Tag Archives: Darwinism

Can you expect the mainstream media to report honestly on science education?

Investigation in progress
Investigation in progress

Whenever policy makers try to get public schools to teach both sides of issues like evolution or global warming, the mainstream media is there to distort the issues.

With respect to evolution, there are criticisms of elements of the theory from within naturalistic science.

For example, here is an interview with famous biologist Lynn Margulis, published in the radically pro-evolution, pro-naturalism Discover magazine.

Excerpt:

Margulis came to view symbiosis as the central force behind the evolution of new species, an idea that has been dismissed by modern biologists. The dominant theory of evolution (often called neo-Darwinism) holds that new species arise through the gradual accumulation of random mutations, which are either favored or weeded out by natural selection. To Margulis, random mutation and natural selection are just cogs in the gears of evolution; the big leaps forward result from mergers between different kinds of organisms, what she calls symbiogenesis. Viewing life as one giant network of social connections has set Margulis against the mainstream in other high-profile ways as well. She disputes the current medical understanding of AIDS and considers every kind of life to be “conscious” in a sense.

Here is something from the interview:

And you don’t believe that natural selection is the answer?


This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.

Now, that’s a criticism of the standard theory from a prominent scientist who is a naturalist. She has a naturalistic alternative that she thinks can do the creating. Can we teach her criticism of the standard theory in the public schools? This is what people mean by “teach the controversy”. We don’t mean teach intelligent design, we mean teach the weaknesses of the theory of evolution from within the naturalistic scientific community. But this is apparently too much for journalism graduates to understand.

This article from The Stream explains:

In states like Louisiana, Tennessee, and the current flash point of South Dakota, we have supported responsible academic freedom laws. These laws allow science teachers to present the strengths and weaknesses of neo-Darwinian theory as an explanation of biological novelties. They don’t introduce or protect teaching about intelligent design, and certainly not about any religious doctrine (like creationism). They explicitly extend protection to science instruction alone, and then only when it enriches students’ understanding of subjects that are already part of the curriculum (which ID is not). Yet journalists routinely assert that these laws would shoehorn intelligent design and “creationism” in public school science classes.

In the same context, when we advocate introducing students to “critical thinking” on evolution, with teaching material drawn only from mainstream science, the media claim that “critical thinking” is “code” for intelligent design, or for “intelligent design creationism.” We know that it’s not, and that the “code word” conspiracy theory is utterly false.

The author of that piece tries to explain the difference between criticism of evolution from within mainstream science, and intelligent design, but the journalists just can’t understand what he is saying. There is an example of it here on Evolution News.

Stephen C. Meyer debates intelligent design with two scientists on NPR

British Spitfire and German Messerschmitt Me 109 locked in a dogfight
British Spitfire and German Messerschmitt Me 109 locked in a dogfight

Evolution News reported on a 27-minute debate featuring Dr. Stephen C. Meyer – probably the best proponent of intelligent design there is.

Description:

We often say that Darwinists are reluctant to debate advocates of intelligent design, but here are two who deserve a tip of the hat. Keith Pannell is a chemist at the University of Texas at El Paso who hosts a program, Science Studio, on the NPR station there. He invited Stephen Meyer on to talk about the science of ID, pegged to the Dover anniversary.

Clearly Pannell is an ID critic so he gets kudos for being willing to have a civil and informative conversation. Perhaps feeling insecure about facing the author of Darwin’s Doubt by himself, Dr. Pannell invited a biologist colleague, Ricardo Bernal, to serve as “co-host.”

So it was two against one, but no worries. Meyer is, as always, superb, and the discussion sounds like it was an education for the two Texas scientists. Listen and enjoy.

I took a back-up of the MP3 file here.

