Tag Archives: DNA

Can naturalism account for the origin of the 20 amino acids in living systems?

Do the Miller-Urey experiments simulate the early Earth?
Do the Miller-Urey experiments simulate the early Earth?

The origin of life

There are two problems related to the origin of the first living cell, on naturalism:

  1. The problem of getting the building blocks needed to create life – i.e. the amino acids
  2. The problem of creating the functional sequences of amino acids and proteins that can support the minimal operations of a simple living cell

Normally, I concede the first problem and grant the naturalist all the building blocks he needs. This is because step 2 is impossible. There is no way, on naturalism, to form the sequences of amino acids that will fold up into proteins, and then to form the sequences of proteins that can be used to form everything else in the cell, including the DNA itself. But that’s a topic for a separate post.

Today, let’s take a look at the problems with step 1.

The problem of getting the building blocks of life

Now you may have heard that some scientists managed to spark some gasses to generate most of the 20 amino acids found in living systems. These experiments are called the “Miller-Urey” experiments.

The IDEA center has a nice summary of origin-of-life research that explains a few of the main problems with step 1.

Miler and Urey used the wrong gasses:

Miller’s experiment requires a reducing methane and ammonia atmosphere,11, 12 however geochemical evidence says the atmosphere was hydrogen, water, and carbon dioxide (non-reducing).15, 16 The only amino acid produced in a such an atmosphere is glycine (and only when the hydrogen content is unreasonably high), and could not form the necessary building blocks of life.11

Miller and Urey didn’t account for UV of molecular instability:

Not only would UV radiation destroy any molecules that were made, but their own short lifespans would also greatly limit their numbers. For example, at 100ºC (boiling point of water), the half lives of the nucleic acids Adenine and Guanine are 1 year, uracil is 12 years, and cytozine is 19 days20 (nucleic acids and other important proteins such as chlorophyll and hemoglobin have never been synthesized in origin-of-life type experiments19).

Miller and Urey didn’t account for molecular oxygen:

We all have know ozone in the upper atmosphere protects life from harmful UV radiation. However, ozone is composed of oxygen which is the very gas that Stanley Miller-type experiments avoided, for it prevents the synthesis of organic molecules like the ones obtained from the experiments! Pre-biotic synthesis is in a “damned if you do, damned if you don’t” scenario. The chemistry does not work if there is oxygen because the atmosphere would be non-reducing, but if there is no UV-light-blocking oxygen (i.e. ozone – O3) in the atmosphere, the amino acids would be quickly destroyed by extremely high amounts of UV light (which would have been 100 times stronger than today on the early earth).20, 21, 22 This radiation could destroy methane within a few tens of years,23 and atmospheric ammonia within 30,000 years.15

And there were three other problems too:

At best the processes would likely create a dilute “thin soup,”24 destroyed by meteorite impacts every 10 million years.20, 25 This severely limits the time available to create pre-biotic chemicals and allow for the OOL.

Chemically speaking, life uses only “left-handed” (“L”) amino acids and “right-handed” (“R)” genetic molecules. This is called “chirality,” and any account of the origin of life must somehow explain the origin of chirality. Nearly all chemical reactions produce “racemic” mixtures–mixtures with products that are 50% L and 50% R.

Two more problems are not mentioned in the article. A non-peptide bond anywhere in the chain will ruin the chain. You need around 200 amino acids to make a protein. If any of the bonds is not a peptide bond, the chain will not work in a living system. Additionally, the article does not mention the need for the experimenter to intervene in order to prevent interfering cross-reactions that would prevent the amino acids from forming.

Usually when you hear the origin of life debated, they sort of skirt about the problem of where the amino acids come from, but there is no reason not to make that an issue. The naturalist has to explain how the first living cell could come about naturalistically.

Positive arguments for Christian theism

 

Stephen C. Meyer and Peter Atkins debate intelligent design

This dialog occurred in 2010 on the Unbelievable radio show.

I made a rough transcript, so please see below for that.

The MP3 file is here. (60 minutes)

Details:

The documentary film “Expelled” is presented by US Actor Ben Stein and makes the case that scientists who question Darwinian orthodoxy and support Intelligent Design are being “expelled” from academia.

As the UK edition of the DVD is released we ask “Is freedom of thought at stake or is Intelligent Design out of bounds when it comes to biological science?”

