Sunday, December 18, 2011

Oh, the news and finals question 16 (thinking about multicellularity)

 Why Almost All Multicellular Organisms Begin Life as a Single Cell

As soon as one turns around, there is a newsy item that directly relates to a Biofundamentals exam question.  Question 16:   In the context of social slime molds consider i) a cell in your brain to one of your eggs or sperm and ii) a sterile worker mole rate to a queen mole rat.  How is this possible, evolutionarily.  

Saturday, December 10, 2011

Tuesday, December 06, 2011

A little perspective.....

Turns out, the largest black hole ever (or rather, so far) has been identified.  Here it is described "a black hole with nearly ten billion times the mass of our Sun, an event horizon that would stretch five times further than the orbit of Pluto if we had the misfortune to have it drop in, and a gravitational sphere of 4,000 light-years."

Lynette Cook's impression of a black hole larger than our solar system in the middle of the galaxy (NGC 3842) composed of trillions of stars (perhaps as many stars as there are cells in one person's brain!!!!!!)

Monday, December 05, 2011

Being eusocial....

Based on today's discussion, it was clear to me that I needed to know more about i) sexual determination in the naked mole rat; ii) something about the organism's genome (link here), and iii) the (perhaps weird and perhaps not) fact that mole rats are extremely resistant to cancer (link here).   So here it is.

Turns out naked mole rats, both males and females are diploid.  In a colony there is one female breeder, and their presence appears to inhibit breeding by other females.
  "Female nonbreeders have small uteri as well as small ovaries without corpora lutea, indicative of complete failure to ovulate. Thus, despite achieving adult body size, the non-reproductive females remain in a pre-pubertal state throughout life." from Holmes et al, 2009.  

If, however, such a non-breeding female is removed from the company of the breeding female, and placed with a male, it can become fertile and breed successfully.  This is how laboratory colonies are started (apparently).

Also, please note that I made a mistake about sex determination in bees. All females are diploid, males are haploid.  Whether a female becomes a female worker or a fertile queen is determined by what it is fed during development.  Female workers can lay eggs, but these are unfertilized and develop into males (drones).  The Wikipedia article on this is good. 

Monday, November 28, 2011

An amazing video....

on the effects of forming sea ice on organisms living on the ocean floor (who would have thought?)
Given that part of the purpose of this blog is to remind me of what I have read and thought, I can report that I finished the Flavia De Luce mystery "I Am Half-Sick of Shadows" as well as Andrew Knoll's "Life on a young planet".  As I was reading Knoll's book, I realized that the section in Biofundamentals on endosymbiosis and the origin of eukaryotes was rather too sketchy, so I revised it.  Knoll's book reminded me of the historic origins of the endosymbiotic hypothesis, in the late 1800 and early 1900s.  

Amazingly, as I was writing the death of Lynn Margulis was announced.  Her major contribution was returning the idea of the endosymbiotic origins of mitochondria and chloroplasts (seem was clearly wrong about flagella).  As is often the case in the popular press, description of her contribution seemed to be inaccurate, exaggerated, and overly-dramatic; endosymbiosis is a perfectly Darwinian (that is biological) mechanisms for evolution.   

As to Knoll's book, which appeared in 2003, I am left (as I often am) concerned about the need to hype the relatively minor contributions of specific people, when in fact the lesson of science is that, more often than not, it is the churning of ideas and observations by the community that separates solid and meaningful insight from mistakes and trivia. I cannot help by hold my head when people talk about life on Earth originating from Mars.  

Wednesday, November 23, 2011

brains and free will and living science

Here is a very interesting interview with Michael Gazzaniga who works on split brains and how brain work.  Also reflects my experiences at CalTech, namely the importance of caring (primarily) about the science compared to secondary concerns about one's career.  

