The Tyranny of Evidence: Do Scientists Use Dogma?

Is evolution a religion? Should we describe the positions of scientists as dogma?
Is science democratic? Isn't there room for debate on the issues of science?
Why can't we teach both sides? Isn't that good science pedagogy?

Here's some links to additional information
1. [Neutral] Aquatic Ape Hypothesis (AAH)
2. Critical of AAH
3. Favorable of AAH

4. [Neutral] Endosymbiotic Theory (EST)
5. Critical of EST
6. Favorable of EST

7. [Neutral] for Intelligent Design
8. Critical of Intelligent Design
http:// Entire scientific community / (hah, joke!)
9. Favorable of EST

[jfedgar]

@longfootbuddy C0nc0rdance 

"scientists care about keeping their jobs, and the funding rolling in...much like religious leaders"

Most scientists work in academia or research centers where they make half of what they could make in private industry working on more immediately practical applications. Instead they spend their time doing "basic research" at jobs that are much more stressful and pay significantly less.

Why do they do this? Because they love science. Because they love discovering new things that are TRUE about our world. It would be kind of a pointless endeavor if they fabricated things intentionally, which is way that is very very rare in a profession that encompasses millions of people. If it were about the money, they would be much wiser to go into private industry and make twice as much money with half the stress.

[Cncrdance]

There is a branch of bioinformatics dealing with genetic information. In simulations, and in practical experiments, the information contained in a population can increase spontaneously (without outside intervention).

The term is Shannon entropy. Information is measured in bits.

You should look this up and educate yourself. The work of Tom Schneider at the National Cancer Institute has been very thorough. On his site, you can even run a simulation and see how it works.

[JimDeferio]

"Evidence" always has to be interpreted. Evidence is interpreted by one's worldview which is a network of presuppositions that are not testable by science. I have assembled 17 presuppositions of science from several sources.

1) the existence of a theory-independent, external world (in other words, the world doesn't have to conform to our theories but there is a REAL world out there and our theories must conform to this real world)

2) the orderly nature of the external world 

3) the knowability of the external world (this is person related)

4) the existence of truth (this is fact related)

5) the laws of logic

6) the reliability of our cognitive and sensory faculties to serve as truth gatherers and as a source of justified true beliefs in our intellectual environment

7) the adequacy of language to describe the world

8) the existence of values used in science (e.g. scientists should "test theories fairly and report test results honestly")

9) the uniformity of nature and induction (the regularity of order - this is different than #2). The spatial uniformity, the temporal uniformity, as well as the continuation of laws of nature into the future.

10) the existence of numbers

11) the law of causality (Norman Geisler includes this as one of the laws of logic but others see it as separate)

12) contingency of the universe

13) desacralization of the universe (for the Hindu, the universe is part of the divine)

14) methodological reductionism (Occam's Razor - though I think this is sometimes taken to far as if it were a law and not merely a presupposition)

15) value of scientific enterprise

16) falsifiability (philosopher of science Karl Popper's gift to the scientific community)

17) principle of analogy 

Please note that there is some overlap among these 17 presuppositions. Sources for these were: Dr. Neil Shenvi (Duke Univ. - Physics & Chemistry), Dr. Norman Geisler (Christian apologest & philosopher), Dr. William Lane Craig (Biola Univ.- apologist & philosopher), Dr. JP Moreland (Biola Univ. - apologist & philosopher), Dr. Phil Fernandez (apologist), and one from me. I added a bit of explanation on some  

[Cncrdance]

What happened was a general receptor for several cortisol-like molecules became more specialized through a series of random mutations that led up to a key amino acid change, resulting in a new conformation.

For it to go backwards, to the general form, AT ALL THE SAME LOCATIONS, there would need to be a series of random mutations that are unselected. This is unlikely because there is nothing to enrich for the reverse mutants.

But a new receptor could arise from a pseudogene to do the job.

[Cncrdance]

"science is without foundation"

Again, you seem unable to keep straight the philosophy and methodology of science. You are using epistemology to attack methodology.

Let me say this slowly, so you will understand:

The METHODOLOGY of science uses TESTING of MODELS of the NATURAL WORLD against EVIDENCE.

Philosophy of science covers what CAN BE TESTED, and WHAT LOGICAL TOOLS are available.

We do not answer philosophical questions with discussion of methodology, and vice versa. Got it?

[Cncrdance]

"If you take any 2 amino acids and switch them, the overwhelming probability is that the resulting protein will not perform the original function."

That's a testable proposition! Excellent.

Will you agree that if that is NOT the case, you will retract this argument and admit that you are wrong on this one point?

[Cncrdance]

I said "dozens of other characteristics". I didn't mention the hymen either... for obvious reasons.

