"In Search of Evolution" - Steve Hays

Just a quickie. I'm a big fan of "Triablogue", mostly because of the amazing Steve Hays. Steve is some kind of machine. He doesn't bother with refuting an argument briefly when he can instead deconstruct it into all of its 250 components and analyse them one by one. The consistency of thinking which he applies to each subject he addresses is particularly impressive. If you like quick posts that can be processed in a moment, Hays isn't for you. But if you want to see the detailed and comprehensive dismantling of an opposing position, and have time for it, then Hays is frequently devastating.

Here's one of Hays' recent posts in which he analyses Douglas Futuyma's textbook "Evolution". It is a veritable guided tour and controlled demolition of many of the common fallacies and misrepresentations of anti-creationist and anti-ID writers.

http://triablogue.blogspot.com/2007/07/in-search-of-evolution.html

David

A Basis for Intelligent Design Predictions

A comment at Telic Thoughts inspired this post. TTer Bilbo made the following remark (in red):

"If we have a property that is closely associated with intelligence, such as language generation, or (what appears to be) the purposeful assembly of parts, and the phenomena reaches such a degree of improbability that to deny intelligent causes is incredible, I think we can have justified belief that the phenomena was intelligently caused, regardless of a lack of hypotheses about the mechanisms used, or the nature of the designer."

It appears as if Bilbo is citing two phenomenon for which there are obvious parallels to intelligent causality namely, linguistic similarities between human languages and biological genomes and a purposeful assembly of parts common to man made machines and cellular structures.

This comment was made in response:

"If you aren't forming and testing empirical predictions that distinguish the claim from other such claims, then you aren't doing science. As the vast majority of scientists disagree with you that "to deny intelligent causes is incredible", you should look to your own position very skeptically."

The second sentence can be taken with a grain of salt. There is no data excluding intelligent causality as an explanation for the origin of life. When scientific data is inconclusive the statement of any scientist can be viewed as a personal opinion.

The first sentence is more compelling in emphasizing that a capacity to predict is an indicator that a proposed theory is scientific. That leads me to the point of this post. Any pathway to life, invoking an unguided series of chemical reactions that culminates in a cell, must envision a gradual, incremental process involving successive changes that approximate ever so closely a functional cell. This type of process, when combined with studies intended to determine the range of a minimal genome, offer clues as to what type of conditions would support the view that life was the outcome of an intelligently designed process.

There are cellular functions which are intrinsic to cellular viability. A capacity to replicate would be basic to an evolutionary process. That, in turn, would entail at a minimum, some sort of genomic structure able to store genetic information, mechanisms that ensure genomic integrity, mechanisms that allow for the expression of the genetic information, mechanisms that enable genomic replication and mechanisms enabling the metabolism of cellular constructs and a means of generating energy.

Minimal genome concepts raise the question of what level of genetic complexity would be sufficient to allow for genetic changes and environmental adaptation? A related question is could that level be attained through a gradual incremental process? Minimal genome experiments could provide empirical answers. The approach would be a top down one seeking an answer though the simplification of existing genomes. There have been studies with results of interest. 'Essential genes of a minimal bacterium' is an example as is 'The complexity of simplicity.'

Experiments indicating that life is not viable when the number of coding genes falls below a certain threshhold would constitute evidence that a gradual, incremental process is an implausible life generating strategy. That would also be evidence for intelligent design. Predictions of threshhold levels would constitute the empirical predictions demanded by the ID critic.

A plug - raising money for education in Africa

This post is a commercial break. Our IntSeq overlord did tell me to blog about whatever I liked, so here we go!

Later this year I'm hoping to run my first marathon, and raise money to fund teachers and schools in a very under-developed part of Kenya (no electricity or water, terrible roads). A little money in that particular place will go a long way. Investing in children's education is one of the most effective to help people in places like these. Can you help?

I'm digging for water. I'd rather go to school!

I have a website up with more information (including dozens of photos), and can take debit/credit card donations securely, and re-claim gift-aid to boost the value of UK gifts by 28%. Please consider donating what you can, and passing on this link to anyone and everyone you know who has an interest in Kenya, development and/or education. Link me from your blog, pass it on to e-mail lists, mention it on your website, print it out - whatever you can. My goal is to raise £10,000; we have 3 months - let's go for it!

http://david.dw-perspective.org.uk/marathon

Please educate us! Go here!

David Anderson

Cosmic Jackpot

I got hold of the book Cosmic Jackpot by Paul Davies. I'll focus on a very small section of it for the purpose of this post. In chapter 9 (Intelligent and Not-So-Intelligent Design) there is a subsection entitled God as a Necessary Being. In a somewhat unorthodox manner Davies broaches the who designed God or who designed the designer question. Davies correctly identifies God as having unique properties including an existence that is not owed to a preexisting cause. Davies then goes on to describe God as a necessary being making it logically impossible for God not to exist. Dwelling on the word necessarily, Davies cites God's choice to create the universe as logically problematic; asking if a necessary being can behave in a way that is not necessary?

