Wintery Knight

…integrating Christian faith and knowledge in the public square

New study: fruit fly DNA reveals unexpected complexity

From Evolution News.

Excerpt:

You know about ENCODE, the project that found 80 percent or more of the human genome is transcribed and appears functional. Now, along comes modENCODE: the ENCODE project for model organisms. Results from the fruit fly are in, and Indiana University shares the surprises (for evolutionary theory, that is): “Study of complete RNA collection of fruit fly uncovers unprecedented complexity.”

The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called “antisense” RNAs are especially prominent during gonadal development; that “splicing factors” (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that theDrosophila transcriptome undergoes large and interesting changes in response to environmental stresses. (Emphasis added.)

Ten of the 41 researchers from 11 universities working on modENCODE came from IU. They found many genes transcribed only under stress, such as exposure to heat, cold, and toxins. “In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions,” they said. As if the “junk DNA” myth needed any more pounding, the lead author testifies:

“As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.

The post on Evolution News also talks about another study from the University of Vienna on the genome of the sea anemone.  Their genome was way more complex than expected, too.

So what is the best explanation for all this specified complexity that enables biological function?

Evolution News explains:

Intelligent design… knows how to explain the observations. Whenever we see a complex, functioning system (like a rollout of a software system), we know intelligence played a role in its origin. We also know that intelligence can explain multiple, independent instantiations of similar systems. We never see, however, complex, networked systems arising de novo by unguided natural processes.

Yes. In the company I work for, we have a release of functional code every month (at least). These explanation for the increase in specified complexity in our applications is that busy little software engineers have been carefully sequencing characters into lines of Java code, for  purpose. No rational person believes that you can get huge increases in specified complexity by random chance. Code is code is code. It all requires a coder, just like the Big Bang requires a Big Bang. 

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Dr. 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 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.

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

Positive arguments for Christian theism

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The long war: a history of the conflict between religion and science

Let’s start with an example of a famous battle in the long war between science and religion.

Canadian science writer Denyse O’Leary writes about the history of cosmology at Evolution News.

Excerpt:

What help has materialism been in understanding the universe’s beginnings?

Many in cosmology have never made any secret of their dislike of the Big Bang, the generally accepted start to our universe first suggested by Belgian priest Georges Lemaître (1894-1966).

On the face of it, that is odd. The theory accounts well enough for the evidence. Nothing ever completely accounts for all the evidence, of course, because evidence is always changing a bit. But the Big Bang has enabled accurate prediction.

In which case, its hostile reception might surprise you. British astronomer Fred Hoyle (1915-2001) gave the theory its name in one of his papers — as a joke. Another noted astronomer, Arthur Eddington (1882-1944), exclaimed in 1933, “I feel almost an indignation that anyone should believe in it — except myself.” Why? Because “The beginning seems to present insuperable difficulties unless we agree to look on it as frankly supernatural.”

One team of astrophysicists (1973) opined that it “involves a certain metaphysical aspect which may be either appealing or revolting.” Robert Jastrow (1925-2008), head of NASA’s Goddard Institute for Space Studies, initially remarked, “On both scientific and philosophical grounds, the concept of an eternal Universe seems more acceptable than the concept of a transient Universe that springs into being suddenly, and then fades slowly into darkness.” And Templeton Prize winner (2011) Martin Rees recalls his mentor Dennis Sciama’s dogged commitment to an eternal universe, no-Big Bang model:

For him, as for its inventors, it had a deep philosophical appeal — the universe existed, from everlasting to everlasting, in a uniquely self-consistent state. When conflicting evidence emerged, Sciama therefore sought a loophole (even an unlikely seeming one) rather as a defense lawyer clutches at any argument to rebut the prosecution case.

Evidence forced theorists to abandon their preferred eternal-universe model. From the mid 1940s, Hoyle attempted to disprove the theory he named. Until 1964, when his preferred theory, the Steady State, lost an evidence test.

Here is a a quick summary of some of the experimental evidence that emerged in the last few decades that caused naturalists to abandon the eternal universe that they loved so much when they were younger.

The importance of having a narrative

Now I want to make a very, very important point about Christianity and the progress of science. And that point is that it is very important that Christians present the evidence in exactly the way that Denyse presented it in that article – in its historical context, featuring the conflict between naturalists and the experimental evidence.

All Christians should be familiar with the following basic pieces of evidence which fit the war between science and naturalism narrative:

  1. The origin of the universe
  2. The cosmic fine-tuning
  3. The origin of life (biological information)
  4. The sudden origin of the Cambrian phyla
  5. The habitability/observability correlation

When you talk about these evidences as a Christian theist to non-Christians, you have to have cultivated a genuine interest in reconciling your beliefs with science. You have to accept that there are two books that reveal God’s character and attributes. The book of nature, and the book of Scripture. And you need to be flexible about getting these two books to fit together. The book of nature gives us natural theology (see Romans 1). It tells us that God is Creator and Designer. The book of Scripture tells us that God stepped into history as a man to save us by taking the punishment for our headlong rush away from God, which the Bible calls sin. Science is one way that humans can recover some of basic knowledge about God. Knowledge that is only possible because God created and designed the universe (and us) in such a way that we are capable of making discoveries, and that the universe is capable of being explored and understood.

