Tag: science

Posted on

…mmmm…fly paper…

So, Nathan said he wanted to know what I’m up to in my research rotation for the next few weeks… I’m working for Dr. Joel Eissenberg (who reminds me quite a bit of Dr. Buckner at Truman…) in the Department of Biochemistry. He works primarily with fruit flies, but most specifically, a protein known as dELL. This protein is known as an “RNA elongation factor.” For those who know anything about genetics, DNA is coded into mRNA by RNA Polymerase II; Pol II will sometimes pause along the transcription process, thereby causing the DNA to be transcribed more slowly. dELL prevents this “transient pausing,” allowing transcription to be carried out more efficiently. dELL has also been linked to leukemia (which is how it was discovered in the first place).

Anyway, Dr. Eissenberg is trying to get various characteristics of dELL from his research. I’m taking part in the work by using a technique known as gel electrophoresis (SDS-PAGE, to be more specific…) to isolate the protein from extracts obtained from fly cells. I then take the gel and apply it to a Western Blot analysis. The protein extracts (nuclear extracts, technically…meaning that they came from the cell’s nucleus…) are obtained by either Size-Exclusion Chromatography or Ion Exchange Chromatography, neither of which I’ll explain, but they’re both pretty cool… On the Western Blots, we use selective antibodies to detect and expose the proteins we’re interested in…one antibody binds to dELL and then a second antibody binds to the first one…but that second antibody has a luminescent “probe” (i.e. chemical) attached that allows us to see it… By carrying out this whole process, we are able to see in which cells/extracts/etc. that dELL is present and/or active.

There’s a lot more to it, honestly…most of which I don’t know. Regardless, I’m just running a bunch of SDS-PAGEs and Westerns right now…both of which are relatively time consuming…so it takes me a good two afternoons to take care of each of them… It’s relatively interesting, but not really what I want to do with the rest of my life. If anything, it’s interesting to see how proteins are isolated and such…seeing how all of this has been done in the past…

…and why everyone hates Western Blots… 😛

Posted on

Of Paltering and People

So, a “palter” is a lie, for the record… Secondly, I refer to a book that is being pushed in Kansas and other states/communities that masquerades as a science “textbook” known as Of Pandas and People.

I only bring this up because I’ve been watching “The Daily Show” this week while they’ve been doing their “Evolution shmevolution” series, looking at the “evidence” for or against evolution, intelligent design, etc. Overall, there’s been something of a liberal bias (…not unexpected…), visiting sites like Dover, TN (the side of the Scope’s Monkey Trial) and talking to the conservatives there (they’re like those crazy townies that live in the trailer park on the other side of town…freaky, yo…).

Anyway, last night, Lewis Black brought up this book…and actually showed it to the audience. He showed the cover…and then slid it around to its side… The stupid thing is only 170 pages long!!! How much “science” can you learn anything from a book like that? There are some classes in college where you read that much in a night! I also found this website (web hosted by the Kansas Citizens for Science) by a professor at Brown University and he points out some serious flaws, places in this book that the author (Percival Davis) refuses to acknowledge (like extinction…something we know to be fact, but it isn’t mentioned in the book). An excerpt:

“When I first opened the pages of Pandas and read the fine words presented by its authors in the name of free and open inquiry, I expected a text that might genuinely challenge students to examine the assumptions of what they had learned and evaluate scientific theory in an objective manner. To say that I was disappointed is to put it mildly. What I found instead was a document that contrived not to teach, but to mislead. The many errors and misrepresentations that inhabit the pages in Of Pandas and People will, quite honestly, serve to hinder teachers as they attempt to cover the stunning range and diversity of contemporary biology.”

So yeah, let me line this out… Scientists and most teachers don’t agree with the book. The politicians are pushing it on teachers. Can’t we trust the teachers and scientists to know what to teach in their classes? Do we want politicians coming into our classrooms and teaching? Do they even have a right to dictate what teachers are supposed to teach their students? It’s bad enough that teachers are having to teach their classes based on standardized tests and can’t teach what’s really important…

…important like…oh…I don’t know…real scientific studies and evidence rather than dogma? 😛

Posted on

Isn't it ironic…

…dontcha think?

“Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.” — Cardinal Christoph Schanborn

That quote comes from an article posted at New Scientist, submitted by Steve Hosack.

I’m not even going to comment on this except to say that the irony of the statement is staggering and ignorant. I’m very glad I’m not Catholic… 😛

Posted on

Isn’t it ironic…

…dontcha think?

“Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.” — Cardinal Christoph Schanborn

That quote comes from an article posted at New Scientist, submitted by Steve Hosack.

