Tag Archives: Naturalism

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Paul Nelson: the most interesting and significant paper we’ve read in years

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Wow, check out this post by Paul Nelson over at Evolution News.

Excerpt:

Now, the paper I retrieved for my co-worker, entitled “The Levinthal paradox of the interactome,” Protein Science 20 (2011):2074-79, explains why the space of “being alive” is so much vastly smaller, and harder to find, than the space of being “not alive.” The paper is short (only six pages) and was written by two structural biologists, Peter Tompa of Vrije Universiteit in Brussels and George Rose of Johns Hopkins University, neither of whom is an intelligent-design advocate. But the paper’s arguments bear so strongly on the design debate, and represent so remarkable a challenge to widely held assumptions about (for instance) the origin of cells, that its effect promises to be far-reaching. As in, revolutionary.

[…]Tompa and Rose draw a number of lessons from their calculations. They argue, first, that any increase in biological realism will only make the Levinthal interactome paradox worse:

Of course, there are additional complicating factors such as alternative splicing, post-translational modifications, non-pairwise macromolecular interactions, incorrect complex formation that is adventitiously stable, and so forth. However, even neglecting such complications, the numbers preclude formation of a functional interactome by trial and error complex formation within any meaningful span of time. This numerical exercise…is tantamount to a proof that the cell does not organize by random collisions of its interacting constituents.But secondly, what they call “the most profound conclusion” from their analysis bears directly on widely held assumptions about the origin of life.

A highly enriched soup of proteins and nucleic acids will never form a functional cell, even if lipid bilayer membranes were provided to help these materials become organized. Indeed, the fully functional contents of a living cell, once the wall or membrane enclosing them has been breached (thus, killing the cell), move irreversibly in the direction of non-living chemistry. Humpty Dumpty, once he cracks, does not reconstitute, but enters what Tompa and Rose call the “zone of chaos,” never to return.

Tompa and Rose have sketched the theoretical basis for why this happens:

[O]ur calculations of combinatorial complexity [show] that the emergent interactome could not have self-organized spontaneously from its isolated protein components. Rather, it attains its functional state by templating the interactome of a mother cell and maintains that state by a continuous expenditure of energy. In the absence of a prior framework of existing interactions, it is far more likely that combined cellular constituents would end up in a non-functional, aggregated state, one incompatible with life…The spontaneous origination of a de novo cell has yet to be observed; all extant cells are generated by the division of pre-existing cells that provide the necessary template for perpetuation of the interactome.

Tompa and Rose spell out other implications of their analysis (e.g., for medicine and synthetic biology), but maybe we’ve piqued your curiosity enough already. This paper deserves your attention. As noted, for a close circle of us at Discovery and Biologic, it’s the most interesting and significant paper we’ve read in years.

Dr. Nelson’s post explains a bit more with pictures.

Polemics

Five myths about intelligent design that many Christians believe

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Consider this article by Melissa at Hard Core Christianity. (H/T Neil Simpson)

Here’s her list of 5 myths about intelligent design:

  1. Intelligent Design (ID) is just a fancy name for Creationism. 
  2. ID has been dis-proven by the fossil record, which supports common descent. 
  3. ID claims that the “intelligent agent” had to supernaturally intervene in natural history over and over again. 
  4. ID uses a disguised form of the “God of the gaps” fallacy.
  5. ID research has not produced peer-reviewed literature.

All five of these myths are also believed by most opponents of ID in the media, and even in academia. So it’s not just Christians.

And here is the detail on myth #4:

MYTH #4: ID uses a disguised form of the “God of the gaps” fallacy.