Although generally a precise thinker Davies allows linguistic ambiguities to guide his own analysis. God's actions are not necessary in the sense that God's behavoir is predetermined by causal necessity. There is no reason to assume an absence of divine freedom of choice.

Logical difficulties are inherent with accounts of beginings- at least from the perspective of finite human minds. Conceptual difficulties are inherent to differing and conflicting accounts of origins. Those who find logical difficulties with a God, who preexists the universe, could find logical difficulties with alternative explanations if they look for them. For example, assume there is no God. There is, however, a universe and attempts to account for its existence lead to infinte regress arguments. If the universe is attributed to a big bang then what caused the big bang? If the big bang was preceeded by a singularity and specified conditions then what led to this and so on. When confronted with the alternative, a God who existed prior to and outside his created universe, no longer can be seen as entailing uniquely difficult conceptualizations.

Does all this mean we can know God through human reason alone? No, but God can and has revealed himself to us. The seal of credibility was the resurrection of the Son of Man.

Recovering Genomic Information

If causes of genomic decay go unchecked is there any way to recover the original sequencing patterns for long dead specimens? The answer appears to be yes according to 'Molecular breeding of polymerases for amplification of ancient DNA.' A promising method exists, according to the authors of the linked abstract from Nature Biotechnology, which notes that DNA lesions accumulate unless repaired. Death stops repair but not the accumulating lesions. Accumulating lesions have implications for DNA found in connection with paleontological, archaeological and forensic endeavors.

Around the Blogosphere 7/16/07

http://bcse-revealed.blogspot.com/2007/07/recommendation-and-few-odds-and-ends.html

More on the BSCE Revealed from David Anderson


http://www.uncommondescent.com/intelligent-design/barbara-forrest-up-to-her-old-tricks/

The Real Wedge Threat


http://www.uncommondescent.com/intelligent-design/programming-and-the-development-of-life/

Life was Programmed


http://www.uncommondescent.com/intelligent-design/miller-the-malignant/#more-2504

Ken Miller and Gutter Sniping


http://www.uncommondescent.com/informatics/paper-and-website-the-jesus-tomb-math/

A Rational Approach to Irresponsible "Journalism"


http://post-darwinist.blogspot.com/2007/07/edge-of-evolution-significance-of.html

More from Denyse O'Leary on Behe's Edge of Evolution


http://www.newcreationism.org/2007/07/internal-clock-external-light-regulate.html

Signaling and Plant Growth

Taking an Axe to the Tree of Life?

Is the tree of life a hindrance to good science? That's the opinion of Dr. Ford Doolittle of Dalhousie University whose views are discussed here. Quoting from the link (in red):

"What’s the danger in believing that all beings of the same class, living and extinct, derive from a single figurative “tree” and its branches?

“It’s not true, that would be the main danger. It misleads us,” says Ford Doolittle, Dalhousie’s Canada Research Chair in Comparative Microbial Genomics."

He does not mean it is not true because he does not want to believe it but rather that it does not accord with the evidence. More from the link:

"Current research is finding a far more complex scenario than Darwin could have imagined, particularly in relation to bacteria, archaea and one-celled organisms. These simple life forms represent most of the earth’s biomass and diversity, not to mention the first two-thirds of the planet’s history. Many of their species swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers from multiple sources."

Horizontal gene transfer has been discussed at Telic Thoughts. Joy has weighed in on this repeatedly in comment sections.

What is the "Fine Tuning" argument?

Some of the other guys on this blog have forgotten more biology than I've ever learned. I hope, though, that I can bring something else to this blog. I want to carry on some discussion of some of the logical arguments used in the intelligent design debate that I hope everyone can profit from.

Last post I talked a little about the "God of the gaps" fallacy, which isn't always as fallacious as materialists suggest. This time, I want to talk a little about "fine tuning". Here again, materialist apologists are misrepresenting what's being said - and missing the point.

Fine Tuning

Within what bounds is life possible? What are the ranges of values that various physical constants must exist within for us to exist? This is the "fine tuning" question. Let me borrow a few examples from another web site to give you an idea of some of the facts involved:

• The electromagnetic coupling constant binds electrons to protons in atoms. If it was smaller, fewer electrons could be held. If it was larger, electrons would be held too tightly to bond with other atoms.~
  
  
• Ratio of electron to proton mass (1:1836). Again, if this was larger or smaller, molecules could not form.
  
  
• Carbon and oxygen nuclei have finely tuned energy levels.
  
  
• Electromagnetic and gravitational forces are finely tuned, so the right kind of star can be stable.
  
