Monday, December 04, 2006

"Genetics and Molecular Biology", by Robert Schleif, 1993

This is a graduate level textbook used at Johns Hopkins University to teach basic concepts of molecular biology that are extended to many other disciplines. It has a considerable Physical Chemistry and Organic Chemistry component which would make it intimidating for the large majority of biologists, but this subject is really foundational to understanding the molecular foundations of genetics. The book also goes a bit into how this relates to proteins and the various other things that drive life.

I bought this book mainly to test the theory that Darwinism was necessary to understanding biology and that it was an obvious deduction based on the structure of DNA. Getting away from the popular literature, I wanted to know to what extent Darwinism was either driving the theory or derived from the theory at the foundational molecular biology level as an actual graduate level molecular biologist would know. The answer was pretty much what I expected: There were a few, rare, single sentence exclamations thrown in (Holy Darwinism, Batman!), but otherwise, the connect was entirely missing. As I suspected, the modern invoking of DNA and molecular biology in support of Darwinism was merely BS. To further support my contention, professor Schleif routinely invokes factories and computer information concepts (intelligently designed all) to help in understanding the basic concepts, whereas Darwinism is entirely absent.

The next question is why would scientists have deliberately made such false statements about the Darwin-molecular biology link? My hypothesis is that the field of molecular biology is simply not understood by the majority of biologists and thus pretty secure from rational debate by laymen. By claiming that this discipline (which they probably don't understand either) proves Darwinism and that Darwinism is vital to understanding molecular biology, the Creationists can be silenced, humiliated and put in their place by simply invoking superior knowledge. More malpractice?

44 comments:

Doppelganger said...

Ah - another creationist engineer pontificating on matters he thinks he understands better than he does.

I do wonder why arrogance is so common a trait in creationists with engineering backgrounds?

So, you read a text and don't see a link to "Darwinism." Did you see a link to Dembskiism? Johnsonism? Beheism?
No? Probably not. I did, however, use molecular biology when I did my graduate research on the evolution of Primates. And understanding the tenets of "Darwinism" as you call it certainly helped explain the results I got.

LK said...

LOL

No references to 'Darwinism' in a genetics text book from 1993.

You creationists crack me up.

In '93 our lab was still doing gel slab sequencing and doing water bath PCRs. Good times.

Maybe a first year course on the history of evolutionary science, Neo-Darwinism, and the modern synthesis would help you put such a book in context. Then read a post-genomic genetics text book. Then go to pubmed and search for comparative functional genomics.

Maybe then you'll finally work out what the limited term 'Darwinism' actually means.

But I doubt it.

LK said...

Actually here is a better idea, read this book

Molecular Evolution: A Phylogenetic Approach [ILLUSTRATED] (Paperback)
by Roderic D. Page, Edward C. Holmes

It's 1998, so it's keeping up with the retronesh of your previous example.

Unfortuantely it's $91, but it's definately worth it

Looney said...

Hmmm. If I recall correctly, Darwinistas has been claiming for nearly 150 years that "Evolution" is a proven fact and only a reeetard would disagree. For almost 100 years they have claimed that biology is impossible to understand without FAITH in Darwinism. Y'all are always invoking something new to justify the claims of an earlier generation when they show up as having been baseless.

Smokey said...

"I bought this book mainly to test the theory that Darwinism was necessary to understanding biology..."

Darwinism is used as a historical term. Your use of it to describe modern scientists and what they think reveals your mindless indoctrination.

"... and that it was an obvious deduction based on the structure of DNA."

Where did you find that?

"Getting away from the popular literature, I wanted to know to what extent Darwinism was either driving the theory or derived from the theory at the foundational molecular biology level as an actual graduate level molecular biologist would know."

An actual graduate-level molecular biologist wouldn't use the term "Darwinism." She'd use terms like "drift," "homology," "Clustal," "tree," etc.

"My hypothesis is that the field of molecular biology is simply not understood by the majority of biologists and thus pretty secure from rational debate by laymen."

That's just laughable, as the majority of biologists ARE molecular biologists.

"By claiming that this discipline (which they probably don't understand either) proves Darwinism..."

Dude, Darwin was shown to be wrong about some things (especially by molecular biologists), but right about most things.

Your use of the term "Darwinism" demonstrates your ignorance, Looney.

Smokey said...

"If I recall correctly, Darwinistas has been claiming for nearly 150 years that "Evolution" is a proven fact and only a reeetard would disagree."