I’m not even going to comment on this except to say that the irony of the statement is staggering and ignorant. I’m very glad I’m not Catholic… 😛

Posted on

…so it begins…

“Why do we need explosive detection methods? Terrorists. Because they all want to increase your entropy?”
– Joel Brockmeyer

So classes have officially started. All I had today was BBS 501: the “BBS” stands for “Basic Biomedical Sciences” and, essentially, this class is Graduate School Biochemistry (officially titled “Beginning Basic Biomedical Sciences I”, I think). Today we began a few lectures on thermodynamics, hence the aforementioned quote regarding entropy…spoken by Joel during my Junior Chemistry Seminar class Junior year at Truman…

If today’s class is any indication of the future, then it shouldn’t be too terribly hard for the first few weeks. We had a review on thermodynamics, and by “review,” I mean back to Freshman year of college. I’m sure it’ll get more difficult, but flipping through the first few weeks of the syllabus, all I can see is stuff I’ve, at the very least, heard of if not studied on multiple occasions in various classes throughout undergrad. I think the primary difficulty will be in the sheer amount of material, however. As in, I’ve got this class weekday mornings at 9:00 am…so when I have my first test in just over 2 weeks, I’ll have had about 11 lectures…which is the equivalent of almost a month of lectures (MWF) at Truman. So yeah, I dunno…it could be easy…could get a lot harder really quickly…

The exams will be completely in essay form and we are assured 3 hours to take the exam and each lecture will be covered by only one question on the test…therefore, we are relatively aware of what’s going to be on the test already…that, and we are being told to a). get the previous tests from upperclassmen and b). that the questions are very similar from year to year.

Graduate school?! So far, it sounds a lot easier than I would have thought in many of my undergrad classes…on the other hand, I’ve only had one day to deal with…but, then again, I only have two real classes to worry about: this one and a class twice a week that deals with reading “classic” papers (i.e. the original Watson and Crick DNA structure paper, etc.).

Only time will tell, I guess…

Posted on

A link, poker table, and AoE II

So yeah, in the same vein as all the evolution posts from the past week or so, Andy S. sent me this link…which is rather amusing… 😛 It’s an open letter to the Kansas state school board…and is very, very sarcastic…

I approve whole-heartedly… 😉

In other news, I think I’m going to wait to build my poker table until I’ve paid some more bills and get my paycheck next week… I haven’t quite decided whether to build a table-top (i.e. fit it on top of our card table) or build an actual table (you can buy folding legs at Home Depot for, like, $20…). I think I’d be happier with a separate table, but we’ll see…

…in other news, I am getting in practice for our AoE II playing this weekend…I can take on a single “hard”-rated computer character and win…sometimes it takes me awhile, though… Back in my prime, I would take on 2 “hardest”-rated computers…but that was Sophomore year…been awhile……

Posted on

Updates and shenanigans…

Well, Kristen left this morning after visiting for a few days. A good visit, in all, yet seemed somewhat rushed at times. Apparently, certain museums in this town are closed on certain days and some don’t open until certain times, so that threw a kink in things…however, we did make it to the zoo, the Missouri History Museum, got some shopping done, went to Union Station and made a valiant attempt at going to a Cardinal’s game…but the game was so full, there was only standing room available…and I wasn’t about to pay to stand there and watch a game… 😛 Hopefully we’ll get to see a game sometime soon, though…

Anyway, I’ve got some errands to run over the next few days…nothing terribly important, but errands nonetheless… I’ll be heading to Kirksville this weekend to get some AoE II action on, so I’m looking forward to that. Regardless, I guess I’m looking forward to classes starting in a few weeks…although, it’s gonna get pretty hard, I’m afraid…

But on the plus side, I decided that I want to build a poker table… 😉

Posted on

Fascinating…

So yeah, as a few of you have noticed, there’s actually been a good and lengthy discussion on my “Lee Strobel is an Idiot” posting on August 3rd, which I find rather fascinating. I’m very much enjoying the stimulating conversation that’s going on there between very diverse people with different backgrounds and understanding. I hope it continues since I’m learning a decent amount from it!

…which brings me to another subject… I’ve been thinking recently about why all these articles and such are coming up about Intelligent Design Theory versus Evolution, or more importantly, why I seem to be making a relatively big deal about it. Yesterday, I noticed that this week’s Time Magazine is publishing a few articles on the subject and even has it on the cover for the week. I guess it represents a crossroads in my life, perhaps. I’ve been going to church for many years; I’m already entrenched at one in St. Louis where I get to play drums every week (score… ;-)). But at the same time, I’m continuing with my graduate school education. I now have a bachelor’s degree in Chemistry and in Biology, so I’ve lived and breathed science for the past 5 years (if not longer), while at the same time attending the Wesley House regularly and hearing the “other side” of the story. I don’t know that I’m making decisions or life plans or anything around this “crossroads,” yet I think I am making progress toward the “truth,” or however close to it one can get.

