Thursday, February 28, 2008

On junk DNA

While we talk about the quirks of DNA and mutations in class this week, here's a good review of junk DNA that you might enjoy spending a few minutes reading. Here's how it begins:

The instructions for "life as we know it" are coded in DNA, but it appears that only a fraction of our DNA is ever used. (This is probably not true of our brains, myths notwithstanding.) At least, only a fraction of it is ever translated into proteins such as enzymes. Some of the untranslated (noncoding) DNA has known functions, such as coding for the RNA part of the ribosomes that translate messenger RNA into protein, but much appears to be junk. Much of the junk is multiple copies of transposons, bits of unusually selfish DNA that reproduce like rabbits and burrow into the chromosomes, sometimes presumably disrupting functional DNA.

But if the noncoding DNA is mostly useless junk, why has some of it apparently been preserved by natural selection?
Go read the whole thing on This Week in Evolution, a blog I hope is becoming part of your weekly wander through the blogosphere.


Wednesday, February 27, 2008

Please Talk to Kids About AIDS? Really?

Not sure if my second-grader is quite ready for this kind of talk yet, although being raised by a couple of biologists, she may know more than her average classmate. But this film is intriguing, and worthwhile if it gets more people learning about AIDS, I suppose. So go watch: Please Talk to Kids About AIDS - Free Streaming Movie.


*cough*... it might just be the flu talking!

If you are wondering about the rather diffuse and widely spread nature of recent posts on this blog, folks, then please bear with me for a little while longer. I've been under the cosh (as many of you know since soon after our last Café Scientifique meeting) from this nasty flu that's laying low much of the great Central Valley this February. I hope to be back to regular speed soon - although I'll have a great deal of catching up to do workwise, so the blog may rely more on student postings which should start trickling in faster soon...

And btw, this video from the local ABC affiliate (also linked above) actually shows some of the local incubators where my particular virus probably came from - my younger child's preschool or the older one's elementary!

Of all the great infectious diseases my immune system was primed to handle growing up around Bombay, the flu was the least of anyone's concern as far as I remember, yet here it is decades later knocking me out for weeks in this temperate zone! Go figure!! And maybe one of you students can tell me why the flu might have been less of a worry in the tropics than in the temperate zone.


Monday, February 25, 2008

Whales evolved from small aquatic hoofed ancestors « Not Exactly Rocket Science

Also from Not Exactly Rocket Science, here's another post relevant to our recent discussions in class on the evolution of whales. As a recent paper suggests, Whales evolved from small aquatic hoofed ancestors. And they did so in India!


Reprogramming our cells to fix those darn mutations

Yes, we seem to be approaching that brave new world where we can fix mutations in our genomes to treat certain genetic diseases. The technology has already reached the point where it can handle at least point mutations as seen in this astonishing piece of recent research where they were able to reprogram cells in mice to treat sickle-cell anemia. You can find a nice description of the work with some background to put it into context in this essay on "Not Exactly Rocket Science", a blog I discovered while updating the bit about sickle cell in my lecture on mutations for today's class. It looks like a blog well worth reading on a regular basis, and has a number of other good examples of commentary on peer-reviewed articles you might emulate for your blogging for this class!

And as you absorb this paper, and marvel at how we might, someday soon, be able to fix some of our genetic defects, ponder the ethical implications of acquiring this ability to tinker with our genes at this level!


Thursday, February 21, 2008

Breaking the Science Barrier with Richard Dawkins

This is from a few years ago, but it is excellent, and well worth the hour or so you might spend watching. Buy the DVD for a mere 15 bucks, or watch it right here in these youtube segments, below the fold (click on Read more to see them):

Part 1, segment 1:

Part 1, segment 2:

Part 2, segment 1:

Part 2, segment 2:

Part 3, segment 1:

Part 3, segment2:


Wednesday, February 20, 2008

Midterm will be @ Testing Center

This is an administrative note for students taking the BioSc 180 class this spring - if you are not one of them, please ignore this post!