Correct. This is because evolution is easily observed and Darwin and MET were about the mechanisms of evolution, a pertinent distinction that is unable to be grasped by your steel trap of a mind.

"For almost 100 years they have claimed that biology is impossible to understand without FAITH in Darwinism."

I don't recall anyone making any such statement about FAITH. Perhaps, since you claim there is a 100-year history, you can offer a few instances of this instead of simply asserting it as a matter of YOUR faith?

Looney said...

Well Smokey, I brought up the scientists of ~150 years ago because everyone knows their knowledge of biology was essentially the same as Moses had and they were obviously liars in claiming that evolution was obvious and provable. They invoked their credentials to prove their word while knowingly making false statements. Nothing has changed in science or high-tech. Corruption is everywhere.

Smokey said...

"Well Smokey, I brought up the scientists of ~150 years ago..."

And you grossly misrepresented their positions.

"... because everyone knows their knowledge of biology was essentially the same as Moses had and they were obviously liars in claiming that evolution was obvious and provable."

See, you're simply impervious to the fact that Darwin and MET are about MECHANISMS of evolution. Evolution is both obvious and observable. Are you really so dense as to not grasp this distinction, Looney?

"They invoked their credentials to prove their word while knowingly making false statements."

You seem to be projecting. This is ironic, given that you are invoking your hopelessly irrelevant credentials to make false statments.

"Nothing has changed in science or high-tech. Corruption is everywhere."

Don't you mean, nothing has changed in the minds of those who blindly follow religion? After all, you can't even wrap your mind around the fact that modern evolutionary theory is about much more than Darwin, including ways in which he was wrong.

That would be a significant change from Darwin, but you are blind to it. Hell, you don't even realize that most biologists nowadays are molecular ones.

Looney said...

Smokey, I can only tell you what I have seen: Groups of smart people routinely make incredibly dumb decisions. If you wander the Dilbert cubicle land of Silicon Valley or Detroit or and to a lesser extent Japan (all of which I have done), you will see this. It is time to leave the fairy tale science we learn when we are young behind.

Smokey said...

"Smokey, I can only tell you what I have seen:..."

That would be a change, because so far, you're only telling me things that you haven't seen.

Are you admitting that you failed to comprehend the distinction between evolution and the mechanisms underlying evolution? It's pretty goofy for an engineer to miss a distinction like that.

"Groups of smart people routinely make incredibly dumb decisions."

But not as routinely as groups of dumb people do.

"If you wander the Dilbert cubicle land of Silicon Valley or Detroit or and to a lesser extent Japan (all of which I have done), you will see this."

That's nice, but those are engineers, not scientists. You demonstrated your ignorance about science when you didn't realize that most biologists are molecular biologists.

Your failure to admit your mistake says it all, Looney.

"It is time to leave the fairy tale science we learn when we are young behind."

I DO science, Looney. I also work to improve science education of today's children, so they understand something you clearly don't--how science works by generation of new data in the testing of hypotheses, not scanning textbooks for outmoded words.

Looney said...

Smokey, engineering = science + intelligent design. If you want to teach that intelligent design is impossible, fine. We will just continue to hire new engineers from China, Taiwan and India.

Smokey said...

"Smokey, engineering = science + intelligent design."

Thanks for revealing the simplistic nature of your mental processes.

"If you want to teach that intelligent design is impossible, fine."

That has got to be one of the most lame straw men I've ever seen. Do you think that it will divert a reader's attention from your other falsehoods? From your inability to distinguish between evolution and the mechanisms that underly it? Or your inability to distinguish between a hypothesis and a theory in your original post?

"We will just continue to hire new engineers from China, Taiwan and India."

If you're representative of engineers from the US, we'll all be better for it.

For the record, I intelligently alter protein structures, and my choices are informed by MET. IOW, I do engineering and design within my science, so your equation is simply laughable.

Looney said...

'"Smokey, engineering = science + intelligent design."

Thanks for revealing the simplistic nature of your mental processes.'

Would you want the person who engineered your car safety systems to apply a different definition?

Smokey said...
This comment has been removed by a blog administrator.
Looney said...

Perhaps the way to do nuclear power plant design is to build multiple deisgns and see which ones melt down and which ones don't?

Smokey said...

Absolutely! I demand testing and selection after intelligent design, because intelligent design is insufficient. That's another reason why your equation is laughable.

IOW, I'd expect those engineers to do extensive selection from among multiple design candidates, as well as multiple recursions through successive design modificatons. In fact, I do screens (selections) in my science when I lack sufficient information for design.