The ID vs Evolution debate is a difficult one that will never be fully completed. I posted an article yesterday that is written by a proponent of the ID side of things. I don’t agree with a few things out of his article, but I do agree that the problem needs to be resolved with healthy debate, much like we are doing in the “Lee Strobel” posting. There are severe problems with the way ID is presented to young school kids. On the other hand, Evolution is still a theory (although, a very well-supported one…) and should be treated as such. Neither is truly “right” as they are being taught today. I guess more time is needed to come to a clear consensus. The issue needs good, healthy discussion before anyone will waver and listen to the other side’s argument…and I certainly find myself leaning toward one side, unable to listen to the other.

The problem is: which one?

Posted on

Lee Strobel is an idiot

So, I mentioned awhile back that I’m reading “The Case for a Creator” by Lee Strobel, who also wrote such books as “The Case for Faith” and “The Case for Christ,” two very popular books on the college scene in such “black and white” groups as CCF and Campus Crusade…

Anyway, so I saw this book at Barnes and Noble and couldn’t help but buy it since it was that trendy author writing about two things I’m interested in: God and science. Thus far (and, granted, I’m only 80 pgs into it…), the book is worthless. Strobel uses “evidence” out of non-evidence. For example:

“The problem with irreducibly complex systems is that they perform no function until all the parts are present and working together in close coordination with one another. So natural selection cannot help you build such systems; it can only preserve them once they’ve been built. And it’s virtually impossible for evolution to take such a huge leap by mere chance to create the whole system at once.” — pg 79

Why not?! The chances of being struck by lightening once, surviving, and then getting struck again in the exact same location as before isn’t likely, but it’s still possible. How do you know it isn’t possible? And now to the whole “evidence by non-evidence” point:

“This is not an argument from ignorance…we’re not inferring design just because the naturalistic evolutionary theories all fail to explain information. We infer design because all those theories fail and we know of another causal entity that is capable of producing information – namely, intelligence. Personally, I find this to be a very strong argument indeed.” — pg 78

Oh really! All those theories fail? Do you know how science works, Mr. Strobel? You know there is no such thing as “proof” in science? That’s because any evidence can come along and change the way we we all see the world. You assume that since we don’t understand a few facets of the world around us, we must assume that “intelligence” as we know it must be involved. We thought the world was flat until we found evidence to support that it’s round. We thought the universe revolved around Earth until we found that Earth revolves around a star…that is one of infinite stars in the rest of the universe. The “intelligence” you’re talking about is human intelligence. God is all-knowing, thereby presenting an entirely different type of intelligence from what we have experienced. Frankly, Mr. Strobel, you don’t know anything about science if this is the “evidence” you’re presenting. You shouldn’t be writing books about things you apparently know nothing about.

The point of all this is: humans understand absolutely nothing about the “known” universe. We don’t know how God works. We don’t know how it was all done. To quote the common phrase, “we don’t know jack.” How can we assume to know how it all works? Isn’t it possible that there are other universes parallel to our own that have completely different physics to our own? How about another planet out there that has beings built out of neon rather than carbon? Or perhaps even that on some planet on some distant galaxy, a milk cow won an election against someone looking strangely like George W. Bush. Frankly, we don’t know. I can’t prove that these things aren’t happening because, well, because it can’t be proven.

Much like Strobel can’t prove anything he’s putting forth in his book. Know why? Well, because “evidence by non-evidence” isn’t evidence at all. It’s ignorance.

Posted on

God vs Evolution

“There are gaps in science everywhere. Are we to fill them all with divinity? There were gaps in Newton’s universe. They were ultimately filled by Einstein’s revisions. There are gaps in Einstein’s universe, great chasms between it and quantum theory. Perhaps they are filled by God. Perhaps not. But it is certainly not science to merely declare it so.”
— Charles Krauthammer, Time Magazine, August 8, 2005

I posted another essay posted in the “Articles” section above…check it out…

There seem to have been more than a few articles about this subject over the past few weeks. There’s a show that’s going to be on the History Channel on August 7th called “Ape to Man: The Evolution of Evolution,” indicating that interest in the subject is still as strong as ever.

We talked about teaching intelligent design (……creationism…) in our public schools in my Evolutionary Thought class this past semester and came to the conclusion, much like anyone who knows anything about science, that it’s a dumb idea. It’s one thing to teach it in a Catholic high school, but to teach it in our public schools is entirely wrong. What happened to a separation of church and state?

Anyway, it’s a good essay…check it out…