Stephen C Meyer is co founder of the Discovery Institute in the USA and a major proponent of Intelligent Design.

Peter Atkins is Professor of Chemistry at Oxford University and an outspoken atheist.

They both feature in “Expelled” and join Justin to debate the pros and cons of Intelligent Design theory.

Mark Haville who is bringing the film to the UK also joins the discussion.

Note: The transcript below is quite snarky and may include paraphrases of Dr. Atkins for the sake of humor.

My rough transcript of the Meyer-Atkins debate

Stephen Meyer:
– started researching on ID while doing his PhD at Cambridge
– the question is whether the information-bearing properties in DNA require a designer
– what cause is adequate to explain the digital code that in the simplest living cell
– alternative explanations like self-organization and RNA-first have failed
– so the best explanation for functional sequences of parts is an intelligent designer
– Darwinists have responded to this argument with insults and suppression of dissent

Peter Atkins:
– intelligent design is creationism
– there is no science at all in it
– information can emerge without an intelligent designer
– structures emerge spontaneously, no agent is needed to generate the structure
– information in DNA is also a structure

Stephen Meyer:
– structure and information are two different things
– many structures emerge spontaneously
– structure may be like the vortex that occurs when water goes down a drain

Peter Atkins:
– the vortex is information

Stephen Meyer:
– structures are different from functionally-specified digital information
– in DNA, there is a 4-digit alphabet that is used to create code sequences
– the thing to be explained is where do the functional sequences come from

Peter Atkins:
– information can grow without an agent
– the second law of thermodynamics
– the universe is falling into disorder
– but there are local abatements of chaos that create information
– evolution can cause the amount of information to grow

Stephen Meyer:
– that’s just an assertion
– I agree that energy flow through a system can produce spontaneous order
– but spontaneous order is not the same thing as information

Peter Atkins:
– spontaneous order is the same as information

Stephen Meyer:
– it’s not order that needs to be explained it’s specified complexity

Peter Atkins:
– what do you mean by specified complexity?

Stephen Meyer:
– the chemical bonds that connect to each letter do not determine the letter
– the chemical bonding sites will accept any letter as easily as any other
– any one of the 4 bases (letters) can attach at any place along the backbone

Peter Atkins:
– the selection of which letter comes next is determined by evolution

Stephen Meyer:
– that is just an assertion
– there is no physical process that sequences the letters to have a function

Peter Atkins:
– do you believe in evolution? YES OR NO!

Mark Haville:
– for him to answer the question you have to define the word
– do you mean macro or micro? biological or stellar? directed or undirected?

Peter Atkins:
– undirected molecules to man evolution by natural processes

Stephen Meyer:
– but even Dawkins doesn’t believe in evolution then
– you’re including the origin of life from non-living matter in evolution
– Dawkins says that there is no known naturalistic explanation for that

Mark Haville:
– you need to define your terms

[They discuss of the movie Expelled and the case of Richard Sternberg]

Stephen Meyer:
– the problem is people don’t want to talk about the science
– they denounce dissent as unscientific
– they will not debate about whther natural causes can explain the information
– I want to talk about the science

Peter Atkins:
– ID people raise interesting questions for naturalists to work on
– but you want to tell us what the answer is (intelligence) before we begin
– you start from the idea that an intelligence was involved

Justin Brierley:
– but you start with the idea that natural mechanisms can explain everything!

Stephen Meyer:
– for Dr. Atkins, only explanations based on material processes are valid

Peter Atkins:
– that is correct

Stephen Meyer:
– but we think that the activities of mind can explain some effects
– e.g. – the best explanation of the Rosetta stone is a mind

Peter Atkins:
– but we naturalists think of minds as material as well

Stephen Meyer:
– that’s a materialist pre-supposition on your part
– we would have to have a debate about mind and body

Mark Haville:
– I think that the materialist position is socially dangerous
– the problem with naturalism is that it is an ideology
– the ideology pushes absurdities, e.g. – the universe came from nothing uncaused
– and naturalists exert power over others to force them to believe nonsense

Stephen Meyer:
– science progresses as the result of scientists disagreeing
– both sides agree to the facts
– the debate is about the interpretation of those facts
– and one side is being ruled out a priori based on the pre-supposition of materialism

Peter Atkins:
– why do you say that an intelligence is involved in DNA but not general relativity

Stephen Meyer:
– it is always logically possible that intelligence can be invlved in any effect
– the main thing is that explanations based on intelligence should not be ruled out

Peter Atkins:
= well you can’t appeal to any non-material process in expaining anything
– those are the rules

Moderator:
– what does intelligent design have to do with religion?