Do you realize that selection is the all-important, highly nonrandom component that's omitted by the multitude dishonest creationists who misrepresent modern evolutionary theory as merely "random chance"?

Looney said...

I am happy to leave the argument here.

Smokey said...

"Perhaps the way to do nuclear power plant design is to build multiple deisgns and see which ones melt down and which ones don't?"

That's why we don't trust their safety, Looney--we can't do that. However, I'll bet that if you polled a bunch of people if they'd be more comfortable living next to a nuclear power plant if the faulty designs were first rejected by testing elsewhere, the approval would soar.

No wonder you're a creationist--you miss the obvious.

Smokey said...

"I am happy to leave the argument here."

I understand completely. ;-)

LK said...

Looney's claim that engineering is science + intelligent design (despite numerous times where smart people make poor design choices leading to disaster), highlights the fact that he hasn't thought very much about what entails intelligent design.

Male nipples, vestigal limbs, cancer, blindness, baldness, extra toes, exposed skin to UV radiation etc etc etc

The list of poorly designed features in man alone is astounding (and I haven't even commented on genetics and wonderful world of recombination). These features of man are poorly designed, suggesting an unintelligent designer or at least a designer who wasn't 100% when he designed us. And yet we are supposedly in his image.

Humans make mistakes in engineering designs all the time: Titanic, the space shuttles, bridge failures, the Ford Pinto to name a few.

If God is perfect and man is fallible, then surely by using the principles of intelligent design (where no single designer is actually implicated) then the poor design of all organisms on this planet suggests that man designed everything including himself. Or aliens. Those pesky aliens. At least God gets off the hook here by doing a botched job.

And yet if you apply an evolutionary framework to these poorly designed features you can begin to answer why we seem to have so much bad luck in the design stakes.

It's a shame that Looney as an engineer hasn't identified poor design choices in the human body, but then engineers arn't biologists so I shouldn't expect him to.

Looney said...

Two responses:

1) There are plenty of poorly designed features in Microsoft Products. Sadly, Intelligent Design includes Stupid Design and Incompetent Design as large subsets.

2) One of the most dangerous things to do is to change a program that you think has a stupid design in it when you don't fully understand what the program does. (Speaking from experience.) Thus, the argument of "poor design" to justify evolution is founded on ignorance. A thousand years later, biologists might understand enough to make such pronouncements.

Anonymous said...

Glad I'm not an engineer.

Smokey said...

"Sadly, Intelligent Design includes Stupid Design and Incompetent Design as large subsets."

How can a design be both intelligent and stupid at the same time, Looney?

"2) One of the most dangerous things to do is to change a program that you think has a stupid design in it when you don't fully understand what the program does. (Speaking from experience.)"

OTOH, as long as you have a selection process, you can make random changes in a program and end up with improvements.

"Thus, the argument of "poor design" to justify evolution is founded on ignorance."

I don't see how that follows from your claim that designs can be both intelligent and stupid.

"A thousand years later, biologists might understand enough to make such pronouncements."

Biologists understand a lot right now, but you can't be bothered to learn it. You think that scanning for a historical word that real biologists don't use to describe their positions is scholarship.

Looney said...

"I don't see how that follows from your claim that designs can be both intelligent and stupid."

It is because a stupid designer will still do better than trillions of generations of random perturbations via genetics. His bad design will involve simultaneous changes at multiple places in the program. This is what genetics can never replace.

Doppelganger said...

For almost 100 years they have claimed that biology is impossible to understand without FAITH in Darwinism.


You really should stop making things like this up.

Looney said...

You should read up on Karl Pearson. I did not make that up.

Anonymous said...

SO, Karl Pearson is making up these things?

Did you not read the actual Dob. quote, and did you not see that it says nothing like what you have been claiming?

And do you really, I mean REALLY - see no difference between the human 'intelligent design' that you refer to and the ID of the IDCreationism movement?

Smokey said...

"It is because a stupid designer will still do better than trillions of generations of random perturbations via genetics."

You're still persistently leaving off the important part at the heart of the creationist lies: it's not just random perturbations, it's SELECTION.

"His bad design will involve simultaneous changes at multiple places in the program. This is what genetics can never replace."

Sure it can. In fact, we can delete an essential binding protein, replace it with a random sequence, and using variation AND SELECTION, restore the binding.

We also can get enzymatically-active enzymes from antibodies, just by designing the selection, not the randomly-varying antibodies. You couldn't design an enzyme if your life depended on it.

Smokey said...

Looney,

Tell me something honestly. Is it honest and Christian to portray a process that involves random variation and selection as random variation alone?

