Posted by: Dan | August 5, 2007

Cells Weekly #41

If biologists have ignored self-organization, it is not because self-ordering is not pervasive and profound. It is because we biologists have yet to understand how to think about systems governed simultaneously by two sources of order, Yet who seeing the snowflake, who seeing simple lipid molecules cast adrift in water forming themselves into cell-like hollow lipid vesicles, who seeing the potential for the crystallization of life in swarms of reacting molecules, who seeing the stunning order for free in networks linking tens upon tens of thousands of variables, can fail to entertain a central thought: if ever we are to attain a final theory in biology, we will surely, surely have to understand the commingling of self-organization and selection. We will have to see that we are the natural expressions of a deeper order. Ultimately, we will discover in our creation myth that we are expected after all.
[Stuart Kauffman, At Home in the Universe, 1995, p112]

In the interests of promoting science posts relating (however broadly) to my interests of cell and molecular biology, here’s my weekly installment of “Cells Weekly,” a showcase of topical blog posts by others from the past week. In in the interest of consolidating the relatively few number of thorough posts on cell and molecular biology, I’m switching to “Cells BiWeekly” as of next week. In the meantime, Enjoy!

Minicells on Target - Moselio explains the use of bacterial minicells to selectively target cancer cells, which is an important goal for oncologists, as they attempt to reduce the side-effects of chemotherapy. At Small Things Considered.

RecA - An Evolution Gene - MikeGene has conceived of the possible existence of “Evolution Genes,” and goes looking for candidates (psst - crank alert!). In actuality, the candidate that he looks at, RecA, influences antigenic variation by homologous recombination; while it therefore facilitates selective change, it does so naturally, and presumably RecA itself evolved naturally from an ancestral gene product (Karlin & Brocchieri, 1996). So it’s only as “intelligently designed” as MikeGene imagines it to be. At The Design Matrix.

Immunofluorescence: Why Color is Bad - Alex reprises a few tips that every budding microscopist should know, while he’s away. At The Daily Transcript.

Carnivals: Gene Genie 12, Encephalon 28, Tangled Bank 85, Skeptics Circle 66, Bio::Blogs 13, Mendel’s Garden 17

And four ScienceDaily picks, below the fold…

Effects Of Aging In Stem Cells

There is little disagreement that the body’s maintenance and repair systems deteriorate with age, even as there is plenty of disagreement as to why. Stem cells combat the aging process by replenishing old or damaged cells–particularly in the skin, gut, and blood–with a fresh supply to maintain and repair tissue. Unfortunately, new evidence suggests that this regenerative capacity also declines with age as stem cells acquire functional defects. In highly purified hematopoietic stem cells from mice aged 2 to 21 months, gene expression analysis indicates a deficit in function, yet an increase in stem cell number with advancing age.

Brain Cell Development Process Implicated In Mental Retardation Uncovered

Scientists have discovered a biological process in brain cell development that may help explain some causes of mental retardation. This understanding may one day help other researchers develop therapies that can reduce specific forms of retardation. Proteins of the Rho family, when excessively present in developing brain cells known as neurons, inhibit another protein, called cypin, that promotes healthy neuron development.

Mechanism Discovered In Adult Stem Cell Regulation

Scientists have discovered an important mechanism for controlling the behavior of adult stem cells. Research with the flatworm, planaria, found a novel role for the proteins involved in cell-to-cell communication. This work has the potential to help scientists understand the nature of the messages that control stem cell regulation — such as the message that maintain and tells a stem cell to specialize and to become part of an organ (e.g., liver or skin).

How To Predict Cells’ Response To Drugs

Researchers have developed a model that could predict how cells will respond to targeted drug therapies. Models based on this approach could help doctors make better treatment choices and drug developers identify the ideal compound. In addition, the model could help test the effectiveness of drugs for a wide range of diseases, including cancer, arthirtis, and immune system disorders.

Categories:

« Religion and Ethnocentrism: Is Religion Adaptive?
Lives of a Cell »

Responses

Hey, great site. I have an interest in a lot of what you write here. How cells work, Biophilia (just read the book this summer by wilson). I found you by follolwing a link by Mary at Five Wells who is part of our group blog at http://whorledleaves.blogspot.com/

I’ll be back

Dave

By: Dave on August 6, 2007
at 11:09 pm

So, not interested in actually addressing the points that Mike Gene makes?

