7 Biology Myths No Electrical Engineer Would Ever Tolerate

As an Electrical Engineer, I am 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.engineer

15 years ago I couldn’t 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 IC’s in the automation and robotics industry. Fought digital networking standards battles in manufacturing.

Wrote an Ethernet book, published by the world’s #1 technical society for process control engineers. And now here I am discussing DNA, evolution, and telling you about scientific discoveries so new, you can’t buy books about them in the bookstore.

I’m loving it. As an outsider to the “biology industry” I bring a very particular perspective: That of an engineer who’s 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 wasn’t 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. Like these men, I am a total outsider in biology.

Yet despite the fact that I wouldn’t 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, you’re 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 can’t see electricity and shouldn’t touch it, EE is abstract and very mathematical. It’s also rigorous. I can’t 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 they’re supposed to? Your car doesn’t. Your dishwasher doesn’t. Your refrigerator needs new parts every few years. The mechanical stuff is prone to problems.

But your TV does exactly what it’s 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, EE’s have very high expectations of theoretical models… because the model has to be built and it has to work.

Engineers don’t 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 I’m an EE. I know that the information in DNA is a signal. By definition, random mutations are noise. 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!

You’ll 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 you’ll 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. Here’s 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 isn’t junk is 22 megabytes. In other words, they’re 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 doesn’t. 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. It’s 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 don’t.

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 wouldn’t 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 don’t computer programs ever evolve by themselves? They don’t and they never will – not unless they’re programmed to do so.

Evolution is not a given; in the real world it’s always a design feature. Software programmers will tell you that self-adaptive code is profoundly difficult to write.

Never happens by accident. This pronouncement by Daniel Dennett is Exhibit “A” of pseudoscience.

4. “Biology is nothing more than sophisticated physics and chemistry.” That’s like saying the Internet is nothing more than sophisticated copper wire and silicon chips.

I’m 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 Donald Trump.

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.

These assumptions continue to get nowhere in Origin of Life research. Information never improves by accident. Information evolves only through highly structured processes.

(By the way, Systems Biology bypasses old-school reductionism and is making great strides.)

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. GA’s refine software programs through an evolution-like process.

GA’s 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 didn’t 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. It’s intelligent evolution.

Every single Genetic Algorithm I’ve ever seen, no matter how simple or complicated, only works if it has pre-programmed goals.

Which requires both a program and objectives. I’ve 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. I’ve never seen an exception. This is no different than computer programs that evolve.

6. “The human eye is a pathetic design. It’s got a big blind spot and the ‘wires’ are installed backwards.”

There are many, many variations on this argument. It’s 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. 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 didn’t 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 – I’m 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 organism’s ancestors.

But human beings must be very careful to not proudly assert that we could ‘obviously do better.’ We don’t know that. We do not understand what’s involved in designing an eye because we’ve never built one.

My friend, if you lose your eye, there’s 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, I’d 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.”

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 he’s 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 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 thermostat’s 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, there’s 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 1’s and 0’s 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 1’s and 0’s have their purpose. The operating system has a purpose, my email program has a purpose and your message has a purpose.

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.

Darwinism as we know it CANNOT stand under the weight of 21st century DNA research. It’s impossible. Because I’ve 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 it’s 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. We’ll 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, we’ll achieve huge breakthroughs in Artificial Intelligence.

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” we’ll 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 don’t 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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184 Responses

  1. Metadoodle says:

    Thanks God Chaser, your info and links were very helpful.

  2. A Brief Point on Darwinism | CalvinDude.com says:

    […] with an atheist regarding Darwinism, and figured I’d post part of my exchange here: [Perry Marshall] isn’t the only one who points out that what constitutes “proof” in biology would […]

  3. Kevin says:

    “I am not saying that there are no sub-optimal designs in biology – I’m sure there are lots of sub-optimal designs.”
    ———-

    Why are you “sure” of this? Can you give examples?

    ———-

    “Furthermore I do believe that life followed an evolutionary process and many designs are “best guesses” engineered by the organism’s ancestors.”
    ————–
    Why do you believe this?

    In what sense are “best guesses engineered” by organisms? Are you simply saying organisms adapt to changing circumstances, and that the encoded information-intelligence to do so within the parameters of the species is an inherent aspect of the subtle encoding?

    Are you extrapolating from this and supporting the transformist thesis?

  4. Arthur says:

    This article makes me angry. The author openly admits to knowing nothing about biology – yet talks about “7 urban legends” biologists believe. She gets so many things wrong that it’s hard to know where to start. Many of the comments highlight her mistakes (e.g. her claim that biologists say 97% of DNA is junk). That’s nonsense. Even when I studied biochemistry 40 years ago, when the purpose of the “junk” DNA was not known, we didn’t say that. We said that it all had a purpose but that was not yet known. In fact, part of DNA research over the last 40 years has been to discover what this DNA actually was far – and it is crucial.