How many times have you done that in this thread?

Isn't that bearing false witness?

Isn't there a Commandment about that?

How strong can your faith be if you have to resort to dishonesty when you perceive a threat to it?

Looney said...

Smokey, random processes come in many forms. GA as I have seen others implement it is always driven by a random number generator. Mutations are also random in nature, although certainly not uniform in distribution. Selection is simply the process whereby we choose the next generation. The engineer does this in GA using firm criteria. In nature, this is done statistically and constitutes one more level of randomness on top of the random mutations. i.e. the engineering GA is guaranteed to converge much faster than a natural GA.

There are no magical properties resulting from the genetics.

Smokey said...

"Smokey, random processes come in many forms."

I know. however, I was asking about your dishonest portrayal of evolution as mere random variation, omitting selection.

"GA as I have seen others implement it is always driven by a random number generator."

That's nice. How is it relevant to your omission of selection?

"Mutations are also random in nature, although certainly not uniform in distribution."

That's odd, because the converse is true in biology. The nature of mutations (transition, transversion, deletion, insertion, inversion, translocation) varies dramatically, while the locations at which they occur (with some exceptions for some of the rarer types) is the random component.

"Selection is simply the process whereby we choose the next generation."

No, that would be artificial selection, as in breeding dogs and horses.

"The engineer does this in GA using firm criteria. In nature, this is done statistically..."

Statistically? You're fabricating again.

"... and constitutes one more level of randomness on top of the random mutations."

Here's your problem, Looney--you're spectacularly wrong. Here you describe selection as random, when it is decidedly nonrandom. Of course, we have a nondarwinian random variation in nature in the absence of selection (drift), which is why your labeling of MET as mere "Darwinism" is so dishonest.

"...i.e. the engineering GA is guaranteed to converge much faster than a natural GA."

Guaranteed? Then why haven't engineers guaranteed a more rapid way to prevent viral diseases than vaccines, which cause the immune system to respond via random genetic variation (mainly recombination, only a little mutation) and selection?

"There are no magical properties resulting from the genetics."

I never claimed there were. I accused you of polemic dishonesty in omitting the power of selection.

You're the one desperately misrepresenting reality so that you can say that magic is the only alternative.

Smokey said...

"The nature of mutations" should be "The frequency of different types of mutations."

Looney said...

"I never claimed there were. I accused you of polemic dishonesty in omitting the power of selection."

There is nothing magical about selection either. Those with the most beneficial properties tend to survive.

Tend = random process.

Smokey said...

"There is nothing magical about selection either."

I never claimed that it was magical. I pointed out that it is both powerful and nonrandom. Observe its power the next time you don't die from a viral infection.

"Those with the most beneficial properties tend to survive."

True, but that is not selection. Selection is about reproduction, not mere survival. See the salmon?

"Tend = random process."

Tendencies are explicitly nonrandom, Looney.

No tendencies = random.

Looney said...

Smokey, much of the problem here is that Darwinists have projected the supernatural, intelligent design capabilities of God onto inanimate genetics. Thus, you must attribute supernatural powers to genetics (while denying such), which I don't.

This is why we have a problem with young engineers thinking that they will be able to do amazing things with GA. They are superstitious, unlike us more practical and worldly fundamentalists.

Smokey said...

"Smokey, much of the problem here is that Darwinists have projected the supernatural, intelligent design capabilities of God onto inanimate genetics."

Looney, you're just lying. Genetics is about inheritance. There's nothing supernatural about it.

Also, your use of "Darwinists" is simply dishonest.

"Thus, you must attribute supernatural powers to genetics (while denying such), which I don't."

False premises often lead to false conclusions.

You never have explained why you kept omitting selection, and why you claimed it was about survival, when in fact it is about reproduction.

Why would your misconceptions about modern biologists justify your rank dishonesty?

Looney said...

Smokey, since you seem to have an idea of what selection is that I don't comprehend, could you explain it to me? I will slow down and read carefully. Thanks.

Anonymous said...

Thus, the argument of "poor design" to justify evolution is founded on ignorance.


And what about the argument of "I just find evolution implausible for no real reason"?

If you are going to use 'design' as support for creation, then it is not ignorant at all to use bad design against it. If you people actually had evidence, you would not have to use such silly arguments. Of course, as you are not a scientist and have no experience in the sciences I guess we should expect you to know any better.

Anonymous said...

His bad design will involve simultaneous changes at multiple places in the program. This is what genetics can never replace.