“and presumably RecA itself evolved naturally from an ancestral gene product ”

Presumably? Well, case closed. Nice detective work, Columbo. What was Mike thinking? Didn’t he know he was going up against a ‘presumption’ contrary to his view?

“So it’s only as “intelligently designed” as MikeGene imagines it to be. At The Design Matrix.”

Yup, because that’s exactly what Mike said. He stated, “therefore, it was intelligently designed”. And that comment can be found in his…. 2nd para….hmmmm,…. it’s in the 55th sentence down from the ……. Oh who really cares? I’m sure that’s in there somewhere.

Again, stunning work to refute his claim.

By: Doug on August 9, 2007
at 12:41 pm

Hi Doug,
Way to spin it Doug. MikeGene is a crank, and one doesn’t need to spend time rigorously refuting a crank. If, however, you wish to criticize the inclusion of “presumably,” then be my guest.

By: Dan on August 9, 2007
at 12:52 pm

Hi Dan,

MikeGene is not a crank. And thankfully, you don’t need to refute him, but just his idea.

I’m not doing nearly the amount of spinning that you were with the, “So it’s only as “intelligently designed” as MikeGene imagines it to be” comment.

Mike is very reserved with using that phrase.

“If, however, you wish to criticize the inclusion of “presumably,” then be my guest.”

I never said that you can’t point this out, but the simple fact of a ‘presumption to the contrary’ of the point that Mike is making doesn’t justify the leap from that to an obvious error on the part of Mike’s thinking (or his imagination about the role & significance of RecA).

By: Doug on August 9, 2007
at 2:52 pm

Doug,
When one’s idea is unsupported by anything other than the most baseless speculation, then that person is a crank. Please, do not push this any further, as natural-theology-posing-as-science is not welcome here, just as my brand of rationalist naturalism is not welcome at Telic Thoughts.

Thanks.

By: Dan on August 9, 2007
at 2:59 pm

“just as my brand of rationalist naturalism is not welcome at Telic Thoughts.”

Come on. Who is not welcomed at TT? Ed Darrel (you’re not him, are you?) wasn’t even banned. Posts don’t even get deleted - the get Memory Hole-bound, still accessible to anyone.

“When one’s idea is unsupported by anything other than the most baseless speculation”

It has more than “baseless speculation” supporting it - if you follow the flow of his posts at the Design Matrix you can see that one causal impetus seems to be tool kit genes and the regulatory role played by them during embryonic developmental stages, the coordination of regulating the expression of particular genes at specific moments.
As well as the role of RecA itself - RecA dependent crossing over.

“Please, do not push this any further, as natural-theology-posing-as-science is not welcome here”

Come on, bro. We can get along. But wouldn’t it be more accurate (though still not correct) to say ‘teology posing-as-science’?

Take care.

By: Doug on August 9, 2007
at 3:46 pm

Doug,
Come on yourself. The insipid indulgence of decidedly unscientific arguments at TT is quite high. To even suggest that the positions espoused there deserve the respect of being properly refuted (much less accepted) is absurd, yet that is just what is called for at TT.

No, the off-handed dismissal of teleology as science (which teleology deserves) is most definitely not welcomed at TT.

And yes, we can get along, but I personally will not stand for calling teleology (even such ‘weak design’ arguments as ‘front-loading’) with any degree of respect, in science forums, any longer.

Nothing personal, to either you or Mike, but that’s the way it is.

By: Dan on August 9, 2007
at 4:00 pm

Bye Doug. I wasn’t going to ban you, just delete the comments and end the thread, but I could not take this discussion off-list (you gave a fake email, or at least one that doesn’t work). Here’s what I tried emailing you:

Doug,
This isn’t philosophy, this is science. And when you promote an ideology sans empirical evidence, that’s just not science, end of story.

It’s true, I have little patience to indulge in such ideas - I have no obligation as your teacher to educate you beyond what you yourself wish to study and inquire about. If I were a teacher, I would endeavor to show greater patience, but even then, a wrong interpretation is still a wrong interpretation.

Good day, but I’ve indulged in this nonsense long enough (I’m sorry, but WordPress does not offer a ‘memory hole’)
-Dan

Also, check back in a day or so if you’d like, I’ll have lifted the ban - if you’d like to discuss Intelligent Design, please search through my postings on that topic (under the category ‘creationism’).