Summary:

  • How did Dr. Meyer get interested in science?
  • What is intelligent design? (origin of life, fine-tuning)
  • What is creationism? (young Earth, different epistemology)
  • Who does Dr. Meyer think the intelligent designer is?
  • Finding the best explanation from multiple competing hypotheses
  • Critic: aren’t you arguing for a designer from ignorance, then?
  • The importance of naturalists acknowledging what they do and do not know about the origin of life
  • We do have experience with intelligent causation, whenever we sequence symbols to have meaning and purpose, e.g. – writing
  • Critic: information in DNA is not digital information, is it?
  • Information in the cell follows a 4-character alphabet
  • the sequences are composed of many parts / symbols
  • the sequences themselves are specified to have function
  • Critic: the complexity just emerges from change over time
  • the origin of the first life is immune to explanation of change over time, because there is no replication – this is the first replicator
  • Critic: but isn’t it just ignorance about the origin of life?
  • what we do is look at a number of competing hypothesis and what they are capable of, and see whether each cause is capable of generating the effects we observe in nature
  • Critic: where is the experimental verification of your theory?
  • well, in the appendices of Signature of the Cell, we predicted that the non-coding regions of DNA (junk DNA) would be found to have function, and that was later proven out
  • the Darwinists said that non-coding regions of the DNA was junk, but that’s not what has been proven experimentally
  • Critic: where was this prediction written up, who wrote it?
  • intelligent design theorists predicted it: Dembski, Kenyon, Mims, Sternberg
  • Critic: but we used the scientific method to disprove the Darwinian predictions, you don’t like the scientific method
  • intelligent design proponents love science, and the scientific method, and they do work in labs to confirm their hypotheses, (WK:for example, the probability of generating a protein by chance)
  • Critic: what about the Dover court case that you lost?
  • the Discovery Institute objected to actions taken by the Dover school board
  • Critic: what about the molecular machines, how are they related to intelligent design?
  • even in the simplest living organisms, there are tiny machines that are tightly integrated, and cannot be built up in a stepwise fashion
  • Critic: I’ve worked with the ATP-synthase and other molecular machines, but “you can kind of begin to tease how some of these molecular machines have come about” – pieces have multiple functions, and they are co-opted into larger systems
  • the problem with the co-option argument breaks down when you look at the specific details of different machines
  • for example – the type III secretory system cannot be an precursor to the bacterial flagellum, it is younger, not older than the bacterial flagellum
  • Critic: what would it take for your view to be falsified?
  • demonstrable undirected processes that are capable of creating functional information in DNA, or processes that can build up an irreducibly complex molecular machine within the time available with a decent probability

If you like this debate, check out Stephen C. Meyer’s two books: “Signature in the Cell” and “Darwin’s Doubt”. They are now out as audio books, too.

Information Enigma: 21-minute video explains intelligent design

Can random mutation and natural selection create new functional information?
Can random mutation and natural selection create new functional information?

The video is here:

I have read and listened and watched a lot of material on intelligent design, but I have never seen so much value packed into such a short lecture. I really hope you’ll watch this and that it’s helpful to you.

Summary:

  • the big question when discussing the origin of life: where did the information in living systems come from?
  • Until 530 million years ago, the oceans were largely devoid of life
  • In a 10 million year period, many new forms of animal life emerged
  • New biological forms of life require new information
  • the discovery of DNA shows that living systems work because cells have information that allows them to build the components of molecular machines: cell types, proteins, etc.
  • can random mutation and natural selection create new functional information?
  • normally, random mutations tend to degrade the functionality of information, e.g. – randomly changing symbols in an applications code does not usually introduce useful new functions, it usually renders what is there non-functional
  • the majority of possible sequences will NOT have functions, so random mutations will more likely give you non-functional code, rather than functional code
  • example: a bicycle lock  with 4 numbers has many possible sequences for the 4 numbers, and only one of them has unlock functionality, the rest have no functionality
  • if you have lots of time, then you might be able to guess the combination, but if the lock as has 10 billion numbers, and only one combination that unlocks, you can spend your whole life trying to unlock it and won’t succeed
  • how likely is it to arrive at a functional protein or gene by chance? Is it more like the 4-dial lock (can be done with lots of time) or the 10 billion dial lock (amount of time required exceeds the time available)?
  • the probability is LOW because there is only one sequence of numbers that has unlock function
  • consider a short protein of 150 amino acids has 10 to the 195th power possible sequences
  • if many of these sequences of amino acides had biological function, then it might be easier to get to one by random mutation and selection than it is with a lock that only unlocks for ONE sequence
  • how many of the possible sequences have biological function?
  • Thanks to research done by Douglas Axe, we now know that the number of functional amino acid sequences for even a short protein is incredibly small…
  • Axe found that the odds of getting a functional sequence of amino acids that will fold and have biological function is 1 in 10 to the 77th power
  • Is that number too improbable to reach by chance? well, there are 10 to 65th atoms in the entire Milky Way galaxy… so yes, this is a very improbable outcome
  • can random genetic mutations search through all the sequences in order to find the one in 10 to the 77th power one that has biological function? It depends on how much guessers we have and how many guesses we get in the time available
  • even with the entire 3.5 billion year history of life on Earth, only about 10 to the 40th organisms have ever lived, which far smaller fraction of the 10 to the 77th total sequences
  • even with a very fast mutation rate, you would not be able to reach a functional protein even with all that time, and even with all those organisms