    The most interesting claim is her first one ““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.” which she claims not to be possible as that’s not how things work. Again, that’s something that biologists have been working on for a long time – to identify a process that filters out bad mutations from good ones. Last month, a paper was published in Nature that explained the process – through an experiment that demonstrated how this worked. http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature17143.html

    Even her claims that biologists dismiss the idea of God and God “steering” evolution to get what we see isn’t valid. God cannot be proven or disproven experimentally. As a result, no scientist can honestly dismiss God on scientific grounds. (They can on belief grounds – but that is still a belief. Even Richard Dawkins – an arch-atheist – has not said that “intelligent design by an external being” is impossible. It just can’t be proven scientifically).

    • You might want to let Larry Moran (http://sandwalk.blogspot.com/) know that all that “junk dna” has a purpose. He still doesn’t think so.

      The article you cited doesn’t deal with random mutations. It deals with population genetics, which is an entirely different thing.

      • Arthur says:

        Perry – you stated at the outset you weren’t a biologist. Your comment regarding the Nature article shows this. The significance of the paper is that it’s NOT about population genetics at all. It’s proof of the “Red Queen” idea for evolution and the paper showed that sexual reproduction led to a concentration of advantageous genes, and a reduction in deleterious / harmful genes. This refutes your claim relating to why beneficial genes shouldn’t succeed using your “electrical engineer” hat. Here’s a slightly simpler explanation that goes through why this paper is important. http://www.yeastgenome.org/the-benefits-of-sex

        As for the Larry Moran junk. The majority of DNA is NOT for coding genes but has other functions – some of which are still unclear but becoming clearer. The likelihood is that most will be linked to the expression of genes – as one key question is what turns genes on and off. So, for example, you have a gene that makes protein X. However the gene protein X is switched off in men, and only expresses itself between the ages of 14-44 (i.e. during a women’s fertile period). How does it switch on and off. The non-coding parts of DNA are part of the answer.

        This article gives more on the topic, and there are many more that explain what Junk DNA’s purpose actually is. http://www.news-medical.net/life-sciences/Functions-of-Junk-DNA.aspx and similar – http://genetics.thetech.org/ask-a-geneticist/junk-dna-not-so-junky

        Of course if you want to reject biology as a science and want to select non-mainstream viewpoints to support a creationist perspective, that’s fine. I’ve no problem with the idea of God pushing along evolution. I have a BIG problem in denying scientific evidence based on non-provable beliefs. If you go this way, then you should go the whole way and reject heliocentrism for the Solar System and perhaps even that the Earth is approximately spherical. There are religious people out there that hold the flat earth / geocentric idea. It’s not that far removed from your rejection of biological science either!

        • I’m afraid you’re not understanding what I mean by random mutations. By that I mean copying errors. Not shuffling of genes through sexual reproduction, mendelian genetics and all that. And by the way none of those things all by themselves produce new forms either. The only mechanisms that produce significantly different new species are symbiogenesis and hybridization. Sympatric speciation is by the way a very interesting study – it doesn’t produce radical changes but it does produce new species.

  5. Arthur says:

    Perry – ALL mutations are copying errors and random (although mutagens can speed up the process). The point is that the majority of mutations are deleterious or neutral. A copying error is a mistake. The majority cause damage. Only a few will be beneficial.

    In asexual reproduction there is no process to select out bad mutations and select good ones so any change is essentially random. In prokaryotes – which reproduce asexually, you get antibiotic resistance growing for example through lateral gene transfers (e.g. via plasmids, phages, etc.). However there’s very little else to select good from bad.

    What this paper CONFIRMED (as it was to test something that nobody had worked out how to do before) was that sexual reproduction allowed for bad genes (i.e. deleterious copying errors) to be weeded out, while good changes were positively selected.

    It’s NOTHING to do with shuffling of genes – except that sexual reproduction involves this.

    Biology is NOT electrical engineering. Name me one electrical engineer (not physicist) who has won a Nobel Prize. There are dozens or biochemists and life-science scientists who have – starting with Watson & Crick, Krebs and many more. Perhaps that reflects the difference between the two disciplines. One is an applied discipline that is methodological and routine – and essentially trivial (unless you look at experimental aspects involving quantum theory which currently has no or limited application). The other (life sciences) is pure science that gets to the source of life.

    • All mutations are not copying errors. Such an assertion has no place in 21st century biology. Study Barbara McClintock, who won a Nobel prize for discovering transposition. Study Lynn Margulis and the theory of symbiogensis. Study Ohno’s 2R hypothesis and hybridization. Study epigenetics. Study horizontal gene transfer. Read Shapiro’s landmark book “evolution: a view from the 21st century.” Not a single one of these mechanisms are copying errors. Cells expend enormous effort to prevent copying errors (3 stage checkpoint process) and that’s precisely what the 2015 Nobel prize for chemistry was about. Look it up.

      Show me one significant evolutionary event that was demonstrated to have come from a copying error. Warning: this is much harder to prove than you might initially think.

      I’ve done my homework on this. I have ample peer reviewed studies to back up everything I have said. I strongly recommend you get yourself up to speed on all the above before you reply. The biology you are citing is 25 years out of date.

      And by the way, next time you post, you are required to use your full name – first name, last name.

  6. Arthur Weiss says:

    We are talking cross-purposes and you have extended the definition of a gene mutation to other biological processes most of which are not seen as a mutation by normal definitions.