Stephen Meyer:
– creationism is about understanding the istory of life using the Bible
– intelligent design is about using the same method of inquiry as Darwin
– we know that information arises from intelligent causes
– humans create information all the time by using intelligence to sequence parts

Moderator:
– are intelligent design proponents disreputable?

Stephen Meyer:
– what’s disreputable is shutting down debate by setting arbitrary rules

Peter Atkins:
– we are both interested in the same questions

Moderator:
– why won’t you let Stephen publish his papers then?

Peter Atkins:
– because it breaks the pre-suppositions of naturalism and materialism

Stephen Meyer:
– you’re shutting down inquiry by using an arbitrary definition of science

Mark Haville:
– we need to define the word science
– science should be based on what we can observe empirically
– we can observe micro-evolution empirically
– but Darwinism goes beyond what is observable to postulate macro-evolution

Peter Atkins:
– but paleobiology is replete with evidence

Stephen Meyer:
– paleobiology uses a method of inference that I think is valid
– but intelligent design uses the same mode of reasoning which is also valid

Peter Atkins:
= you’re intellectually lazy
– we’re smart, we’re using our brains

Moderator:
– you’re saying that appeals to intelligent causes ends science?
– is ID the view that some things are too complex to be explained with naturalism?

Peter Atkins:
– yes, and to teach children that materialism is false is child abuse

Stephen Meyer:
– let’s drop the insults and the rhetoric and focus on the arguments
– the ID argument is not based on what we don’t know, it’s based on what we DO know
– first, we can ask what undirected natural processes can and cannot do
– second, we can ask what we know about intelligent causes from our own experience
– what we do know seems to me to require an intelligent agent as a cause

Peter Atkins:
– GOD! Do you mean God!? Do you mean God!?

Stephen Meyer:
– I personally mean God, but all that the arguments proves is a generic intelligent cause
– and I am using the same method of investigation that Darwin used to get there
– what we know from our experience is that a mind is needed to create information

Peter Atkins:
– NONSENSE! ABSOLUTE NONSENSE!

Stephen Meyer:
– in my book, I list 10 predictions made by ID, so it’s not a science-stopper
– furthermore, the enterprise of science began with th goal of understanding God
– consider the earliest scientists, people like James Boyler and Johannes Kepler

Peter Atkins:
– that was 300 years ago, we’ve moved on

Mark Haville:
– what about Max Planck then?

Stephen Meyer:
– how about James Clark Maxwell?

Mark Haville:
– we need to focus on the facts

Peter Atkins:
– what do you mean by the facts?

Mark Haville:
– well the fact is that Darwinism has no mechanism to produce new information

Peter Atkins:
– well copying errors introduces beneficial mutations

Stephen Meyer:
– let’s focus on where we get the first information from the simplest organism
– you can’t account for the first organism by appealing to copying errors
– to add functionality to a program, you need new lines codes from an intelligence
– once you have life, you can generate some new information
– but you can’t generate macro-evolution either

Peter Atkins:
– if we give you your explanation for teh origin of life, will you give this up

Stephen Meyer:
– of course! I’m a former theistic evolutionist
– but right now the evidence is not there for it
– we have to decide these questions based on what we see with our own eyes today

Peter Atkins:
– but I pre-suppose materialism as the starting point of all explanations
– you’re just intellectually lazy to abandon my pre-supposition

Stephen Meyer:
– why is it is less intellectually lazy to insist that materialism is true
– we are making plenty of predictions, and isn’t that what science is about?
– consider Junk DNA – you guys said it had no use
– now we know it has a use

Peter Atkins:
– naturalists were open to the idea that junk DNA might have a use before ID

Moderator:
– Dr. Meyer, what about the wall that locks out intelligence as an explanation?

