Tag Archives: Darwinism

News

New study: fruit fly DNA reveals unexpected complexity

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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. 

Podcasts

Brian Auten interviews Dr. Angus Menuge on philosophy of mind

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Click here for the interview. It’s up at Apologetics 315!

Details:

Today’s interview is with Dr. Angus Menuge, Professor of Philosophy  at Concordia University, and author of Agents Under Fire: Materialism and the Rationality of Science. He talks about his background and work, the philosophy of mind, what reason (or reasoning) is, what materialism is as a worldview, things excluded from a materialistic worldview, methodological naturalism and materialism, accounting for free will, materialistic accounts of reason, the epistemological argument from reason, the ontological argument from reason, finding the best explanation for reason, problems with methodological naturalism, implications of materialism, practical application of the argument from reason, advice for apologists, the International Academy of Apologetics, and more.

If what Dr. Menuge says in this interview is true, and I think it is, then a person who believes in materialism can neither ground free will nor rationality! So atheism wouldn’t really be freethought so much as it would be… un-free… non-thought.

In case people don’t want to listen to the podcast, then I’ve got some things for you to read below.

The ontological argument from reason

Dr. Menuge presented a paper at the real Evangelical Philosophical Society conference for students and professors of philosophy, and you can download the paper here in Word format. (here’s a PDF version I made)

Here is the introduction to the paper that Dr. Menuge read at the EPS conference:

The argument from reason is really a family of arguments to show that reasoning is incompatible with naturalism. Here, naturalism is understood as the idea that foundationally, there are only physical objects, properties and relations, and anything else reduces to, supervenes on, or emerges from that. For our purposes, one of the most important claims of naturalism is that all causation is passive, automatic, event causation (an earthquake automatically causes a tidal wave; the tidal wave responds passively): there are no agent causes, where something does not happen automatically but only because the agent exerts his active power by choosing to do it. The most famous version of the argument from reason is epistemological: if naturalism were true, we could not be justified in believing it. Today, I want to focus on the ontological argument from reason, which asserts that there cannot be reasoning in a naturalistic world, because reasoning requires libertarian free will, and this in turn requires a unified, enduring self with active power.

The two most promising ways out of this argument are: (1) Compatibilism—even in a deterministic, naturalistic world, humans are capable of free acts of reason if their minds are responsive to rational causes; (2) Libertarian Naturalism—a self with libertarian free will emerges from the brain. I argue that neither of these moves works, and so, unless someone has a better idea, the ontological argument from reason stands.

The paper is 11 pages long, and it is helpful for those of you looking for some good discussion of one of the issues in the area of philosophy of mind.

You may also be interested in Alvin Plantinga’s epistemological argument from reason, which is related to this argument. It shows that even to have the ability to think, you have to have a certain anthropology and you have to have mental faculties that are designed for reason, not survival.

Methodological naturalism

Dr. Menuge also wrote an article entitled “Is methodological materialism good for science?”.

Intro:

Should science by governed by methodological materialism? That is, should scientists assume that only undirected causes can figure in their theories and explanations? If the answer to these questions is yes, then there can be no such thing as teleological science or intelligent design. But is methodological materialism a defensible approach to science, or might it prevent scientists from discovering important truths about the natural world? In my contribution to The Waning of Materialism (Oxford University Press, 2010), edited by Robert Koons and George Bealer, I consider twelve of the most common arguments in favor of methodological materialism and show that none of them is convincing.

Of these arguments, perhaps the most prevalent is the “God of the gaps” charge, according to which invoking something other than a material cause is an argument from ignorance which, like a bad script writer, cites a deus ex machina to save our account from difficulty. Not only materialists, but also many Christian thinkers, like Francis Collins, worry that appeal to intelligent design commits the God of the gaps fallacy.

As I argue, however, not only is an inference to an intelligent cause not the same as an inference to the supernatural, it is a mistake to assume that all gap arguments are bad, or that only theists make them. If a gap argument is based solely on ignorance of what might explain some phenomenon, then indeed it is a bad argument. But there are many good gap arguments which are made both by scientific materialists and proponents of intelligent design.

So how do you make an argument like that?

As Stephen Meyer has argued in his Signature in the Cell, intelligent design argues in just the same way, claiming not merely that the material categories of chance and necessity (singly or in combination) are unable to explain the complex specified information in DNA, but also that in our experience, intelligent agents are the only known causes of such information. The argument is based on what we know about causal powers, not on what we do not know about them.

Since the inference is based on known causal powers, we learn that the cause is intelligent, but only further assumptions or data can tell us whether that intelligence is immanent in nature or supernatural. It is a serious mistake to confuse intelligent design with theistic science, and the argument that since some proponents of design believe that the designer is God, that is what they are claiming can be inferred from the data, is a sophomoric intensional fallacy.

If you think this is interesting, then do have a listen to the podcast. Dr. Menuge is not an ordinary academic – he is very direct. He calls materialism “a catastrophe” in the podcast!

Polemics

Is there any science in the new “Cosmos” series, or is it all naturalistic religion?

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I noticed a couple of reviews of this television series, produced by an atheist producer of cartoons.

The first review comes from J. W. Wartick.

Multiverse:

The universe is actually so huge that we can’t actually observe the entire thing because there is more beyond what we can see. But “many… suspect” that our universe is but one in an extremely huge number of actual individual universes (here shown as little bubbles spreading out continually over the screen).

Origin of life:

The origin of life “evolved” through biochemical evolution.