    Symbiogenesis is the hypothesised process where prokaryotic cells became eukaryotes. It appears to only have occurred a few times (mitochondria, chloroplasts) – and this is not generally viewed as a mutation in the traditional sense. Although such changes can be explained scientifically, they do not discount God as the driving force (except to atheists).

    Transposition is also not viewed as a gene mutation although it does result in significant change. You will notice I actually mentioned transposition mutagenesis in the context of antibiotic resistance, resulting from plasmids or phages (i.e. horizontal gene transfer – which I referred to as lateral gene transfer).

    Epigenetics is also not viewed as a gene mutation and such changes result from methylation of DNA bases resulting in genes being switched on or off permanently. They do not change the base DNA itself.

    The NIH defines gene mutation as a permanent alteration in the DNA sequence that makes up a gene, such that the sequence differs from what is found in most people. Mutations range in size; they can affect anywhere from a single DNA building block (base pair) to a large segment of a chromosome that includes multiple genes. The latter can occur due to transposition, as you correctly say. However ultimately it is a copying error where one copy of DNA does not get copied correctly into a new cell. And I agree that cells try and stop copying errors. Nevertheless they DO occur and sexual reproduction appears to have evolved to limit the impact of deleterious errors.

    You can view it like a colour photocopy where instead of copying 10 pages, for some reason, the machine goes wrong and copies 10 pages missing one colour AND inserts 20 pages in the middle from a prior document (perhaps inserted into the memory of the photocopier). The result is different from what was placed in the machine. It’s a copying error!

    The point is
    1) Does evolution exist or is Intelligent Design a better explanation
    2) Does God have a role in biology.

    I would argue that point 2 is unprovable and for me, the answer is yes. God drives forward evolution – as observed by biologists.

    With regards to point 1 – Intelligent Design is not provable at all. It tries to supplant the best explanation there is for biological change and seeks to show that evolution is false. That is taking a non-scientific idea that cannot be tested and using it to replace one that not only can be tested but has been tested many times. That is not scientific.

    • Based on what you’re saying, then gene mutations (by the traditional definition) are not responsible for evolution. Certainly no one has clearly demonstrated that this is so – ref. Margulis 2003.

      The alternate mechanisms I described are the actual sources of evolutionary novelty. This has been exhaustively proven since McClintock. See Shapiro’s excellent book.

      There is a hugely pervasive notion that random copying errors are an occasional source of evolutionary novelty. Millions of biologists have believed this for a century. However the concept of something like this simply does not exist in software or any other branch of engineering. It violates Shannon’s information theory and it is flat wrong. Biggest urban myth in the history of science. And nobody in biology has actually demonstrated that it is true. It’s time to lay that notion in the grave where it belongs.

  7. Arthur Weiss says:

    I’ll agree that nobody has shown that gene mutations are solely responsible for evolution – and that some of the other mechanisms are likely to be responsible too. This is not new. When I studied biochemistry 35+ years ago, this was talked about. Transposons, plasmids, etc. were new discoveries but were recognised as being significant vectors for genetic change. I still remember the idea of “lateral evolution” being discussed as possible (hypothetically at the time) and even epigenetics (although that term was not used). Whereas a few years before the concept of “Lamarckian” evolution was totally rejected, it wasn’t completely off the radar at my university BECAUSE of the issues of antibiotic resistance and how that spread laterally. It wasn’t referred to as Lamarckian evolution – and still isn’t. However essentially epigenetic change can be viewed in this context. (Of course the two are not the same as the latter has a chemical basis whereas Lamarck was essentially postulating that evolution came from changes in behaviour).

    I was lucky as I studied under John Maynard Smith who was very open to ideas if they had a scientific provenance. (Richard Dawkins also owes Maynard Smith for many ideas – e.g. in his book “The Selfish Gene”). He was the one who discussed lateral evolution as a way that organisms could evolve. One of Maynard Smith’s main areas of study was the evolution of sex – because it is such a biological problem. (That is another reason the Nature paper I mentioned is so significant).

    The whole issue of random copying as a source for evolutionary novelty is a big problem. Logically it does not make sense that this could be a mechanism as random change is not going to result in beneficial selection in the way we see it. In fact, it makes more sense that random changes will be weeded out – even if they are beneficial or neutral – purely because they will be so rare, that it is unlikely they would persevere. THIS is why biologists have looked for a mechanism that would filter out negative mutations and positively select beneficial ones. Essentially the mechanism is that a random copying error occurs. As you say, this should be filtered out. It’s a bit like a software program – where you change ONE letter in the code. The chances are the code will no longer make sense and will fail.

    The difference is that biological systems are more resilient. Engineering systems & software, etc. are created by human beings that do not have the ability to build in that resilience yet (although the latest experiments on AI – with DeepMind’s GO problem suggest this is being solved). Biological systems were designed by God – with the ability to change.

    If you equate a biological system to an engineering one, then essentially you are saying the two are equivalent i.e. that God cannot be involved. For me, one of the miracles that provides indirect evidence of a creator IS that things were designed in a way that human systems cannot emulate. (I do NOT believe in creationism. I believe God designed the world so that it follows scientific rules that man must discover – and that He pushed evolution along to these rules. These rules do NOT have to be the same as human rules including rules relating to human designed information systems).