  
• Our sun is the right colour. If it was redder or bluer, photosynthetic response would be weaker.
  
  
• Our sun is also the right mass. If it was larger, its brightness would change too quickly and there would be too much high energy radiation. If it was smaller, the range of planetary distances able to support life would be too narrow; the right distance would be so close to the star that tidal forces would disrupt the planet's rotational period. UV radiation would also be inadequate for photosynthesis.
  
  
• The earth's distance from the sun is crucial for a stable water cycle. Too far away, and most water would freeze; too close and most water would boil.
  
  
• The earth’s gravity, axial tilt, rotation period, magnetic field, crust thickness, oxygen/nitrogen ratio, carbon dioxide, water vapour and ozone levels are just right.
  
  (http://www.creationontheweb.com/content/view/3841)

Impressive, is it not? The most memorable quote that sums the situation up is from eminent Cambridge physicist Fred Hoyle: he said that it appeared as if "a super-intellect has been monkeying with physics". The set-up seems rigged.

The question is, is this a valid argument? Many materialist apologists strongly argue that it isn't, and pour scorn on the fools who disagree. Here I include a quotation from blog of "the atheist experience", a "weekly live call-in television show sponsored by the Atheist Community of Austin." Here's what they think:

The whole assumption about fine tuning is a fallacy called affirming the consequent, or arguing from your conclusion. ... Douglas Adams goofed on this in a now-immortal passage in his Hitchhiker's Guide to the Galaxy series.

". . . imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in, an interesting hole I find myself in, fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!'"

http://atheistexperience.blogspot.com/...godandscienceorg-part-1-of.html

I like the illustration - it makes the point very well. Because we are here, therefore we know that the right conditions for us to be here must exist, therefore the discovery that those conditions do in fact exist proves nothing. The probability of making this discovery is 100%. Ta-dah! Cue atheist victory lap.

Hang on a minute...

If you've been concentrating really hard, though, you may have noticed that Adams' objection makes a subtle switch in the calculation being made. Adams' illustration uses this calculation:

P ( the conditions exist for life | life exists)

i.e. "The probability that conditions are tuned for life, given than life exists". As the event space being considered is completely included within the event space that is given, the answer is certainty, and the calculation is not particularly useful. Life is known to exist, so calculations about its probability have no value. The interesting calculation is to look at how narrow the boundaries are for the various conditions that make life possible.

As scientists seek to discover the extent of these boundaries, the possible results have two extremes:

1. There are very wide ranges of conditions within which life is possible.
   
   
2. The range of conditions within which life is possible is very small.

If you've got that point, you'll see where Adams went wrong. The question isn't "is life possible?" - we know that the answer to that is "yes, with absolute certainty". The question is "was life very possible, or rather unlikely, or somewhere in between?".

Imagine that a man tosses a coin 500 times, and I call out "heads, tails, heads, heads, tails", etc., to give a sequence 500 guesses long. Suppose that after I do so, a man hands me a prize. What did I get the prize for? You don't know, so you do some investigating.

Suppose that I got given the prize for getting more than 50% of my guesses correct. That's not massively impressive, is it? But suppose rather that you discovered that the prize was only given to me because I got 100% of my guesses correct. That would be staggering. The chances of doing that are about 1 in 3 * 10^150 - an incredible number, beyond the number of atoms believed to exist in the universe.

If we keep in mind Adams' illustration, then Adams has said: "he's got the prize, so we know that he guessed up to the necessary standard - so it proves nothing". Actually, though, the question is to find out what room for error I had in order to get that prize. What we then find out is that "to get the prize was phenomenally unlikely - I suspect someone's monkeyed with the coin".

Looking More Closely At The Outcome

Look at those two extremes for the outcome again. The first is that scientists might discover that there is a broad range of circumstances within which life would be possible. What would this prove? Would it indicate that life arose by chance?

In fact, it would prove nothing. A wide range allows both that life might have arisen by chance, or might not - you have to look elsewhere to find out which. If I score a tap-in in a game of soccer, I might be a soccer genius; or I might not; you'll never know - the evidence can't decide.

On the other hand, if scientists discover that the range within which life is possible is extremely small, then this is positive evidence for intelligent design. The point is not that the system is fine-tuned (as in Adams' mistake); the point is that the fine tuning was absolutely necessary. If I take ten free-kicks in soccer from long distance and curl them all into the top corner, then the thesis that "David can't play soccer" takes a severe beating. (I can always dream!).

The signficance of this is that the "fine tuning" argument is valid, puddles notwithstanding. The discovery that life requires extreme fine-tuning is a highly significant piece of evidence. Science is turning up more and more evidence that our world is intelligently designed.