It’s very important to present these five basic evidences to non-Christians in the historical context. And here is the story you must tell: “In the beginning, there was the naturalism, and the naturalism tried to argue from ignorance that God was not Creator and God was not Designer. And then came the science, and now people have to give up their naturalism in order to not be crazy and irrational”. That’s the narrative you use when talking to non-Christians about science.

In the beginning was the naturalism:

  1. In pre-scientific times, atheists maintained that the universe was eternal
  2. In pre-scientific times, atheists maintained that a life-permitting universe was as likely as a life-prohibiting universe
  3. In pre-scientific times, atheists maintained that the cell was a simple blob of jello that could spontaneously emerge in some warm pond
  4. In pre-scientific times, atheists maintained that the sudden origin of the Cambrian phyla would be explained by subsequent fossil discoveries
  5. In pre-scientific times, atheists maintained that there was nothing special about our galaxy, solar system, planet or moon

But then science progressed by doing experiments and making observations:

  1. Scientists discovered redshift and the cosmic microwave background radiation and more!
  2. Scientists discovered the fine-tuning of gravity and of the cosmological constant and more!
  3. Scientists discovered protein sequencing and exposed the myth of “junk DNA” and more!
  4. Scientists discovered an even shorter Cambrian explosion period and the absence of precursor fossils and more!
  5. Scientists discovered galactic habitable zones and circumstellar habitable zones and more!

And now rational people – people who want to have true beliefs about reality – need to abandon a false religion (naturalism).

Now naturally, science is in a state of flux and things change. But you have to look at the trend of discoveries, and those trends are clearly going against naturalism, and in favor of Christian theism. No one is arguing for a deductive proof here, we are simply looking at the evidence we have today and proportioning our belief to the concrete evidence we have today. People who are guided by reason should not seek to construct a worldview by leveraging speculations about future discoveries and mere possibilities. We should instead believe what is more probable than not. That’s what a rational seeker of truth ought to do. Proportion belief to probabilities based on current, concrete knowledge.

It is very important that Christians keep abreast of the progress of science, and give proper respect to science when forming our worldviews, and keep in mind what is really going on with atheism. There is a lot of loud worshiping of science by people like Dawkins and Atkins and Krauss, but if you dig into things a little, you’ll find that they are actually filled with rage and enmity against what science has revealed about nature. And not just in one area, but in many, many areas.

Atheism, as a worldview, is not rooted in an honest assessment about what science tells us about reality. Atheism is rooted in a religion: naturalism. And the troubling thing we learn from looking at the history of science is that this religion of naturalism is insulated from correction from the progress of science. Nothing that science reveals about nature seems to be able to put a dent in the religion of naturalism, at least for most atheists. Their belief in naturalism is so strong that it repels all scientific evidence that falsifies it. Atheists simply don’t let science inform and correct their worldview.

It falls to us Christian theists, then, to hold them accountable for their abuse and misrepresentation of science. And that means telling the story of the progress of science accurately, and accurately calling out the religion of naturalism for what it is - a religion rooted in blind faith and ignorance that has been repeatedly and convincingly falsified by the progress of science in the modern era.

Positive arguments for Christian theism

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New study: Y-chromosome Adam and mitochondrial-Eve dating tightens up

Mysterious Melissa brought this interesting new study to my attention. It was published in the peer-reviewed journal Science. It was reported on Science Daily.

Excerpt:

More than 7 billion people live on this planet — members of a single species that originated in one place and migrated all over Earth over tens of thousands of years.

But even though we all trace our family lineage to a few common ancestors, scientists still don’t know exactly when and how those few ancestors started to give rise to the incredible diversity of today’s population.

A brand-new finding, made using advanced analysis of DNA from all over the world, sheds new light on this mystery. By studying the DNA sequence of Y chromosomes of men from many different populations, scientists have determined that their male most recent common ancestor (MRCA) lived sometime between 120,000 and 156,000 years ago.

It’s the first time the human ancestry has been traced back through the male line by sequencing the DNA of many entire Y chromosomes.

And, it agrees reasonably well with previous findings about our female most recent common ancestor, made by studying DNA carried down through the human race’s female line. Such studies used DNA from mitochrondria — structures inside cells — and placed that time of the most recent common ancestor between 99,000 and 148,000 years ago.

[...]The reconciliation of the timing of “Adam” and “Eve,” however, may be this study’s most important immediate implication.

“This has been a conundrum in human genetics for a long time,” said Carlos D. Bustamante, PhD, a professor of genetics at Stanford and senior author of the study. “Previous research has indicated that the male MRCA lived much more recently than the female MRCA. But now our research shows that there’s no discrepancy. In fact, if anything, the Y chromosome may be a bit older.”

So the new dates for Adam and Eve would allow them to actually date. Ha ha!

Now those dates are still too far in the past to satisfy an old-Earth creationist like me, but it solves that problem about them existing durring completely different dates. I’ve been waiting for that one to be solves for a decade! It’s progress.

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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

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