I was once having a discussion with a woman about the research that Axe did at the Cambridge University lab. He published four articles in the Journal of Molecular Biology. I held out one of the papers to her and showed her the numbers. She said over and over “I hate the Discovery Institute! I hate the Discovery Institute!” Well, yeah, but you can’t make the Journal of Molecular Biology go away with hating the Discovery Institute. JMB is peer-reviewed, and this was experimental evidence – not a theory, not a hypothesis.

We have been blessed by the Creator and Designer of the universe in this time and place with overwhelming evidence – an abundance of riches. For those who have an open mind, this is what you’ve been waiting for to make your decision. For the naturalists who struggle so mightily to block out the progress of experimental science, they’ll need to shout louder and shut their eyes tighter and push harder to block their ears. Maybe if they keep screaming “Star Trek” and “Star Wars” over and over to themselves, they will be able to ignore the real science a little longer.

Are endogenous virus genes evidence for common descent?

Investigation in progress
Investigation in progress

This is a guest post by JoeCoder.

It’s often argued that when two or more organisms share viral genes in the same place, it is evidence those organisms evolved from a common ancestor.  Wikipedia’s Evidence for Common Descent page frames it as follows:

Endogenous retroviruses (or ERVs) are remnant sequences in the genome left from ancient viral infections in an organism. The retroviruses (or virogenes) are always passed on to the next generation of that organism that received the infection. This leaves the virogene left in the genome. Because this event is rare and random, finding identical chromosomal positions of a virogene in two different species suggests common ancestry.

This argument presupposes that the viruses inserted themselves into genomes randomly and stick around as junk DNA baggage, rather than genomes originally being designed with viral-like genes that perform useful functions.  However this argument has unraveled as we’ve discovered useful functions for many viral-like genes, including functions that specifically require a viral-like sequence.  Some examples among many:

  1. ERV sequences protect against viral infection through interference–a matching-but-opposite strand of RNA is created to bind to and disable RNA from a virus.
  2. Likewise, ERV’s seem to function “during embryo implantation to help prevent immune recognition by the mother’s immune system”
  3. In worms, an ERV has been observed to create actual viruses that transfer DNA from somatic cells (skin/brain/heart/etc.) to germline (sperm/egg) cells whenever the worm is exposed to too much heat, allowing them to rewrite their own DNA for future generations.
  4. Viral envelopes from ERV transcripts attach to cell membranes in the placenta and causes them to fuse as a normal part of development: “The HERV-W [a human ERV] envelope glycoprotein named syncytin 1 is expressed in all trophoblastic [part of the placenta] cells and directly involved in human trophoblast fusion and differentiation [cells taking on specialized roles]”

These aren’t isolated cases of function.   Phys.org interviewed one researcher:  “When we investigated public data from embryonic cells, we found that many RNAs originated from regions in the human genome that are ERVs.  We did not only observe isolated events, but systematic activation of these ERVs. Every cell type showed transcription of specific classes, something that is very unlikely to occur by chance”.