    We may be discovering how evolution sifts out good from bad – and the mechanism. It is NOT the same as software. (A software programme needs to have built in systems to recognise that “colour” and “color” or “program” and “programme” are synonymous. If a letter was changed in the program to make “colour” into “color” it would work – even if that was a copying error. However only if built in. That could be beneficial as it would make for a smaller program so a faster programme – just taking out the letter “u” (and “me” from programme).
    The biological systems will be much more complex but could be similar and allow some random copying to be beneficial and selected. However I agree that without such a mechanism you would be right.

    • Arthur,

      It actually sounds like our views overlap quite a bit. A few remarks:

      The difference is that biological systems are more resilient. Engineering systems & software, etc. are created by human beings that do not have the ability to build in that resilience yet …

      YES and engineers always recognize resilience as a design feature. It certainly never happens by accident. I’m casting my vote the same direction you are – that there are undiscovered laws that lead to this order. The only proviso being that nobody knows what these are even though some people have been searching for them. Short of that, design is a valid hypothesis that is reasonably inferred from the data; in fact we don’t have inference to any other explanation. So it’s inappropriate and unscientific to cast scorn on the ID paradigm. I do think the ID crowd is remiss for not searching for evolutionary mechanisms.

      If you equate a biological system to an engineering one, then essentially you are saying the two are equivalent i.e. that God cannot be involved.

      Hmmm I might be missing your point but it seems to me that saying “biology = engineering” tends to imply that God IS involved. Either that, or those undiscovered laws of self organization I mentioned earlier.

      What I can say is that computer information and biological information are isomorphic. Both are accurately modeled by information theory, though information falls far short of adequately describing biological systems in their totality.

  8. DMT says:

    As an electrical engineer myself, I found this to be an interesting perspective. If the intent was to argue against atheism and its claim that the universe and everything in it (including life) is a happy accident, then I am in general agreement with you. However, if this is some backdoor attempt to argue that science validates religion and scripture (regardless of which religion or scripture) then you’ve wasted my time. Whatever it is that brought about the universe (or multiverse) is far, far beyond man’s comprehension—any man’s comprehension. Religions, and the scriptures they are based upon, are nothing more than inventions of man, not “god.” More specifically, religion was invented by small groups of men as an attempt to have control and dominion over large groups of other men (and women). While science has gotten better and better at describing the behavior of the universe, it cannot explain the fundamental what or why. Although those will always be legitimate questions, the answers are beyond us, that includes any explanation of “god.” Put another way, your pet gold fish has a better chance of comprehending the nature of the electrical system that powers the light above its aquarium than man has of comprehending the fundamental nature of matter and energy and whatever brought them into play.

  9. Christopher Gieschen says:

    I am currently in the editing process of my book due out in fall called, “Don’t Let Evolution Make A Monkey Out Of You.” I handle the textbook claims of evolution and show them to be specious at best when it comes to Macroevolution. Feel free to respond back to me if you want me to put you on an email list fir info when it comes out.

  10. adb says:

    the fact that dna evolves via control mechanisms is no surprise. there is a big difference between the crap they teach in elementary school and the complex reality. there is no reason at all that likely truth speaks against initial evolution originating from random event. essentially you would need to check the probability that a minimal sized effective (replicating in ideal conditions) RNA would sporadically assemble in an appropriate energized brew of chemicals and then verify that that level of event holds any feasibility against the available environment’s size, time span, etc. it is my understanding that that IS feasible when you’re talking about a world boiling with chemicals and bathed in energy for several millions of years, but not when you’re looking at 20 gallons of goo for a few years in a laboratory.

  11. Alex says:

    An Ethernet card is not a mouse. You are correct in the sense that if biologist don’t understand many aspects biology. However I think it’s pure arrogance and hubris to believe that you understand biology. By definition if we did understand biology we would be rewriting life in any form we see fit, although. A comprehensive understand by definition would entail the ability to reform and rewrite life.

    “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.”

    Biological systems are much more complex and adaptive that anything engineers have built. They are self repairing and self reproducing. Computers are and sports cars are much simpler so they zero capacity for change. What would happen if you put diesel fuel in a sport’s car? I shudder to think or plug your computer into a 220v outlet? Yet biological systems are capable of tolerating far more extremes, you and I can chose whether or not we want salad rice or beef for lunch. A measure of adaptivity that simply doesn’t exist in any man made device.

    Life does not work the same way a switch or sports car works. If it did I’m sure we would have created all sorts of new life DECADES AGO.

    • I don’t disagree with a thing you’ve said.

      So given how much more complex and adaptive living things are than anything engineers have built, how can anyone have the audacity to believe they arose by accident? Is that not the biggest flying leap of faith you have ever seen in your life?

      Makes tarot cards and horoscopes seem tame by comparison.

      • Carol Sperling says:

        There’s that argument from incredulity again. And it is wrapped around an equivocation on “accident”. You truly are the master of the logical fallacy, Perry.

        • Where is your demonstrable evidence that information based systems come from accidents, Carol?