David Anderson

Advancing Efforts to Decipher a Chromatin Code

A Science Daily article entitled New Method For Reading DNA Sheds Light On How Cells Define Themselves reveals how a technological advance, that sequences DNA, is facilitating our understanding of functions associated with chromatin. The Broad Institute of MIT and Harvard issued a news release related to a published paper (Mikkelsen et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature; DOI:10.1038/nature06008). The article's first paragraph:

"As a fertilized egg develops into a full grown adult, mammalian cells make many crucial decisions -- closing doors of opportunity as they adopt careers as liver cells, skin cells, or neurons. One of the most fundamental mysteries in biomedicine is how cells make such different career decisions despite having exactly the same DNA. By using a new kind of genomic technology, a new study unveils a special code -- not within DNA, but within the so-called "chromatin" proteins surrounding it -- that could unlock these mysterious choices underlying cell identity."

Chromatin has been known to have a genomic packing function but it is also known that the location of chromatin proteins affects gene expression. Chromatin regions known as bivalent domains indicate control regions of key genes involved in expression. Analyses of bivalent domains enables one to get both a history and a prediction of future gene activity. This in turn has implications for developmental biology. The mapping of chromatin could help identify RNA producing genes in addition to those encoding proteins.

DNA Polymerase Epsilon and Genomic Stability

NIEHS researchers identify enzyme critical in DNA replication is an article focused on the importance of DNA polymerase epsilon in the replication of DNA. You can read the full but brief article at the link.

Researchers working with yeast discovered that: "DNA polymerase epsilon was found to be a key determinant of genome stability and of cellular responses to DNA damage resulting from exposures to environmental stress." Advances in our understanding of the role of replicating enzymes can help elucidate other mechanisms involved in maintaining genomic stability. These include identifying detailed functions of other polymerases having essential roles in making replication fidelity possible. One of the primary themes of this blog is emphasizing the essential nature of genomic repair mechanisms which are critical to our understanding of mutations and, of course, any natural selection process dependent on mutations to generate adaptive responses.

A UD Exchange Over 'Edge of Evolution'

There is a lively exchange ongoing at Uncommon Descent over Behe's new book 'Edge of Evolution.' Ken Miller, the honest Darwinist, is the name of the post authored by Sal Cordova. Sal takes Miller to task for his dishonest statements directed at Behe.

There are many commenters who include Sal, a critic of Behe who goes by the moniker of JAM and Jehu, an effective defender of ID, who I've noticed at both UD and TT. Much of the exchanges center around chloroquine resistant malaria. Here is a sample comment by Jehu:

"Wrong again. Here is what White says, “This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10^20 parasite multiplications .” Notice JAM that is “per-parasite probability.” White distinguishes between “developing resistance” and the “de novo selection of resistance.” The calculation of the per parasite probability of developing resistance 10^20 is based only on the population of malaria in people who are sick, where probability of selection of de novo resistance is very high. As White states, “Taken together, the balance of evidence strongly favors acute symptomatic infection as the source of de novo antimalarial resistance.” Gametocytes carrying the resistance genes reach transmissible densities when the resistant biomass has expanded to a population size close to that necessary to produce illness (>107 parasites). Furthermore the relative fitness of CQR strains is .76 or .85, so it is not immediately deselected for lack of fitness in an environment without selective pressure for CQR. At any rate, Behe offers 10^20 as a rough estimate only so your is completely de minimas.

You started off accusing Behe of claiming that CQR always required mutations at 76 and 220. When it was pointed out that Behe said “almost always” you claimed Behe contradicted himself. When Sal asked you to produce a quote where Behe contradicted himself you dishonestly cited pages that said nothing of the sort. When I called you on your pitiful lies you changed your story"

Criticism of Behe has been over the edge. Separating accurate critiques from the inevitable dishonest carping is something that regretably will be, for the most part, the exclusive preserve of ID blogs.

A Biological Revolution

The RNA revolution; Biology's Big Bang, an article from 'The Economist,' makes an analogy between recent scientific history and present day developments by comparing 20th century physics to 21st century biology. The driving force behind the biological revolution is identified as RNA. Just as momentous technological and social changes resulted from advances in 20th century theoretical physics, the same is anticipated for the biological revolution.

In fact vital technological innovations, centered around RNA, which affect research and medicine, already have taken place. RNA interference plays an important role in the business of many biotechnology firms. One well known biotechnology enterprise states the following at its website:

"Long double-stranded RNAs (dsRNAs; typically >200 nt) can be used to silence the expression of target genes in a variety of organisms and cell types (e.g., worms, fruit flies, and plants). Upon introduction, the long dsRNAs enter a cellular pathway that is commonly referred to as the RNA interference (RNAi) pathway."

This silencing tool can identify previously unknown biological functions and helps to pin down interactive biochemical relationships.

New evidence indicates that the generation of RNA is more common than previously believed. Even our concepts of origin could be affected by the dynamics of RNA and the resulting knowledge it leads to. These developments are worth watching.