By: Dan on August 9, 2007
at 8:14 pm

Doug,
Also, looking at the additional comment you left, you’ve clearly turned to trolling. If you continue to troll, you’ll be banned permanently.
Thanks.

Comment change:
Doug, in an unaccepted comment, you said:

And where’s your empirical evidence that science can limit teleological notions?

If that were acceptable logic, we wouldn’t dismiss the flying spaghetti monster as a farce, now would we?

Dan, I don’t mind educating you at all. You might want to read up on the fate of the positivists.

Oh, that’s right - you, the creation advocate, want to teach me science and philosophy. Oh, that’s rich.

The positivists though, you say? Let’s take a look at the major points of modern positivism:

1. A focus on science as a product, a linguistic or numerical set of statements;
2. A concern with axiomatization, that is, with demonstrating the logical structure and coherence of these statements;
3. An insistence on at least some of these statements being testable, that is amenable to being verified, confirmed, or falsified by the empirical observation of reality; statements that would, by their nature, be regarded as untestable included the teleological; (Thus positivism rejects much of classical metaphysics.)
4. The belief that science is markedly cumulative;
5. The belief that science is predominantly transcultural;
6. The belief that science rests on specific results that are dissociated from the personality and social position of the investigator;
7. The belief that science contains theories or research traditions that are largely commensurable;
8. The belief that science sometimes incorporates new ideas that are discontinuous from old ones;
9. The belief that science involves the idea of the unity of science, that there is, underlying the various scientific disciplines, basically one science about one real world.

That sounds pretty spot-on to me. I’d be happy to follow the fate of the positivists, as would any scientist that I know.

Byebye Doug. Email me (cellsnbirds-at-gmail.com) if you have a change of mind and want to honestly and correctly debate science or philosophy, but until then, the ban is not lifting.

By: Dan on August 10, 2007
at 10:00 am

Dan, I really enjoy your site. I disagree with some of your views regarding religion, but for the most part though I find your site to be interesting.
Philosophy of science is my area of interest and you seem to be handling it in an off-handed manner.
Saying, ‘this isn’t philosophy, this is science’ seems very ignorant. I’m not saying you are ignorant, but this comment certainly is. It neglects large areas of contention in the philosophy of science as well as in science itself.

‘I’d be happy to follow the fate of the positivists, as would any scientist that I know.’
–Please tell me you don’t mean this. You don’t have to be a theist to see the enormous errors in the thinking of positivism (self-refuting claims). Do you know what the fate of positivism was? Do you know where the modern resurrection of positivism is heading?
I hope you were just frustrated and reacting off of emotions with Doug when you made this comment. If you made this comment while being cool headed and rational then I am truly amazed with you. Not in a good sense.

By: BrianJ on August 11, 2007
at 8:55 pm

Hi Brian,
Sorry that I wasn’t clear - I actually am not overly familiar with positivism, and so did a quick look-up to get the gist of what positivism entails so far as the philosophy of science is concerned, coming up with the list above. That was what I took Doug’s reference to positivism to mean, which sounds precisely like a description of the scientific method itself. In that sense, I’d be proud to go the way of someone who followed such beliefs, and as a result, call myself a scientist (which I do).

I’m aware the existence of (though not well-read on) sociological controversies pertaining to positivism, but they clearly have nothing to do with a discussion of cell and molecular biology or teleology. So if that’s what Doug and you mean by ‘positivism,’ then my initial conclusion would be that you don’t know what you’re talking about.

But all of this is extremely off-topic. This thread was not about philosophy, nor am I interested in making it about that; it was about cell and molecular biology and science. I mentioned MikeGene because clearly he is actively seeking for material that has the appearance of being about science to fit into a preconceived and religiously-motivated conclusion. That, my friend, is self-evidently not science.

I’m really quite sorry, but if that’s the direction that this thread is going, I’m going to have to close comments here. (unless anyone would actually like to discuss RecA, homologous recombination, or the other stories that I’ve linked to in this post)

Best,
-Dan

By: Dan on August 11, 2007
at 9:27 pm

[...] 12th, 2007 by Dan In last week’s ‘cells weekly’, I made a reference to MikeGene’s disingenuous search for anything science-looking that could [...]

By: Open Thread: Positivism and Philosophy of Science « Migrations on August 12, 2007
at 1:32 pm

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