          What empirical date do you have that would even INFER accidents create information based systems?

          Your evidence, please.

      • Michael Price says:

        ” how can anyone have the audacity to believe they arose by accident?”
        “By accident” isn’t a very good descriptor, “as a result of a process without planning is better” and the answer is the same anyway, because the evidence is overwhelming. Nothing makes sense unless it’s true. There is nothing inherently implausible about highly complex systems

        “Is that not the biggest flying leap of faith you have ever seen in your life?”
        No it’s the opposite because there is no other explanation. To explain it by design would be a massive leap in faith because it would require a far more complex being that was itself not designed for which there is no evidence.

        • Bring your proof.

        • Brian Shipley says:

          Gosh, you redefine accident so it sounds fancy and plausible, when in fact, its way, way beyond such.
          “No other explanation? Why not? As long as you are inventing miracles to make your theory, anything goes, right?
          “Nothing inherently implausible about highly complex systems”
          Are you not contradicting yourself? Isnt the theory that it all started with “simple organisms”? Or does it change to suit?
          “For which there is no evidence”
          Just because you refuse to consider it, or maybe don’t understand it, does NOT work out to “no evidence” stick to facts instead of accusations.
          Why couldn’t there be a “far more complex being”? This is a presumption on your part for which you present no evidence, and refuse to consider. We have always known God is a spiritual creature, who lives in a different universe, subject to different laws. So many yap about the multiverse and infinite universes, but go back to their security blanket if God is even whispered. Amazing

  12. Rowlinson says:

    Reading your original article you mention “design” in life and that chemicals are not life and are only “tools” (my interpretation) in the processes in life.
    I agree but (may be you have addressed this elsewhere) what do you say about the origins of the design (known outcome) and the Designer?
    I know and am wondering if you know?
    Thank you.

      • Michael Price says:

        Ok you’ve claimed that all codes were created by intelligent beings. Problem is that’s your CONCLUSION, not your premise. You can’t just state it. You have to show why it’s theorectically impossible to create codes by random variation combined with differential reproduction. You cannot, and you know that’s not the case.

        You’re fully aware of instances where random changes, which you call “noise” have created meaning. For instance the “METHINKS IT IS LIKE A WEASAL” example. There is no need for a “new law” that creates information, random alternations will eventually do that for any system that isn’t perfectly ordered, as I’ve already explained.

        Just in case you want to pretend that you don’t understand here is another example. Suppose that got a copy of “Hotel California” which was perfect except the base player played his last note a fraction of a second early. A copying error could introduce an extra null byte on that track, delaying that last note by a fraction of a second, making the performance better. See how your moronic claim that random changes couldn’t increase information is dumb?

        In fact of course you know it’s dumb because you know evolutionary simulations have random changes adding information all the time. Otherwise they wouldn’t get coherent results. So you’re lying not stupid.

  13. Dianne Patti says:

    Mr. Marshall, thank you so much for your rich, rich article here. It is intellectual pure gold, and this retired bio teacher is absolutely thrilled with it.

    I shall look for a link where I can follow your blogs.

  14. Cheese says:

    I take it you’ve never heard of the experiments, performed by *electrical engineers*, in which electrical circuits for useful proses were created by something like (I forget the details; you should be able to Google for it) connecting programmable chips ttogether at random and applying evolutionary mechanisms and principles. The resulting circuits performed their intended* functions in ways human engineers would never have imagined, let alone designed. There were some circuits that required a great deal of study before the engineers could even *understand how* they worked. More than one circuit exploited subtle manufacturing defects in the chips themselves, external environmental factors the engineers had overlooked, etc. All of this tookaemail sort time. So it is not merely possible, but *proven*, that you *can*, because somebody *did*, design circuits that way.

    And that’s relatively new stuff; *software* design by genetic algorithm, again using evolutionary principles, has been a viable and successful technique for decades now. Some people *do* write software that way.

    *By “intended” function, I indicate that circuits were deemed to “survive to reproduce,” or not, by how well, or poorly, they performed a function chosen in advance — but choosing-in-advance was necessary only because it was a simple experiment of limited scale. Humans had to perform the mechanics of circuit mating and reproduction because the circuits were, of necessity, both complex enough to require outside attention for reproduction, and simple enough to not be able to do that for themselves. It would be just as true to say that the circuits existed (“lived,” so to speak) in a world where the ability to petgorm thst function protected them from predators (the engineers) that “killed” the circuits that couldn’t perform that function. At this point you’re pretty close to talking about living animals, which indicates that the analogy is valid.

    Oh, and this works for software, too. “Genetic algorithms” have been a thing for at least twenty years now, literally *evolving* useful software out of simple, random precursors mating and mutating, living and dying, under evolutionary pressures straight out of Darwin. So, some people *do* develop software that way.

    • I devote an entire chapter to this in my book “Evolution 2.0.” But fitness functions have to be intelligently designed first, before GA’s can do anything useful. Show me one GA that operates according to nothing but pure random mutation and natural selection. I’ve never seen one.

