see
how:
"METHINKSDAWKINSDOTHPROTESTTOOMUCH"
can evolve into:
"BUTIMSUREDAWKINSBELIEVESHEISRIGHT"
by changing the first sentence one letter at a time, and having it always retain some
comprehensible English meaning along each small step of its evolution. This seems like a
reasonable request, as it is not highly different from what Darwinists are telling me can
happen in nature.

How would Dawkins reply? Would he get angry and complain that this is "the kind of
27

question only a creationist would ask"? Or would he dodge the question like he did in his
"The Information Challenge" article? Personally, I'd like to see an answer to the question.

Part 3: Dawkins "Junk"-DNA Blunder.
Dawkins' article has other problems. He writes that "most of the capacity of the genome of
any animal is not used to store useful information." This is another good example
demonstrating how Neo-Darwinism led may scientists to wrongly believe that non-coding
DNA was largely junk. Dawkins' statement is directly refuted by the findings of recent
studies, which the Washington Post reported that scientists have now found that "the vast
majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of
previously invisible tasks." That strikes a fatal blow to Dawkins' argument:
Dawkins then (1998) Scientists now (2007)
Position
regarding
"Junk"-DNA:
"most of the capacity of the
genome of any animal is not used
to store useful information"
"the vast majority of the 3 billion 'letters'
of the human genetic code are busily
toiling at an array of previously invisible
tasks"

Dawkins claims that there is "lots of repetitive nonsense" in the genome. But is it really
"nonsense"? Recent studies are finding increasing function for allegedly non-functional
repetitive DNA. Richard Sternberg surveyed the literature and found extensive evidence for
function in repetitive DNA (also called repetitive elements, or "REs"). A listing of functions
for REs reprinted from Sternberg's paper is shown below:
satellite repeats forming higher-order nuclear structures;
satellite repeats forming centromeres;
satellite repeats and other REs involved in chromatin condensation;
telomeric tandem repeats and LINE elements;
subtelomeric nuclear positioning/chromatin boundary elements;
non-TE interspersed chromatin boundary elements;
short, interspersed nuclear elements or SINEs as nucleation centers for methylation;
SINEs as chromatin boundary/insulator elements;
SINEs involved in cell proliferation;
SINEs involved in cellular stress responses;
SINEs involved in translation (may be connected to stress response);
SINEs involved in binding cohesin to chromosomes; and
LINEs involved in DNA repair.

(Richard Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified
28

Genomic-Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981:154-
188 (2002).)
Dawkins not only got repetitive junk-DNA wrong, he provides a shimmering example of the
fact that neo-Darwinism has led many scientists to wrongly presume that junk-DNA has no
function. Some Darwinists have tried to counter that claim by arguing that Neo-Darwinism
also led other biologists to presume function for junk-DNA, since its mere presence in the
genome implies that natural selection has preserved it for some purpose. Even if that were a
good argument, the fact remains that the false junk-DNA mindset was born and bred out of
the Neo-Darwinian paradigm. That paradigm misled many scientists on this point, and in fact
continues to mislead them.

But it isn't even clear that Darwinists have a good scientific justification to believe that junk-
DNA, if it exists, would be naturally selected out of the genome. According to the 2006
edition of Voet and Voet's Biochemistry, there is insufficient selection pressure on
functionless repetitive "junk"-DNA to remove it from the genome:
No function has been unequivocally assigned to moderately repetitive DNA, which has
therefore been termed selfish or junk DNA. This DNA apparently is a molecular parasite
that, over many generations, has disseminated itself throughout the genome through
transposition. The theory of natural selection predicts that the increased metabolic burden
imposed by the replication of an otherwise harmless selfish DNA would eventually lead to its
elimination. Yet for slowly growing eukaryotes, the relative disadvantage of replicating an
additional 100 bp of selfish DNA in an 1-billion-bp genome would be so slight that its rate of
elimination would be balanced by its rate of propagation. Because unexpressed sequences are
subject to little selective pressure, they accumulate mutations at a greater rate than do
expressed sequences.

(Donald Voet and Judith G. Voet, Biochemistry, pg. 1020 (Jon Wiley & Sons, 2006),
emphasis added.)
In other words, Darwinists like Dawkins had every reason to presume that non-coding
repetitive DNA was, in Dawkins' words, functionless "nonsense" that was, in Voet and Voet's
words, a "molecular parasite," even though it persisted in the genome. But Voet and Voet are
wrong to presume that such repetitive DNA is mere parasitic junk, given that examples of
functions for it abound. Sternberg's article concluded that "the selfish DNA narrative and
allied frameworks must join the other 'icons' of neo-Darwinian evolutionary theory that,
despite their variance with empirical evidence, nevertheless persist in the literature."
Sternberg, along with geneticist James A. Shapiro, concludes elsewhere that "one day, we will
think of what used to be called 'junk DNA' as a critical component of truly 'expert' cellular
control regimes." (Richard Sternberg and James A. Shapiro, "How Repeated Retroelements
format genome function," Cytogenetic and Genome Research, Vol. 110:108-116 (2005).)