I've decided to use the new Testing Center for the midterm exam scheduled for this week, and will have more specific instructions for you soon. Basically, the exam will be available at the new Center located at Family and Food Science, Room 210, for 3 days, starting on Monday, Feb 25 to Wednesday Feb, 27. Given the logistics of getting everything set up there, I'm pushing back the start of the exam period to Monday instead of this Friday, so you get the weekend to prepare as well (and I suspect none of you mind that!).

We will have regular lecture as scheduled on Friday at noon, so I'll see you then. Meanwhile, you will hear from me electronically with more details on the exam logistics.


Friday, February 15, 2008

The Evolution of Neuroscience: Curing the Blind

Recently, on an article was posted summarizing the recent research from a Neuroscientist at Harvard Medical. The article was titled, “Restoring sight to the blind with deep brain stimulation – a World Changing Idea.” This article discusses that visual systems in the commonly blind, lack a functioning retina, however, the rest of the visual system within the brain is still properly functioning. Utilizing this information, electrical stimulation of the lateral geniuclate nucleus (LGN) may produce visual perception. The LGN is part of the thalamus and receives information or action potentials directly from the retina via the optic nerve.

This was done in a primate system and showed very encouraging results. The results indicated it may be possible (and relatively soon) to produce a neuroprosthetic device for the blind. This is amazing! The human device, in its crude state has been suggested to be a pair of glasses that has a digital camera placed upon it and this camera would wirelessly send the information from the visual field to a signal processor that would appropriately tell a deep-brain stimulator to stimulate the LGN in accordance with what was seen in the visual field by the digital camera.

The implications of this research are vast. Not only will this tell us a dramatic amount of information about our brain (the complex organ that resulted in the invention of this research) but it will assist people who are deprived of something we take for granted, vision.

Albeit an amazing discovery the question might be posed, “This is an evolution class, why did you select this article?” A large amount of science can be understood via evolution but it might not always be obvious. I think this is an important article in terms of evolution because it is an extremely interesting example of artificial selection. It is to be stressed that our restoration of vision to the blind is NOT natural selection by any means. Humans are capable of artificially selecting for traits within their species that would rarely be naturally selected for, if it were any other species. Deadly ailments that exist in nature rarely allow for an organisms survival or reproduction but due to our extreme intellect, we are able to devise means to artificially select for these traits to persist. Evolution has allowed for the development of the consciousness that we use for our values and morality and emotion that decides that we cannot allow people to suffer – that we must cure disease. But are we evading reality? And in accordance with my previous question, it is interesting to note that the article for the summary of this primary research was posted under neurophilosophy on

Would a rabbit likely be preyed upon if it were blind? Would it be able to find a mate and reproduce readily? Mutations or traits such as blindness may have been selected against over the billions of years of evolution, and though I have not been here to witness such events, it is an interesting topic to think about.

Full citation of original paper:
J. S. Pezaris and R. C. Reid, 2007. Demonstration of Artificial Visual Percepts through Thalamic Microstimulation, PNAS 104:18: 7670-7675. doi:10.1073/pnas.0608563104

[Contributed by Steven Miller]


Thursday, February 14, 2008

Wireless Technology: Helpful or Harmful?

Some people are more inclined than others to have the top of the line, most up to date technology spanning their homes. These individuals might be familiar with DLink and its wireless ability to stream information downloaded on their computer directly to the television. So, a person on the couch can watch stuff from their computer on their big screen TV. Knowing this one might ask, are there medical repercussions to sitting in between the two devices while they are operating? A new study is being done to see if there are any detrimental effects from the radio frequency energy that is produced by wireless electronics such as cell phones, internet access and the plethora of other wireless devices available to the public. The article, “National report calls for more research on health effects of wireless technologies” touches on the fact that a study like this is very complex. The potential problems people face from radio frequency are thought to be acquired over time and could take years to investigate.

It is scary to think that everyone using wireless technology in their day to day life could be increasing their risk for medical problems. The article above mentions how we live in a world that is far from risk free, and that people are continuously putting their health on the line. Although this is true, it will be interesting to see if there are, in fact, risk factors involved with the wireless technology that is becoming increasingly popular around the world.