  15. David Tatham says:

    As an Electrical Engineer and a born again Christian I started out totally in agreement with you until I got to this statement ” Furthermore I do believe that life followed an evolutionary process and many designs are “best guesses” engineered by the organism’s ancestors.” But you also said this which I agree with and which contradicts your first statement that life followed an evolutionary process “But I’m an EE. I know that the information in DNA is a signal. By definition, random mutations are noise. 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! ” I absolutely agree. “Evolution” is impossible. Devolution is possible describes what is going on now. All life was created perfect but then man disobeyed God and the perfect organisms started to devolve, not evolve, with “noise” which you so well describe being added to the signal. Were it not for the creators check sum (dual DNA) we would have devolved into idiots long before now. There are more and more harmful mutations, cancer, autoimmune diseases, etc. and only modern medicine and nutrition is keeping us living as long as we are.

  16. Brian Shipley says:

    Very elegantly argued.
    I think its probably Neo-Darwinism’s biggest weakness, depending on ‘random mutations” Come on! Try introducing random mutations to your by pouring gravel into its fuel system. Do it for a billion years. Make note of the improvements. Or, poke a screwdriver randomly about in your computer. Do it to a trillion computers, over a billion years, see how many get improved.
    Even were it true, history would be littered with overwhelming numbers of failed species and mutations. A successful one would be the very rare exception.
    Classical Darwinism seems deliberately fashioned to prove a personal theory, rather than an actual one. More to consciously exclude God, or any such purposeful factor in the design. ID makes incredible sense when regarding purpose, even if you assume a non-conscious purpose designed in. Random is ridiculous on its face.
    Something I noticed, is how careful the author was to walk carefully around any direct reference to God, Creator, etc. Presumably to avoid hurting the feelings of, or triggering the fury of the bitter clingers of the old religion. I have to admit, the authors article really opened my eyes. It was very well argued, and anyone of fair mind would have to admit, it fits the facts far better than anything else, rather than theories stretched to the point of fantasy, in an effort to make the theory fit personal prejudices. As I said, elegant.

    • Thanks for your perceptive comments. Glad to have you as part of the discussion.

    • “history would be littered with overwhelming numbers of failed species and mutations”

      It is.

      • Brian Shipley says:

        That is disingenuous.
        Yes, even species of Man have become extinct, but only after long periods of success, proving they were viable. I am talking about borderline or less than viable species. Even if there were only one mutation that was born, but died because it had no stomach. Or was blind and only lived til its mother stopped feeding it. Given real randomness, the historical record would show these random failures as the overwhelming majority, and only a few, rare successful ones. In fact, random variation is about the quickest way imaginable a species could choose if it wanted to become extinct! The vast majority of random variations are going to be non-viable. Destroying the species chances of survival. But we don’t find the fossil record littered with vast numbers of one-off, non-viable freaks. Instead we have an intelligent progression. Given random variation, its like winning the lottery every single day for millions of years. In actuality, its hard evidence of purpose.

  17. I think the problem may be that you don’t quite understand the biology.

    “Have you ever had a data glitch on your computer that improved your files? Ever?”

    Yes. I’ve written code that intentionally gets glitches precisely to get better algorithms.

    “All the Natural Selection in the world is powerless without a beneficial mutation.”

    Beneficial and neutral mutations happen all the time.

    You have at least 200 mutations different from either of your parents.

    If you had a non-beneficial one you probably wouldn’t pass it on.

  18. Chalisque says:

    There are a number of issues, to my reading. (My background is pure mathematics and mathematical logic, for reference, though I have
    since developed quite broad interests.)

    A. “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.”
    When producing a 16bit CD recording from a 24bit source, dithering is a known technique for improving the result. What dithering does is to introduce a small amount of noise (shaped in spectral content) so as to mitigate the effects of quantisation in going down from 24bit to 16bit. That is one example. Indeed whenever things need to be divided into a small number of categories, (producing a signal with a small bit-depth from one with a large bit-depth), the adding of a small amount of noise has the effect of making the average of the resulting signal better match the original. That is one example, and I believe there are more.

    B. My issue with biologists understanding of evolution is the lack of rigour. I do not believe (as you appear to do) that point 1 is false, just that biologists massively oversimplify it (much like saying that computers work by doing lots of simple arithmetic very quickly, and ignoring the inherent complexity that that entails). First, there is the issue of what ‘random’ actually means. If, for example, I deliberately change the DNA of an embryo (animal or human, for the purpose of the matter here it does not matter), and put it back into the wild, natural selection will play a role, based on how well the organism survives. But can that be said to be a ‘random’ mutation? In some senses, it can, in others it cannot. It is important to be precise about what is meant by ‘random’, and when reasoning, being careful not to eqivocate by changing between multiple similar but distinct meanings.

    C. Still with point 1, there are many other uses where randomness is important, in engineering, computer science, and other sciences. That we have learned to harness randomness in these disciplines, it would be astonishing if nature did not harness randomness (and I believe it does, and evolution is an example of that).

    D. Interestingly, if you take a basic 2-channel audio interface and feed the output back into the input, and put some DSP processing in the loop, you can see the effect the Darwinians love happenning very quickly: some frequencies pass round the loop and meet themselves in phase better than others (and there is much well developed theory to make rigorous what I mean here by this informal description). What you have a is a system whose present state depends upon the immediate past in a way where differences between one moment and the next are bounded. In a one-dimensional signal fed back to itself, things are not all that interesting compared to a ‘signal’ which is the state of the entire universe. (I wish I had a better way to explain this line of thinking.)