Stephen Meyer:
– if these are interesting questions, then we should allow freedom of inquiry
– that’s how science advances

Peter Atkins:
– for all their science-talk really they are just saying God did it
– people who don’t agree with me are not using their brains, like I do
– to give up on my pre-supposition of materialism is a denial of humanity

Mark Haville:
– there are important issues that are affected by our view of origins
– everyone who hasn’t seen Expelled movie should definitely see it

Convergence detected in the genetic structure of bats and dolphins

Apologetics and the progress of science
Apologetics and the progress of science

We have to start this post with the definition of convergence in biology.

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

It is the opposite of divergent evolution, where related species evolve different traits.

On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats.

All four serve the same function and are similar in structure, but each evolved independently.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me.

Excerpt:

The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, according to new research led by scientists at Queen Mary University of London and published in Nature this week.

The scientists investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution to examine the frequency of the process at a genomic level.

Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).

The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.

They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several ‘hearing genes’.

[…]Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

“We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Nature is the most prestigious peer-reviewed science journal. This is solid material.

There is an earlier article from 2010 in New Scientist that talked about one of the previous genes that matched for hearing capability.

Excerpt:

Bats and dolphins trod an identical genetic path to evolve a vital component of the complex sonar systems they use to pursue and catch prey.

The finding is unusual, because although many creatures have independently evolved characteristics such as eyes, tusks or wings, they usually took diverse genetic routes to get there.

Analysis of a specific gene has now demonstrated that although bats live in air and dolphins in water, where sound travels five times faster, they independently evolved a near-identical gene that allows them to accept high-frequency sound in the ear – vital for sonar.

The gene makes prestin, a protein in hair cells of the cochlea, which is the organ in the inner ear where sonar signals are accepted and amplified. Prestin changes shape when exposed to high-frequency sound, and this in turn deforms the fine hair cells, setting off an electrical impulse to the brain. So the protein has the important jobs of detecting and selecting high-frequency sounds for amplification.

When researchers examined the molecular structure of the prestin gene from a range of animals, they found that the variants in echolocating bats and dolphins were virtually indistinguishable.

Indistinguishable genes in animals that don’t share a common ancestor? Maybe a better explanation for the evidence we have is – common designer.

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

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

How similar are human DNA and chimpanzee DNA?

How did life begin?
How did life begin?

Now, I’m not an expert in DNA sequencing similarities, here is paper from Nature which argued for more distance between human and chimp genomes than the 98% similarity commonly asserted by Darwinists.

Evolution News covered that one:

A Nature paper from January, 2010 titled, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.” Of course, the paper attributes these dramatic genetic changes to “rapid evolution during the past 6 million years.”

One of the scientists behind the study was quoted in a Nature news article stating, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” The news article states that “many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human” since “the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans.” According to the news piece, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa, whereas this is true for less than 2% of the remainder of the genome.”

But not wishing to offend the “myth of 1%”, the Nature news article carefully adds, “The remainder of the chimp and human genomes are thought to differ in gene number by less than 1%.”

A more recent paper (PDF) from PNAS (edited by arch-evolutionist Francisco Ayala, no less) has more.

Here’s the abstract:

The rise of comparative genomics and related technologies has added important new dimensions to the study of human evolution. Our knowledge of the genes that underwent expression changes or were targets of positive selection in human evolution is rapidly increasing, as is our knowledge of gene duplications, translocations, and deletions. It is now clear that the genetic differences between humans and chimpanzees are far more extensive than previously thought; their genomes are not 98% or 99% identical. Despite the rapid growth in our understanding of the evolution of the human genome, our understanding of the relationship be-tween genetic changes and phenotypic changes is tenuous. This is true even for the most intensively studied gene, FOXP2, which underwent positive selection in the human terminal lineage and is thought to have played an important role in the evolution of human speech and language. In part, the difficulty of connecting genes to phenotypes reflects our generally poor knowledge of human phenotypic specializations, as well as the difficulty of interpreting the consequences of genetic changes in species that are not amenable to invasive research. On the positive side, investigations of FOXP2, along with genomewide surveys of gene-expression changes and selection-driven sequence changes, offer the opportunity for “phenotype discovery,” providing clues to human phenotypic specializations that were previously unsuspected. What is more, at least some of the specializations that have been proposed are amenable to testing with noninvasive experimental techniques appropriate for the study of humans and apes.

Again, I’m not sure what the exact numbers are, this is not my area, but I think it’s interesting. I know that ICR is doing some work on computing the average level of difference across both genomes.