You have not the simplest understanding of genetics whatsoever, that much is clear.


You keep avoiding my simple question -


Do you REALLY think that the human intelligent design of things like computer programs is the same thing as the Intelligent Design of the Intelligent Design Creationism movement?

Looney said...

Doppelganger, again, engineering = science + design. Not design - science.

High-tech isn't the result of ignoramuses.

"Do you REALLY think that the human intelligent design of things like computer programs is the same thing as the Intelligent Design of the Intelligent Design Creationism movement?"

Yes, and further, ID is far more basic to high-tech than Darwinism. If you can't do ID, a company would probably fire you for incompetence and they wouldn't care if you are a creationist or an evolutionist.

You said you "explained" something regarding the connect between apes and humans. Good. I hear conflicting explanations all the time. It means nothing unless you can do ID with your explanation. I have also seen a lot of worthless dissertations.

Smokey said...

"Smokey, since you seem to have an idea of what selection is that I don't comprehend, could you explain it to me? I will slow down and read carefully."

Wow! The first whiff of humility!

The bottom line is that selection is about reproduction, not survival. Survival only enters into it as a prerequisite for reproduction.

The best system to illustrate this without setting off the signals that close your mind is the immune system.

It works by random shuffling and mutation of antibody and T-cell receptor genes, followed by both positive and negative selection: those that recognize self are selected against (undergoing programmed cell death), and those that recognize antigens are selected for (they get signals to divide).

Most importantly, this example of random variation+selection is fully documented and is observable in real time--there is no way you can discount it as "just a theory," although I wouldn't put it past you.

Now, if you are correct in assuming that:

1) God designed your body, and
2) you are correct in concluding that
a) "the engineering GA is guaranteed to converge much faster than a natural GA."
b) "Ditto for genetics in life. The order of convergence on genetic algorithms is similar to a random search."


Coupling those assumptions with the incontrovertible fact that your immune system recognizes foreign antigens by a genetic variation + selection scheme, there are several obvious questions you need to answer:

1) Since God designed our immune systems to employ GA, is He stupid?

2) Are you smarter than God?

3) Finally, there's the empirical test:

a) There is a market for clinical diagnostic tests (pregnancy, HIV, etc.) in the hundreds of billions of dollars.

b) These tests work by leveraging the ability of animals' immune systems to produce antibodies that recognize vanishingly small amounts of a specific molecule in an incredibly complex mixture. (Mass spectrometry requires purification.)

c) These antibodies, derived by a GA, are the most expensive and labile components of such tests.

d) Therefore, if you are correct, you simply need to engineer an intelligent design that works better than His chosen Darwinian (in this case the term applies) method. Then you license it and will become one of the richest men in the world, if not the richest.

The question is, if you really believe your own claims, why aren't you or any other ID proponent doing that?

See if you can amp up the humility and answer these questions, since you've judged yourself to be superior to God as an engineer.

Looney said...

Smokey, the answer to your last was best done in a new post.

Anonymous said...

Doppelganger, again, engineering = science + design. Not design - science.

You said applied science + design.


High-tech isn't the result of ignoramuses.

I didn't say it was. Of course, neither is biology or geology or etc...



"Do you REALLY think that the human intelligent design of things like computer programs is the same thing as the Intelligent Design of the Intelligent Design Creationism movement?"

Yes, and further, ID is far more basic to high-tech than Darwinism.


Again with the non-sequiturs and nonsense.

I'm sorry, but I find it laughable that someone that implicitly sets themself as some sort of superintellect actually believes that an analogy is evidence.
How, pray tell, does the supernatural design of the bacterial flagellum impact 'high-tech'?



If you can't do ID, a company would probably fire you for incompetence and they wouldn't care if you are a creationist or an evolutionist.


You can't do ID either. You can do human id, but you cannot Design life. Why can you not see the illogic?


You said you "explained" something regarding the connect between apes and humans. Good. I hear conflicting explanations all the time. It means nothing unless you can do ID with your explanation.

Wow. You are nothing if not career-centric...


I have also seen a lot of worthless dissertations.

I have seen a lot of terrible design from engineeers. IN fact, I saw a show on the Mars lander a year or so ago. A whole team of engineers were working on designing - using Intelligent Design - the entry parachute. It woked in all their models, then they made a prototype and tested it and - gulp - it failed! It took the suggestion of a technician to fix the thing. Engineering is wayyy overrated.

Smokey said...

Looney,

There were no answers to my questions in the new post.

That's a very clumsy evasion. Do you think any of the commenters here were fooled by it?