Those cases all involve RNA viruses and that’s old news.  But two weeks ago, a single-celled eukaryote called Cafeteria roenbergensis was found to harbor maviruses within its own DNA that remain dormant until it is attacked by a large virus known as CroV.  When this happens the maviruses activate to form an attack fleet, as NewScientist reports:

A voracious marine predator plagued by a giant virus has a defence system we’ve never seen before – it fights back by making its very own virus… Rather than waiting for maviruses to arrive by chance when CroVs attack, it actually carries the genes that code for mavirus inside its own genome.  These genes are usually dormant, but they get turned on when Cafeteria is invaded by CroV. “It acts as an inducible antiviral defence system,” write Fischer and his colleague Thomas Hackl in a new preprint paper.

This process kills the Cafeteria roenbergensis cell, but is useful in defending other members of its own species.  In this experiment maviruses were deliberately inserted into the Cafeteria roenbergensis genome (see the original paper), but more interestingly, sequences similar to the Cafeteria roenbergensis viral genes have been found in a wide range of animals:

A wide range of animals, from sea anemones to crocodiles, harbour genetic elements called Maverick transposons that closely resemble the mavirus genes. It’s possible that some of these organisms can also unleash viruses that attack giant viruses.

In spite of this, New Scientist still argues “our genomes are littered with the mutant remains of viruses and genetic parasites.”  But these discoveries reveal this as a rapidly-shrinking argument of the gaps. 

Save this for the next time someone insists that viral genes are useless junk DNA and therefore evidence of common descent.

Stephen C. Meyer lectures on intelligent design and the origin of life

Christianity and the progress of science
Christianity and the progress of science

A MUST-SEE lecture based on Dr. Stephen C. Meyer’s book “Signature in the Cell“.

You can get an MP3 of the lecture here. (30 MB)

I highly recommend watching the lecture, and looking at the slides. The quality of the video and the content is first class. There is some Q&A (9 minutes) at the end of the lecture.

Topics:

  • intelligent design is concerned with measuring the information-creating capabilities of natural forces like mutation and selection
  • Darwinists think that random mutations and natural selection can explain the origin and diversification of living systems
  • Darwinian mechanisms are capable of explaining small-scale adaptive changes within types of organisms
  • but there is skepticism, even among naturalists, that Darwinian mechanisms can explain the origin of animal designs
  • even if you concede that Darwinism can account for all of the basic animal body plans, there is still the problem of life’s origin
  • can Darwinian mechanisms explain the origin of the first life? Is there a good naturalistic hypothesis to explain it?
  • there are at least two places in the history of life where new information is needed: origin of life, and Cambrian explosion
  • overview of the structure of DNA and protein synthesis (he has helpful pictures and he uses the snap lock blocks, too)
  • the DNA molecule is composed of a sequence of bases that code for proteins, and the sequence is carefully selected to have biological function
  • meaningful sequences of things like computer code, English sentences, etc. require an adequate cause
  • it is very hard to arrive at a meaningful sequence of a non-trivial length by randomly picking symbols/letters
  • although any random sequence of letters is improbable, the vast majority of sequences are gibberish/non-compiling code
  • similarly, most random sequences of amino acids are lab-proven (Doug Axe’s work) to be non-functional gibberish
  • the research showing this was conducted at Cambridge University and published in the Journal of Molecular Biology
  • so, random mutation cannot explain the origin of the first living cell
  • however, even natural selection coupled with random mutation cannot explain the first living cell
  • there must already be replication in order for mutation and selection to work, so they can’t explain the first replicator
  • but the origin of life is the origin of the first replicator – there is no replication prior to the first replicator
  • the information in the first replicator cannot be explained by law, such as by chemical bonding affinities
  • the amino acids are attached like magnetic letters on a refrigerator
  • the magnetic force sticks the letters ON the fridge, but they don’t determine the specific sequence of the letters
  • if laws did determine the sequence of letters, then the sequences would be repetitive
  • the three materialist explanations – chance alone, chance and law, law alone – are not adequate to explain the effect
  • the best explanation is that an intelligent cause is responsible for the biological explanation in the first replicator
  • we know that intelligent causes can produce functional sequences of information, e.g. – English, Java code
  • the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein
A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone
Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Positive arguments for Christian theism