Make sure you visit the site mentioned in the description under "Critical of AAH". It certainly took the wind out of my sails.

[Cncrdance]

"I know from first hand experience that something is very off."

Really? You've been a reviewer for a major scientific journal? Which one?

[Cncrdance]

And I responded "in bits" by Shannon Entropy.

What is so hard to understand about this:
Gene duplications happen all the time. Eventually, the unconstrained drift results on two genes that differ from each other. We've seen this happen in gene families like TNFAR. Some genes even appear to be the result of endogenous retrovirus integration.

Why are you limiting yourself to RM and NS? There are dozens of other forces acting on allelic frequency and genetic diversity.

[Cncrdance]

(2/2)
changing back to a particular moment in time once other mechanisms have come to rely on it, and the reverse situation. What is the chance that ANY protein does a particular function in ANY way.

For example, glucocorticoid receptor. It can't alter function without causing strong effects in the cell, but a related gene, pseudogene, or non-coding sequence could.

His mistake is in presuming that a SPECIFIC set of events is the ONLY set of events that can lead to a given outcome.

[Cncrdance]

I think most of the needed physical evidence relates to distribution of protohominid fossils.

Are they found primarily in regions that were shallow seas and lakes? Can we find collections of fish and shell fossils nearby? Can we overlay the movements of these hominids with shores and shallows?

There's also going to need to be some modeling data for predation and foraging rates, ecological data on savannah vs. lake at that time period, and physical adaptations and nutrition.

[IDtaksovr]

" mere causal observation reveals that a protein is an interacting whole, the function of every amino acid being more or less (like letters in a sentence or cogwheels is in a watch) essential to the function of the entire system. To change, for example, the shape and function of the active site (like changing the verb in a sentence or an important cogwheel in a watch) in isolation throughout the molecule, destabilizing the whole system and rendering in useless. -Evolution: A Theory in Crisis.

[tehKapw]

@Aresftfun the point of that comic (the caption) was cropped... but basically "it's easier to run the cartoon gauntlet than to survive the peer review process".

[Cncrdance]

@GSFY
Take XMRV, a virus that is implicated in prostate cancer. It's closely related to a mouse endogenous virus. I'm basing an assay on the mouse virus, using it as the standard. We're also trying to uncover whether this is a mouse virus that jumped to humans, or a broken viral sequence that was inherited from a shared ancestor with mice.

I used to do a lot of disease association studies and bioinformatics. Both are entirely based on the mathematics of evolutionary biology.

[Cncrdance]

@GSFY
"algae that formed into clusters when an attacking organis [sic]"
You mean that the environment affected the frequencies of alleles in a population over time?! What would happen if that change continued to happen for a few million years?

What prevents adaptive changes from accumulating? What if two halves of one population face different environmental pressures?

[Cncrdance]

I'm not sure there is a sharp line between those two terms. I work with DNA, RNA, and sometimes protein. The techniques I use are molecular biology methods, and the goals are either viral or cancer related. I don't have the same level of specialization or control that an academic researcher would. I work on projects assigned to me that usually result in a diagnostic test. Sometimes I participate in team research or development, or optimize methods for others.

[Cncrdance]

It's not a strawman. It's what the word irreducible MEANS. "Impossible to be made smaller or simpler." He's using it in place of "interdependent".

What force prevents two genes from fusing? What keeps a nuclear GTPase from fusing with a transmembrane domain? If four parts of a new structure are already present, and we know these things fuse or transpose all the time, the real question to Behe is what force prevents the observed, natural process from happening?

[Cncrdance]

From Wikipedia:
"In modern usage, particularly in the United States, Darwinism is often used by creationists as a pejorative term."

I don't care what Dawkins uses. Evolution is the name of the scientific theory, and while it owes a debt to a 19th century naturalist, it's not ABOUT Darwin or his views. It's a theory built on observations of the natural world.

As I have indicated, we do not refer to people who accept a scientific theory as "-ists".

[Cncrdance]

@GSFY
Humans didn't evolve from fish. Humans shared an ancestor with modern fish. No fish has ever become a non-fish.

Humans and fish are both chordates. Our last common ancestor was almost certainly an early chordate. If that is true, we should see genetic homology in conserved chordate genes. For example, the homeobox proteins that induces bony spine formation during development.

It's called Lhx3. It's an 85% match in zebrafish. Your spine and a fish spine are made by the same gene.

[Cncrdance]

"This [modern evolutionary theory] is an immensely impressive and powerful theory."...
"All scientific theories are conjectures, even those that have successfully passed many severe and varied tests."
--Karl Popper

Again, his work was on Demarcation and the Inductive Problem. This is basic philosophy and rationalism. The procedural contribution he made was against justification and towards falsification to avoid inductive fallacy.

ID's negative case is an example of inductive fallacy.