It looks like Dawkins has some work to do if he is to update all of his arguments against ID
and answer "The Information Challenge."
29

3.0 Does a computer networking expert have something new and
important to say about the Evolution vs. Intelligent Design
Debate?
by Perry Marshall
Im author of the book Industrial Ethernet published by ISA, now in its 2
nd
edition, and have
written many dozens of magazine articles and white papers on computer networks. Now you
may ask, what do computers have to do with DNA and all those endless arguments about
intelligent design? Actually, a lot.
Just like all those 1s and 0s that make our modern world go round, DNA is also a digital
communication system. All the same formulas and communication theory that created our
modern digital age apply to DNA too. In fact many methods that are commonplace in the
information technology field have been adapted and applied to genetics research and the
Human Genome Project.
Now, discover what our knowledge of modern communication systems now tells us about the
Origins Debate.
Download Power Point in Adobe PDF
Read Transcript - Download Printable Version in PDF

Executive Summary:
Part 1: Language, I nformation, and the Origin of DNA (Read Transcript)
Most arguments about evolution and intelligent design offer only anecdotal evidence and are
inherently incapable of actually proving anything. We must get better evidence in order to get
to the bottom of this! Fortunately, the science of modern communications easily provides us
with the tools we need to get answers. Although the details are complex, the concepts are
easily grasped by anyone with a high school education.
Patterns occur naturally - no help required from a 'designer'.
Many patterns occur in nature without the help of a designer
snowflakes, tornados, hurricanes, sand dunes, stalactites, rivers and
ocean waves. These patterns are the natural result of what scientists
categorize as chaos and fractals. These things are well-understood
and we experience them every day.
Codes, however, do not occur without a designer. Examples of
symbolic codes include music, blueprints, languages like English and
Chinese, computer programs, and yes, DNA. The essential distinction
30

is the difference between a pattern and a code. Chaos can produce patterns, but it has never
been shown to produce codes or symbols. Codes and symbols store information, which is not
a property of matter and energy alone. Information itself is a separate entity on par with
matter and energy.
Proof that DNA was designed by a mind: (1) DNA is not merely a molecule with a
pattern; it is a code, a language, and an information storage
mechanism. (2) All codes we know the origin of are created by a
conscious mind. (3) Therefore DNA was designed by a mind,
and language and information are proof of the action of a
Superintelligence.
We can explore five possible conclusions:
1) Humans designed DNA
2) Aliens designed DNA
3) DNA occurred randomly and spontaneously
4) There must be some undiscovered law of physics that creates information
5) DNA was Designed by a Superintelligence, i.e. God.

(1) requires time travel or infinite generations of humans. (2) could well be true but only
pushes the question back in time. (3) may be a remote possibility, but it's not a scientific
explanation in that it doesn't refer to a systematic, repeatable process. It's nothing more than
an appeal to luck . (4) could be true but no one can form a testable hypothesis until someone
observes a naturally occurring code. So the only systematic explanation that remains is (5) a
theological one.
To the extent that scientific reasoning can prove anything, DNA is proof of a designer.
Part 2: A Christian and an Atheist Go the Zoo (Read Transcript)
Did the Antelope evolve into the Giraffe? According to Darwinian
evolution, the necessities of the environment, random mutation and natural selection working
together caused the antelope to grow a longer neck and become a giraffe. OK, then what does
communication theory say about that hypothesis?
Natural Selection is perfectly valid and has been proven time and time again. But most
people will be very surprised to discover that no one has ever actually demonstrated that
random mutation can create new information. Information theory shows us why this is so: In
communication systems, Random Mutation is exactly the same as noise, and noise always
destroys the signal, never enhances it.
31

In communication systems this is called information entropy, and the
formula for information entropy is exactly the same as thermodynamic entropy. Once lost,
the information can never be recovered, much less enhanced. Thus we can be 100% certain
that random mutation is not the source of biodiversity. A tool is provided,
www.RandomMutation.com, that allows you to experiment and see for yourself that random
mutation always destroys information, never enhances it.
This observation is also confirmed biologically by Theodosius
Dobzhansky's fruit fly radiation experiments, Goldschmidt's gypsy moth experiments, and
others. Decades of research were conducted in the early 20
th
century, bombarding fruit flies
and moths with radiation in hope of mutating their DNA and producing improved creatures.
These experiments were a total failure there were no observed improvements only weak,
sickly, deformed fruit flies. Giraffes may have evolved from antelopes - I never said that
couldn't happen, and I remain open to the possibility that it did. But it certainly wasn't because
of Random Mutation!
We have proof that life on planet earth was designed by a mind - and that if life did
evolve, the capacity to evolve had to be designed in. The word Evolution in the English
language always refers to an intelligent process (in business, society, technology etc.) and the
only usage in which it allegedly doesn't is naturalistic Darwinian evolution. But
communication theory shows us that Evolution by Random Process is a hypothesis without
proof.
Finally this presentation concludes with a brief observation: There is an interesting
correspondence between Judeo-Christian theology and modern information theory, the
statement words and language are the essence of creation: And God said In the beginning
was the WORD; that the worlds were spoken into existence.