J.W. comments:

The depiction of the multiverse with little-to-no qualification was alarming, for there is much debate over whether there even is such a multiverse, and if there is, to what extent it may be called a multiverse. The portrayal within this episode was essentially a fictitious account being passed off without qualification as something a lot of people believe. The wording used was that “many… suspect” there is such a universe. Well yes, that may be true, but to what extent can we test for these other universes? What models predict them and why? I am uninterested in how many people hold to a belief; I am interested in whether that belief is true.

[…][T]he brief snippet used to explore the origin of life: “biochemical evolution” was astonishingly insufficient. I’m sure we’ll get into that in the next episode, but the origin of life is one of the great unsolved mysteries within science and to just hand wave and say “biochemical evolution” is, well, notable to say the least.

I agree with Wartick. What I am looking for is the story of how scientists experimented, observed and tested in order to find out about the universe. I’m not interested in people working theoretical physics who presupposed naturalism at age 14 because their Sunday School teacher was mean to them. Presupposing a philosophy of naturalism is just religion. I want to see the science. Here are my responses to the multiverse speculation and the origin of life speculation.

The series quote Carl Sagan at the beginning, but he a person who let his religion of naturalism lead him away from the scientific evidence for a beginning. Instead of accepting the standard Big Bang model, which implies a transcendent Creator, Sagan chose to embrace a faith-based eternal oscillating model of the universe, which tries to avoid a Creator. I wrote about the problems with Sagan’s naturalistic speculative cosmology in this post.

Now let’s see Casey Luskin’s review on Evolution News.

Excerpt:

During the first episode, Tyson devotes lengthy segments to promoting the old tale that religion is at war science, and strongly promotes the idea that religion opposes intellectual advancement. He tells the story of the 16th-century astronomer cultist philosopher Giordano Bruno, who he says lived in a time without “freedom of speech” or “separation of church and state,” and thus fell into the clutches of the “thought police” of the Inquisition for disagreeing with the church’s geocentric views. Never mind that his show made it appear that President Obama endorsed Sagan-style materialism, but I digress… Of course the main religious authority of that time was the Catholic Church, and the program shows angry priests with evil-sounding British accents dressed in full religious garb throwing Bruno out on the street, and eventually burning him at the stake.

Just to make sure that other Christians who aren’t Catholic also understand their religions too hinder scientific progress, Tyson goes out of his way to point out that Bruno was opposed by “Calvinists in Switzerland,” and “Lutherans in Germany,” including the great protestant reformer Martin Luther himself. He never mentions that Protestants aren’t the ones who burned Bruno at the stake, nor does he ever mention that most of the founders of modern science were Christians. But I digress…

It’s a lengthy scene, all to highlight some of the darkest chapters of Christianity in Europe. But the entire retelling of Bruno’s fate lasts a good portion of the first episode’s hour. Why make the religious persecution of scientists some four hundred years ago a major focus of a widely publicized television series that is ostensibly about promoting science?

Luskin took issue with the idea that religious people hold science back. On the contrary, religious Christians were largely responsible for the birth of modern science. Luskin also reports on over a dozen cases where naturalists have suppressed critical thinking about whether science disproves the religion of naturalism.

Here’s are a few:

A congressional subcommittee staff investigation found that biologist Richard Sternberg experienced retaliation by his co-workers and superiors at the Smithsonian, including transfer to a hostile supervisor, removal of his name placard from his door, deprivation of workspace, subjection to work requirements not imposed on others, restriction of specimen access, and loss of his keys, because he allowed a pro-ID article to be published in a biology journal.

In 2005, over 120 faculty members at Iowa State University (ISU) signed a petition denouncing ID and calling on “all faculty members to … reject efforts to portray Intelligent Design as science.” These efforts were significant not just because they opposed academic freedom by demanding conformity among faculty to reject ID, but because they focused on creating a hostile environment for pro-ID astronomer Guillermo Gonzalez, co-author of The Privileged Planet, who was denied tenure at ISU in 2006 due to his support for ID. Both public and private statements exposed through public records requests revealed that members of ISU’s department in physics and astronomy voted against Gonzalez’s tenure due to his support for ID.

In 1993, San Francisco State University biology professor Dean Kenyon was forced to stop teaching introductory biology because he was informing students that scientists had doubts about materialist theories of the origin of life.

In 2005, pro-ID adjunct biology professor Caroline Crocker lost her job at George Mason University after teaching students about both the evidence for and against evolution in the classroom, and mentioning ID as a possible alternative to Darwinism. While her former employer maintains that it simply chose not to renew her contract, she was specifically told she would be “disciplined” for teaching students about the scientific controversy over evolution.

In 2013, Ball State University (BSU) President Jo Ann Gora issued a speech codedeclaring that “intelligent design is not appropriate content for science courses” at BSU, after atheist activists from the Freedom from Religion Foundation charged that a “Boundaries of Science” course taught by a well-liked physics professor (Eric Hedin) was violating the Constitution by favorably discussing intelligent design.

You can read more about the problems with Carl Sagan’s religion-driven rejection of experimental science in this post by Phillip E. Johnson. For a better take on cosmology with more evidence and less religion, check out this lecture by particle physicist Michael Strauss. I think you’ll find that science is better when it’s done by a practicing experimental scientist, and not by the creator of cartoons like “Family Guy”.

UPDATE: On the Christian Apologetics Alliance blog, Dr. Tim McGrew wrote that the portrayal of Bruno had even more inaccuracies. Isn’t it amazing that that a cartoonist can get something filled with myths and misrepresentations to be televised? And many people will believe it, too, just like many people accepted the (now-discredited) oscillating model of Carl Sagan. I still have atheists proposing this to me when I present the standard model to them. That’s the hazard of having a TV-driven worldview, I guess. A worldview based on Star Trek.