    Now onto your point 2.

    E. Given how useful it is with modern computers to have a store of random data, having a store carried in our DNA may not be all that stupid.

    F. When on a modern computer we delete a file, all that usually happens is that the reference to the file in the directory entry is removed, and the data of the file remains until overwritten. With human DNA this may well be the case. (We do not, at present, know. It is important to take care with what you do and do not know, and not to overstate certainty or otherwise jump to conclusions: that is a failing which I see routinely in the less rigorous sciences).

    G. As for the size difference, it would be good to remember the past when fantastic software programs were written using a small amount of code. Back then programmers could not afford to be profligate with storage when it came to the size of compiled binaries and supporing data. Now that storage has become cheap, much of the software engineering world has become sloppy. Nature cannot afford to be profligate with the storage space available in DNA, so isn’t. And if an adaptation that was once necessary to survival isn’t needed, the most efficient way to adapt is to switch it off and leave it there (possibly to decay). In the event of a threat to survival, the sensible thing is to switch on those old deprecated bits of code at random and see what works, using the results of that to guide progress.

    Now for point 3

    “You only need 3 things for evolution to occur: heredity, variation and selection.”

    H. Heredity should really be understood as a continuity condition between ‘now’ and ‘the past’ in the sense that change is limited in some way. In addition, for statistical effects to happen, you need a large number of ‘trials’, and thus you have need of producing a large number of copies of the same ‘DNA program’ to trial. Without heredity, past attempts at solving a problem have no connection to present attempts, and as such you end up with a process which is just guessing with no memory as to how well previous guesses worked. (To me, refining guesswork as a problem solving strategy is an old tried and tested mental technique which resembles evolution in many ways).

    I. Thinking again in terms of attempts to solve a problem, lack of variation means repeatedly trying exactly the same guess. If it didn’t work the first time, trying the exact same guess on the exact same problem isn’t going to work second or third time. So you need variation.

    J. Selection is where one must be careful. What constitutes a selection mechanism. That said, if there is any connection between previous attempts to solve a problem and the current attempt, there is some sort of selection mechanism.

    K. The idea of evolution is that the problem is simply survival, that variation arises from changes to DNA, no matter how they happen (and changes to DNA do happen), and that heredity refers to the input to future trials being the output of past trials.

    (My problem is not that the process of biological evolution is ‘wrong’, but rather it is an example of something much more general, and something which biologists are not well equipped to understand.)

    Your point 3.

    L. The argument you give here is too much of a strawman. The idea that biological evolution can magically do anything is stupid, and any sensible biologist would not pretend that it could. There are limits to what biological evolution can do. Similarly there limits to what can be achieved by taking typical software for a modern computer and randomly modifying its binary code. The trouble with talking in terms of abstract concepts such as ‘resitance to anti-virus software’ and so on disguises the underlying mechanism, and trying to think solely in terms of high level abstractions can lead your thinking astray.

    M. The last book I read on evolutionary computing mentioned an important aspect of an evolutionary algorithm: _if_ it converges to a solution. It may not converge in a sensible timeframe; it may not converge at all. The idea that evolutionary approaches _always_ solve the problems presented to them in a sensible timeframe is a myth that grows up when people think solely in terms of the ‘magic of evolution’ without a solid understanding of the underlying mechanisms. In the case of evolutionary computing, we are better equipped to understand that underlying mechanism, due in part to most of it being deliberately designed by humans and our having access to information on how and why computing devices work the way they do. With nature we have no similar priveleged access to its inner workings and any deliberate design that there may be.

    N. As for “Nobody writes software that way. Nobody.”, that may have been the case in the past, but the rise of deep learning is changing that.

    Your point 4.

    O. A major point about useful scientific theories is that they are succinct enough for people to understand. Explaining biology in terms of the underlying physics would take so much detail that it would be impractical for anybody to actually use. (This is like a hypothetical mathematical theorem whose shortest proof would take more paper than could fit into the solar system.)

    P. Related to my point O is that it is important when describing how to solve problems, to express things in terms of a sensible choice of abstraction. (An abstraction is a means of sytematically disregarding information about a problem, used in the hope that sufficient salient detail will remain to solve the problem: it is a technique for simplifying thinking about problems.)

    Your point 5, I basically agree with.

    Q. Such examples are good to illustrate how evolutionary approaches can solve problems. But going from ‘Genetic Algorithms’ to ‘proving Darwinian Evolution’ is a massive leap: it is important to anybody who wants to argue the ‘Genetic Algorithms prove Darwinian Evolution’ to explain how GA’s prove Darwinian Evolution.