Here is a interesting lecture on the Mind-Brain System

Wednesday, November 16, 2011

cell phones + microwaves + cancer

from Bob Park's newsletter:

Of the world’s 7 billion people, an incredible 5 billion have cell phones 
(“mobiles” in most countries).  The safe use of mobiles is therefore a 
global health concern. The response of the World Health Organization was to 
conduct a huge epidemiologic study aimed at demonstrating a link between 
cell-phone radiation and brain cancer.  The effort was seriously misguided –
no such link exists.  The study served only to raise widespread public 
alarm over a nonexistent hazard.  Epidemiology, which is the study of 
health patterns in populations; is important, but it’s not a substitute for 
science.  Science is the organization of knowledge into testable laws and 
theories.  It has been known for more than 100 years that electromagnetic 
radiation at frequencies below the ultraviolet is non-ionizing, and thus 
cannot create the mutant strands of DNA that constitute incipient cancers.  
In 1905, Einstein’s “miracle year,” he theorized that electromagnetic 
radiation consists of discrete units of energy, now called “photons,” which 
are equal in energy to the frequency multiplied by Planck's constant. It 
marked the origin of wave-particle duality and earned Einstein his 1921 
Physics Nobel Prize.  His theory is verified every time a cell phone 

Friday, November 11, 2011


What great discussions in today's class, but as to the discussion of colorblindness, I have to admit I am befuddled. The national institutes of health (NIH) websie suggests that

"Expectations (prognosis)

Color blindness is a lifelong condition. Most people are able to adjust to it without difficulty or disability."

I will keep checking...

Saturday, November 05, 2011

Shouldn't politicians (and people who seek office) be scientifically literate?

Congratulations to Michael Bloomberg [link] for saying what anyone with a brain, and an education, and a backbone should say.  

Tuesday, November 01, 2011

DNA stretching by origin recognition protein

In E. coli (and other bacteria), the origin of replication (known as oriC) is recognized by the DnaA proteins.  In this recent paper in Nature [here], structural studies show that the binding of DnaA molecules to the oriC DNA region leads to the stretching of the DNA molecule, and the stabilization of single stranded DNA, which appears to be part of the process for assembling the DNA replication complex. Yet another cool molecular machine.

The red structure is the single-stranded DNA, the other colors are the proteins.  Can you determine whether DnaA is primarily composed of beta-sheets or alpha-helices?

Saturday, October 29, 2011

Talking about old proteins....and DNA organization

Consider bacteria which are, in theory, immortal 

Do they age? [good review article].  

Now there is evidence that as bacteria divide [news report here, and original paper here], the two daughters are not equivalent, one is molecularly younger than the other (can suggest how this is possible before reading the papers?)  

Also, I thought I would remind you of the problem associated with putting ~ 5 million base pairs of DNA into a single bacterial cell.  

In this picture, the bacterial cell (the dark blob in the center) has been opened up to allow its DNA to escape (the thin strands around the cell).  

Pretty amazing, so you can imagine the issues associated with finding a gene in this mess.  

Here is a nice overview article, if you are so inclined.

Thursday, October 27, 2011

The value of being random (and dinosaurs migrating)

Apropos of our recent discussions of random processes and gene expression, here is an accessible (and free!) article on how noisy systems can be selected for.

At the same time, here is a piece on how looking at the composition of fossil teeth can lead to a hypothesis of dinosaur migration.  

Tuesday, October 25, 2011

Chimps and People, major differences after all....

Not withstanding the current absurd levels of political shenanigans, many people thought that there had to be greater differences between humans and other primates than those identified by sequencing the genes encoding various proteins.  Now it appears the differences lie in the regulatory regions, and involve large duplications and deletions of genomic DNA that influence gene expression (and perhaps act in part as a species barrier - you have to wait until the Life cycle section to get this).        Previously this group suggested that the "propensity for cancer in humans versus chimpanzees may have been a by-product of selection for increased brain size in humans."  Ah Well, if true it supports the idea that there is no free lunch (or brain).  (image from Olson & Varki 2003.)

Saturday, October 22, 2011

Resurrecting old genes....

This has been an interesting area of research for some time (see the reconstruction of the Sleeping Beauty transposon); it often provokes responses from various pseudoscientific religious fundamentalists.  Here is a recent example, the reconstruction of an ancestral glucocorticoid receptor.  
At Panda's Thumb, P.Z. Meyers (post 1post2) and Jack Scanlon respond to various distortions of the science.  

Thursday, October 20, 2011

The origins of new genes.......

HERE (LINK) is a nature education article on the topic of how new gene originate (in case you want to go beyond biofundamentals).

Then there is a molecular evolution article on the identification of new genes in the primate/human lineage associated with brain function (link HERE).  The surprising observations: i) there are lots of new genes and ii) that are expressed early in neural development.

Here is a nice review of the major mechanisms responsible for Gene Duplication and their subsequent evolution or elimination (link HERE).