[Contributed by Sheena Edmonds]


Tuesday, February 12, 2008

Happy Birthday, dear Charlie Darwin!


Aren't you glad that our campus is finally joining in the global celebrations of Darwin Day?

I recommend starting your morning off with some excellent reading material, and audio-visuals as well, courtesy the Guardian's special pullout section celebrating Darwin. Of course, those of us on the wrong side of the pond can't really pull-out that special section, but we can partake in much multi-media goodness on their excellent website. Any chance our local rag might at least mention Darwin today, you think? (unlikely - I couldn't find anything on their website) And who better to get you going than Darwin's rottweiler, Richard Dawkins, who writes:

Charles Darwin had a big idea, arguably the most powerful idea ever. And like all the best ideas it is beguilingly simple. In fact, it is so staggeringly elementary, so blindingly obvious that although others before him tinkered nearby, nobody thought to look for it in the right place.

Darwin had plenty of other good ideas - for example his ingenious and largely correct theory of how coral reefs form - but it is his big idea of natural selection, published in On the Origin of Species, that gave biology its guiding principle, a governing law that helps the rest make sense. Understanding its cold, beautiful logic is a must.
Go read the rest of it at the Guardian or on Dawkins' own site.

I trust you will later be taking a stroll on campus to check out our interactive christo-esque project to spark a conversation about Darwin and Evolution:
There will be a Christo-esque display of major ideas about evolution, both pro and con, hanging from a line that will run from the Satellite College Union to Joyal Administration. Paper will be provided so you can add your comments to the display. Come see the display and participate by adding your ideas.

And to round off the day, come learn about how parts of our own bodies are evolving:

Professor Fred Schreiber of the Department of Biology will present a public lecture and discussion titled


5:00 – 7:00 P.M., TUESDAY 12TH FEBRUARY, ROOM 109, SCIENCE 2.

Dr. Schreiber will cover topics as diverse as skin color, the epiglottis, varicose veins, malaria and lactose intolerance. All are welcome.

“Darwin’s theory provides the theoretical and conceptual foundation for all of the biological sciences, and remains one of the most momentous intellectual developments in human history. The Department of Biology is committed to accurately representing Darwin’s ideas, and takes great pleasure in this opportunity to emphasize his seminal contribution to science and society.”

So let's remember Charlie, in his own words:
Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science.

- Charles R. Darwin

Happy Darwin Day everyone!


Monday, February 11, 2008

Evolution in Five minutes

Venu Polineni found this interesting video and wants to share it with the rest of the class.


Wednesday, February 6, 2008

Student essays from Spring 07

Several students have asked me about how and what they might contribute to this blog during the course of this semester. So let me repost a list I had compiled at the end of the 2007 Spring semester showcasing all the student contributions at that time:

What happens when you ask a bunch of undergraduate students to contribute short pieces for a class blog on evolutionary topics (with the minor incentive of extra credit)? Turns out to be quite an educational experience, if you follow the links below! About half the students in the Spring '07 Evolution class here at Fresno State contributed a variety of essays on what they've been reading outside class, what they find fascinating and worth sharing in the world of evolutionary biology.

Having been unsure of what to expect, and frankly, being a bit nervous about this experiment, I am really glad I opened up the blog to students - what a way to get a small army to go out and find interesting tidbits from the frontiers of evolutionary biology! And gratifying to think that by the end of a seemingly long semester, one hasn't entirely killed their interest in the subject! (well, I might be flattering myself there - perhaps the interest remains despite my best efforts!) I think you will enjoy these diverse essays as much as I did - so if you know these students, pat them on the back (and you students can pat yourselves!).