    R. The example of evolving from garbage text to something useful is an example of an evolving system with a deliberately crafted selection mechanism. A question which I haven’t heard being addressed, and which is quite probably intractible, is a ‘reverse’ problem to this: given an evolving system, what exactly is the selection mechanism that is being used? If you can’t answer this reliably, then you can’t look at nature and reliably say whether the evolution of life we see is ‘totally random’ or is ‘directed in some way’. We just can’t tell the difference. Thus it may make sense to assume things one way or another, but one must not forget that they have take on such assumptions in their reasoning (and thus that they cannot prove such assumptions true from that reasoning without fallacious circularity).
    Evidence provides an envelope within which our thinking is constrained. The problem with academic dogma is that it can easily provide additional constraints, and these constraints can lead people to rule out explanations which are valid. Taking care in the reasoning process is both essential and unnatural. Learning such care is hard work, and if the modern research environment does not strongly reward such care and avoid rewarding approaches which lack this care, our friend ‘evolution’ will tend to push academia towards less rigorous methods. I have read more than a few laments about how exactly this is happening.

    S. From a mathematical perspecive, I think it is ‘in principle’ feasible for a selection mechanism to evolve. As such, in nature the selection mechaism is survival, and other selection mechanisms are often influenced by the needs of that selection mechanism. The question of whether this is all is the problem. Can we tell? If no, then why be so confident either way. If your perspective is a matter of choice, be clear that it is a choice, not something you are forced to concluded from evidence. If we can tell, then how?

    Your point 6.

    T. The development of evolutionary approaches in computing has led to a few examples of how evolutionary approaches often tend to (try to) solve _exactly_ the problem they are faced with, not necessarily the problem you intend them to solve. If you try and breed an FPGA design, and are not careful, you can end up with something which depends on details of the FPGA’s tested on and do not work on a slightly different but supposedly equivalent FPGA; or where there are seemingly meaningless bits of circuitry that appear to serve no purpose but without which the evolved circuit no longer works. (The work talked about at http://www.damninteresting.com/on-the-origin-of-circuits/ is worth being familiar with.)

    Your point 7 is where much of the problems happen:

    U. What reliable method to we have to ascertain whether or not there is ‘purpose in nature’ (for any reasonable given notion of ‘purpose’)?
    This is where it is easy to jump to a position that there is ‘no purpose’ and then resort to rhetoric and ridicule to back up said position. Too much modern science is getting politicised, or become big business and is thus being bent to serve political or business purposes. When this happens, your being ‘right’ is more important than actual correctness. (A well known problem, which Schopenhauer’s book The Art of Controversy does a good job of explaining.)

    V. Hiding problems by changing the language is tempting, and many are tempted by it. Orwell’s ‘newspeak’ in 1984 gave a good illustration of what happens. But by making it harder to express something you don’t prevent its expression, merely cause a short term decrease together with a pressure to find a new way to express the same thing.

    W. The example with the Thrush you give illustrates how one can ignore purpose: “the player swung the racket, and the ball flew off it and and landed in the corner” vs “the player hit the ball into the corner”. In doing so, you are moving from a sentence of the form ‘A did B intentionally’ to ‘A did B, whether intentional or not’. It is good to be aware of the difference, especially if we are lacking in means to discern intent, but it is foolish IMHO to dictate the people express things on way or the other in general.

    A scientist should be careful, clear and deliberate; and should not overstate conclusions, ignore gaps or difficulties, and should be happy to be shown to be wrong.

    To conclude:

    It is important to challenge dogma in science, and to offer mutual criticism of criticism.

    • A. There is a section on dither in my book “Evolution 2.0” in Appendix 1 “All About Randomness.” I have professional experience in analog and digital signal processing. Dither does not add content to the signal, it only masks imperfections.

      B. What biologists generally mean by random is that there is no correlation to the outcome. This is wrong, as exemplified by cell repair and all of Barbara McClintock’s discoveries. Cells actively edit genomes in response to threats.

      C-D. In order to harness randomness, a non-random process must confine it. Randomness can never be allowed to take over or the system breaks.

      O. I disagree. Nature is always driven by elegant underlying mechanisms. As is the case with weather, you may never be able to completely model it but it can be understood. At present we are only barely beginning to understand the real mechanisms of evolution and they are nothing like what Dawkins and friends represent.

      U. Purpose in nature: You detect teleology by seeing if a system will attempt multiple paths to achieve the same objective. If it cannot go over, it will go under, or around, etc etc. Cells do this and evolutionary mechanisms do this. We see this in convergence – same thing appears too many times over and over again in evolution to ascribe to chance (like eyes).

  19. Dianne Patti says:

    Mr. Marshall,

    I simply wish to thank you so very much for your great diligence in providing critical insight to the unscientific pronouncements of biologists of our day. It has been a source of concern for many for the past several decades.

    And then you stay with your readers and render further support to them. Your work is deeply appreciated.

    This retired biology teacher gives you a gigantic A+!

  20. Will says:

    Even though I’m not an Atheist (I happen to be a Roman Catholic), this article has multiple leading sentences that don’t mean what the author thinks they mean (and I’m talking whole sentences, not single words). When you say, “I’ve read the literature,” in a Biology context, for future reference Perry, that means you’ve read ORIGINAL PEER-REVIEWED PAPERS, not just any books available on Amazon no matter how many papers may be cited in a book. That is just the most blatant example out of several.

    Sorry for the all-caps, but I really can’t stress that point enough.

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