Tuesday, October 18, 2011

Room for optimism and mutations in humans

Turns out that (compared to chimps) people are more drawn to cooperation.  That would explain a lot.  Check it out here.

Also, if you want to read more about mutations in humans, here is a paper by Michael Lynch, which although dense, can can be understood (I believe).  HERE IT IS

Sunday, October 16, 2011

How is one to schedule one's future (classes)?

when the rapture may be occurring on the 21st of October; that would be very inconvenient, since we are planning to cover mutations and DNA repair.    If you are an MCDB 1150-03 student, you have to do your highlighting before you leave......

Thursday, October 13, 2011

Fix your genes & shining evolutionary light on genomic dark matter

Now that we are moving into molecular and cellular biology, this becomes a very interesting story.    Here is the original paper....

In addition, using genome sequencing of 29 placental mammals (including a bat and an elephant, and humans, of course), an evolutionary model uncovers some of the previously unknown structure/function relationships within DNA - something that no intelligent design model could even begins to approach.  Check it out:  here

the original paper is here.

Friday, October 07, 2011

Oh no, people......

And here is an exciting article on mitochondrial evolution (if you are having trouble sleeping!

Fianally, a reference to intracellular parasites

Wednesday, October 05, 2011

Amazing images....

This year's Nikon small world winners are out (luckily I did not compete, because given how great these images are, I would not have placed!!! )  but the pictures and their subjects are amazing:  link here

Saturday, September 24, 2011

and here is a great talk on what Darwin did not know about
adaptation by Hopi Hoekstra;  points if you can find mistakes
(I found one).

 The good thing is that all biofundamentalists'  understand what is wrong with this view of reality...    [from non sequitur}

Thursday, September 22, 2011

Making the most of darkness and color

All becomes clear in the light of evolutionary logic, even random mating in the sparse dark and peacock spiders[].  
oh no, and now an essay on female promiscuity, what is the world coming to (ruin and despair, I am afraid).

Sunday, September 18, 2011

oh my, what a catchy tune......

Thinking about the nature of the universe, I find myself whistling this tune @

Thursday, September 15, 2011

On BS, Vaccines, Science and Presidential politics

What is particularly difficult to deal with is when politicians use BS to score political points.  Most recently, we have a politician making unsubstantiated claims about the safety of the anti-HPV vaccine. If only people harmed by this self-serving BS could sue, and recover damages.  

BS is spouted by members of all political groups, and often has serious economical and medical consequences. That there are people (in Boulder) who seriously think that their can be "zero-waste" anything speaks to the failures of our educational system.  That said death, disease and vaccines are more serious  – see here for an example: body count  

Monday, September 12, 2011

Homework & reading

Interesting article from son Andy, on homework and learning. While I am clearly seriously non-objective, it does seems to me that the students in the class are more engaged, and more interested in the discussion, something I attribute to their ptevious interactions with the text.

Hopefully, group assignments will be getting easier (after the first exam on friday, we will expand from 16 to 20 groups). I am hoping that students will get more comfortable questioning the text, pointing out its flaws and responding to each other, rather than just dutifully answering questions (although even that is an improvement on total passivity).

Next we need to generate a response anlysis system, since there is lots of data (insights) to extract.

I think this this will lead to a revolutiom in how useful texts will "evolve"; It could lead to a new generation of drawfed (i.e. focussed, research-based) texts - I feel an essay coming on.

Well, that explains (almost) everything....

While I always expected that something like this was going on, I now realize my tragic mistake – clearly, one too many nights reading "Good Night Moon".   This will have to be on the biofundamentals test, with regards to sexual selection and mating strategies and the complex interactions associated with biological systems. 

Sunday, September 11, 2011

Thinking about evolutionary oddities

Just finished yesterday Survival of the sickest, a book about evolutionary novelties.  To my mind this is an interesting example of modern popular science writing; it includes a number of interesting stories about unexpected evolutionary scenarios, but all too often treats the most recent "reports" (whether in "prestigious" or less prestigious journals) as facts, and relies on the self-serving beliefs, theories, and speculations of their proponents as if they are significant.  It fails to project how often "breakthroughs" decay into more commonplace observations, once the real complexity of the system is appreciated.  Science is a communal activity, and reliability emerges with replication and extension.

It also fails to consider the forces that drive publication in prestigious journals (which are, after all, generally businesses, and not dispassionate, disinterested reporters)  – all too often it is not scientific rigor, but rather publicity or appeals to current scientific fads (arsenic bacteria and RNA worlds come to mind.)