The true story: ID does not say “We don’t yet know how life emerged from non-life, therefore an intelligence must have done it.” Rather, it makes a two-fold argument: 1) Neo-Darwinian explanations for the emergence and divergence of life are sorely insufficient in their explanatory power and 2) there are features of nature, such as the specified complexity of the digital information in DNA, that are best explained by intelligent agency. We already know from direct experience how to detect intelligence in other branches of science, so inferring intelligence based on the same type of observed effects is completely reasonable. In scientific practice, we infer the existing cause that is KNOWN to produce the effect in question. Since biochemistry contains information, ID theorists infer that there must be an informer, because there are no other sources of information. Ironically, whenever a materialist says, “We don’t yet know how life emerged from non-life, but one day science will explain it,” they are actually using the Science of the Gaps fallacy.

When discussing ID, it’s important to do two things. First, define ID. Second, block any attempt to bring God, the Bible, religion, church, feelings, personal experiences, personal faith, philosophers, or philosophy into the discussion.

To define ID, point the person to this book from Cambridge University Press.

If anyone is debating ID with you and brings up God, the Bible, religion, evil and suffering, sub-optimal designs or philosophy, then immediately tell them that you will not debate natural theology or the problem of evil with them. Anyone who thinks that ID requires the best of all possible words, optimal design, etc. doesn’t understand ID. The ID argument concludes design, if successful. It has nothing to say about goodness and badness and feelings and religion. Intelligent design asserts that an intelligent cause is the best explanation for some specific effect in nature. We can’t say from the data if the cause is good or evil, only that it is intelligent. ID is not natural theology, it is mathematics.

After we infer design based on the science alone, THEN we can talk about who the designer is, and whether he is a nice designer or a mean designer. Those are two separate questions.

If you want to debate intelligent design, then watch this lecture by Stephen C. Meyer, and read Melissa’s article. That’s all you need to get started. If you want to understand even more about it, listen to this debate with Stephen C. Meyer and Keith Fox.

Polemics

Pseudogenes: how Darwinian mythology negatively impacts the progress of science

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The latest discovery that falsifies Darwinian religion wasn’t without cost. Our search for cures for cancer was negatively impacted by more of their prejudices about pseudogenes.

Uncommon Descent explains the new discovery and why Darwinians opposed it. (H/T ECM)

Excerpt:

Because they are generally noncoding and thus considered nonfunctional and unimportant, pseudogenes have long been neglected. Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer.

And the paper concludes:

The function of the great fraction of the human genome (98%) composed of sequences that do not encode proteins remains a mystery. Pseudogenes are technically part of this fraction, and the examples described here clearly demonstrate that they perform a broad and multifaceted spectrum of activities in human cancer. Therefore, the name pseudogenes, which underlies their close sequence similarity with parental counter-parts, should not imply a negative connotation. They might be “pseudo” genes because they do not encode a protein or because they encode a protein that does not function in the same way as that encoded by their cognate genes. Nonetheless, they are functionally disabled but can perform different functions than their parental gene counterparts.

Here are a few of the more recent errors made by religious Darwinians:

Why do these people believe weird things in the absence of evidence, only to have their speculations falsified when the gaps in our knowledge are closed by scientific progress? Well, evidence doesn’t matter to people who are motivated by naturalistic faith. Like belief in a flat-Earth, the delusion of naturalism is not accountable to scientific evidence. They believe what they want to believe. It’s not up for debate. For some people like Richard Dawkins, a prior lifestyle commitment makes theism (and the moral law!) an impossibility a priori. So there is at the root of atheism a fundamentalist close-mindedness that leads to intellectual dishonesty – not just deceiving others but deceiving themselves. They cannot admit to what reason and evidence is telling them. And it really does affect our progress in many areas, such as cancer research.

The war between atheism (anti-rational hedonism) and science is everywhere, across many scientific disciplines. Science makes discoveries about the Big Bang, the fine-tuning, the origin of life, the usefulness of non-coding DNA, pseudogenes, etc. Instead of accepting what science says and living consistently with science, the naturalist turns to speculations about something coming from nothing, multiverses, aliens, “junk” DNA and other irrational nonsense. The truth of the matter is that atheists will literally believe anything no matter how irrational it is.