So here's a list of all the essays contributed thus far:
  1. 28th Annual CCRS - a report
  2. Barn Swallows: Bringing sexy back
  3. Are chimps more evolved than humans?
  4. Gene links longevity and diet
  5. Language, Learning, Logic and the Chimp Genome
  6. To See Or Not To See: The Mexican Tetra’s Question
  7. Walking on eggshells... evolutionarily
  8. Corals more complex than you?
  9. From DNA analysis, clues to a single Australian migration
  10. Hollywood knows what's to come
  11. Why do ducks have big d..cks?
  12. Promiscuous females cause male zebras to have bigger testes and act all weird
  13. How the itch came about: Humans and Gorillas get intimately close
  14. Eat like a python = run like a horse? Or how digestive regulation has evolved
  15. Positive parasites?
  16. Sexual dimorphism and adaptive radiation
  17. Fascination of the cetacean cognition
I might have to try this again in future classes...


Quintessence of Dust: Tangled Bank #98

The latest Tangled Bank (#98) - a virtual "traveling carnival" of blog writings - is up for your reading pleasure at Quintessence of Dust


Grey-Faced Sengi - in action

And if you want to communicate directly with the discoverer Francesco Rovero, tune in to Conservation International's live chat today (@ 1:00 PM EST).


What is this I'm eating?


If you ever pause to wonder about what exactly is in the (likely highly processed) sandwich you are eating for lunch, and if whatever's in there is really good for you, you might want to swing by this noon to listen to my colleague Jim Prince's take as part of the Ethics Center's Spring Lecture series:

Jim Prince: “What is this I'm eating?”

Biologist Jim Prince will lead a discussion of the science and ethics of genetically modified food. What are the risks? What are the benefits? Can we afford to tinker with our food sources? Can we afford not to?

Jim Prince is Professor of Molecular Genetics at Fresno State. He received his Ph.D. in plant molecular biology from Cornell University. He did postdoctoral work at the USDA and Cornell University.
The class agreed to attend this talk rather than listen to me drone on in another lecture (the seminar being in the same time-slot as our Evolution class), so I expect a strong showing from the BioSc 180 students! Meanwhile, here's a few more thoughts to chew on.

Molecular biology, genetics, and biotech seem to be particularly good, among all technologies, in raising our hackles about opening Pandora's box, perhaps because they have the potential to hit us directly in our bodies - where it hurts! And perhaps as a result, breakthroughs and developments in this area seem to always stir up shrill rhetoric from both sides: those who tout the technology as almost magical solutions to world hunger and disease, and those who would raise the specter of Frankenfoods to scare the pants off of us. Take the recent green light given by the FDA for food produced from cloned animals. James McWilliams argues, as you may have seen on the Op-Ed page of the NY Times yesterday, for a more moderate, rational middle ground exploring this frontier of the precautionary principle, and I agree with his perspective. A friend of mine wrote last week to ask me what I thought about the FDA decision, and my immediate email response was that it was hard to imagine serious health issues for humans from cloned meat or other animal products. After all, we've been eating cloned plants for centuries without anyone worrying too much about it. Why do we draw a different line when it comes to cloned animals?

What do you think?



Friday, February 1, 2008

Size Matters - a pre-Valentine's Day Café Scientifique

80BDC612-24B0-41EA-AA68-BEB3034D6D19.jpgFollowing up on last month's interesting discussion of sex, sex determination, and sexual genders by Fred Schreiber, we have pre-Valentine's Day special coming up in the Central Valley Café Scientifique meeting on Monday, February 4, 2008:

Size matters: a tale of male mating strategies in nonhuman primates

Dr. Kaberi Kar Gupta

Monday, February 4, 2008, 6:30-8:30 PM

Lucy's Lair

10063 N Maple Ave,
Fresno, CA 93730
(559) 433-9775
How do you choose your mate? – is a basic question for all primates including humans. Who are successful in finding mates? Should a female prefer a large bodied, stronger male or a male with better territory? How do males choose their mates? In this pre-Valentine’s Day special Dr. Kar-Gupta will guide us through the biological and evolutionary implications of mating in primates, and how that in turn plays a major role in regulating relationships within primate social groups. To round off the talk, she will present her own studies of the mating strategies of male slender lorises in the wild. The slender loris is an endangered nocturnal primate (cousin to the bushbaby) that is endemic to south Asia
If you are in the Fresno-Clovis area and looking for something to do of a Monday evening, join us for what promises to be a fun evening!



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