While the first half of the book is interesting, the second half really goes off the tracks - pushing the idea that epigenetic regulation is more than it is; no conceptual break through, but rather a growing appreciation that how DNA is packaged within the cell matters and can be regulated.  Gene regulatory networks are rather more complex than previously appreciated.

In all of this I see the hand of the "believing mind" (see the essay by Matt Ridley) that highlights Michael Shermer's newest book; we are all susceptible to various "just so" stories, and fail to adequately appreciate the complexity and ambiguity of our actual understanding.  

This is illustrated by the use of the term "theory" when what is really meant is a person's point of view, prejudice, self-serving position, rank speculation, tentative model, etc.  

Thursday, September 08, 2011

jumping genes and early ancestors

jumping genes and evolution:  According to this report P-elements have been present in Drosophila melanogaster for only 80 years; clearly I have to read the paper.

At the same time, more hype about a possible human ancestor (or was it a dead end) and the origins of heavy metals from meteors (hints is clearly the right word).  Hype appears to be order of the day.

Finally, we (that is highlighter) made a breakthrough and we went from 20 to 50 students signed up.  Now a little group sorting and we are really off to the races.

Wednesday, September 07, 2011

Medical needs

Should  women have a choice about caesarian delivery (regardless of need?)

Tuesday, September 06, 2011

Family Relations:  Following our discussion of human ancestors and evolutionary lineages, this work suggests that reproductive isolation was not absolute

Monday, September 05, 2011

Still working to get groups functions working, finding some weird problems. 

Wednesday, August 24, 2011

Working outing out the bugs

Lots of small things to getting highlighting working seemlessly. Have to emphasize getting students to respond to one another, rather than just answering all of the questions on their own, which is why getting the tricks to highlighting worked out is so improtant, but on the whole things are going ok. Now we start getting into serious biological thinking.

Tuesday, August 23, 2011


zombies. A new PLoS One article about strange interactions between organisms. This is vey like the two other examples of zombies, who impose their own reproductive agendas on hapless insects; see 'Zombie ants' controlled by parasitic fungus and
Ant Parasite Turns Host Into Ripe Red Berry

Monday, August 22, 2011

Groups appears to be working

I think I will start migrating a few groups of students to it on wednesday.

An interesting first day of class....

As with much software, the groups function of highlighter was not ready for class, so a little duplicating and copying produced 12 Biofundamentals sites, with students assigned to each in groups of six.  

The real test will come on Wednesday, when we start into the materials.

Wednesday, February 16, 2011

No cancer, but at what cost?

Based on a paper published in ScienceTranslationalMedicine by Guevara-Aquirre et al on a group of Ecuadorian dwarfs, Nicholas Wade has a very interesting article in the NY Times on the effects of mutation in the growth hormone receptor (GRH) gene on the development of cancer and diabetes - this mutation essentially eliminates both (see also this paper).  Unfortunately, in addition to dwarfism, these mutations are also associated with childhood mortality, death associated with convulsions, and impaired mental function.  All of which serve to inform us that (as Ray Troll would say), there is apparently, no free lunch.  

At the same time, it is probably worth noting in the light of standard scientific/news hype, that this is a highly isolated population, and that it is likely that genetic variations at other genetic loci, are likely to make important contribution - things are likely to become more complex.  This could be, yet another case, of where the "truth wears off."

Thanks to Nicholas Wade for clarification and helpful direction. 

Saturday, February 12, 2011

Darwin Day Talk @ UC Boulder

While there is no sound (perhaps, I will add a soundtrack later), these are the slides I used for my talk for the Skeptical Students groups at UC Boulder:  "Why understanding evolution is hard and hard to accept". 

Friday, February 11, 2011

It dawns on me (rather belatedly) that one can use a blog ....

as a place to store various thoughts and web references - something of an intellectual (rather than emotional diary.)

So after a bit of a hiatus, I am back, using the web site post various references and observations, in large part so that I can find them again.   

Bill O'Reilly and the Galaxy Song

After giving a Darwin week talk for the Secular Students and Skeptics Society at UC Boulder, I was thinking about the meaning of the recently posted youtube video by Bill O'Reilly about tides and intelligent design.  A little too late I recognized that the correct response was the Galaxy Song by Monty Python.