Tag Archives: animal

Fine – Octopi are awesome, I get it.

Screen Shot 2015-08-17 at 11.49.37 PMBut aliens?


The Irish Examinier posts, ‘Don’t freak out, but scientists think octopuses ‘might be aliens’ after DNA study.‘ I guess this is just an eye-catching title to bring in readers for a pretty straight-forward article about how octopi are different from other animals. This article is referring to new data published in Nature following  DNA analysis of the octopus, Octopus bimaculoides.

Octopi can escape confinements, like this one that was sealed inside a jar with a screwcap:

They can move over land as well as in the water (especially when motivated by food):

They can mimic other animals:

And use camouflage to hide:

Briefly, though, I would like to take a second to look critically at the basic claim – not because it’s realistic, but because it’s useful to think about what we would or wouldn’t expect to find in a real alien.

claim:      “octopus DNA is highly rearranged – like cards shuffled and reshuffled in a pack – containing numerous so-called “jumping genes” that can leap around the genome. ”

answer: it’s  interesting that their DNA is rearranged in ways that we don’t see in other species, but it’s still DNA, right? And it still follows the same ‘universal codon’ rules dictating what codons (3 letter nucleotide sequences) call for what amino acids. That all life uses the same DNA and rules for its use is one of the most convincing pieces of evidence that all life on earth is related to one another.

claim:    Octopi have “eight prehensile arms, [a] large brain and … clever problem-solving abilities”

answer: This all just makes them interesting specimens, not alien.  Albert Einstein was extraordinarily smart and was not caught up in group-think (at least early in his career). This made his a great scientist, not an extraterrestrial.

claim:     “Analysis of 12 different tissues revealed hundreds of octopus-specific genes found in no other animal, many of them highly active in structures such as the brain, skin and suckers. ”

answer: This is actually great evidence of a large gap between octopi and other organisms, perhaps even stumbling upon new genes or gene combinations that allowed them to rapidly evolve away from homologies with their closest phylogenetic neighbors. Perhaps this phylogenetic tree might be hinting at such a separation for mollusks?


claim:  “Hox genes – which control body plan development – cluster together in almost all animals but are scattered throughout the octopus genome. ”

answer: Pretty cool. But I’ve always wondered what kept these genes together in other animals rather than why are they scattered in the octopus. Difference is always intriguing though, so I get why this is notable. from the paper that elicited the Irish Examiner article, Albertin, et al, comes this cartoon of the arrangement of hox genes in other species compared to the scattering across several chromosomes in octopi:


Rather than call them aliens, which I agree might grab the interest of Discovery Channel viewers, I prefer Albertin, et al’s description, “Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.”

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Posted by on August 17, 2015 in Uncategorized


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Delving into the Bigfoot Aliens who built the Pyramids in Giza

ImageThe Science Channel and Animal Planet have some excellent science and nature programming that I enjoy watching with my son. It makes me happy to see his interest piqued by Big Cat Diaries or How It’s Made or The Wonders of the Universe.

ImageBut it troubles me that sometimes these shows will end and immediately something about Bigfoot’s Ghost comes on. The positive effect of quality program rapidly erodes when juxtaposed against pseudo-science hogwash and I’m not sure how to handle it other than to constantly talk to him about what good science looks like compared to a well choreographed hoax or wild goose chase. ‘Does the Loch Ness Monster really control the US Stock Market?’

‘We may never know….’


Explore an expanding Universe and a shrinking Intellect back to back on the science channel

‘But wait!’ you say.’Isn’t there some merit to asking the question? I mean, we don’t know for sure do we?’

Of course. The robot overlords may actually be the ones who keep making us forget where we left our car keys. But is it really the most likely answer? Maybe you weren’t paying attention when you put them down because you also had groceries, your iPhone and a couple of old coffee cups in your hands when you came home.


Gad Zooks! A ghost bite!

Do we have no way of sorting out probable causes from improbable ones?

Discovery Communications, owners of The Science Channel, The Discovery Channel, TLC and other media outlets offers this mission statement:



Hey, Ghostbusters was entertaining and engaging. But was it enlightening?


Posted by on February 28, 2014 in Uncategorized


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Getting Oxygen Where It’s Needed

Oxygen is required by many organisms for survival, luckily it is plentiful in the air, but how does it get into all the tiny cells all over the body?

periodicFirst, Oxygen is a highly electronegative atom. This means that it attracts electrons very well and can pull them away from other molecules. Only one other atom is more electronegative and that’s the most reactive element in the periodic table, Fluorine. Electronegativity becomes useful biologically because electrons are capable to storing energy that can be passed along from one molecule to the next. But , to do this, each molecule must be more electronegative than the last. Therefore, it is not surprising that Oxygen is used as the final electron acceptor in the electron transport chain of cellular respiration. This reaction is required by many organisms, and can be highly beneficial even to some organisms that can live without Oxygen. An electron transport chain is a process by which molecules in a membrane pass en electron down the line using its energy in a controlled way to extract even more energy from sugar.

But how does Oxygen get to the cells that need it? Two molecules account for much of this action, myoglobin and hemoglobin, both illustrated below:


Hb- hemoglobin, Mb-myoglobin.

What this image also elegantly portrays is the amazing similarity between the molecules that belies their evolutionary relationship.

Each of these molecules is capable of binding Oxygen, but each occurs in a different tissue. ImageHemoglobin is present in Red Blood Cells, making them capable of transporting oxygen from the lungs to other tissues. Myoglobin occurs in these ‘other’ tissues, particularly muscle cells.

Despite the fact that they both bind oxygen, they do not bind it equally well under all conditions. While hemoglobin is just as good at binding Oxygen in high concentration environments (like the lung after inhalation), it is not as good at retaining oxygen when found in less Oxygen-rich environments (such as tissues like muscle).  Under these conditions, myoglobin is much better at binding Oxygen and can pull the molecules away from hemoglobin.

Recently, several groups have published new data about how subtle differences amongst proteins involved in Oxygen transport through blood and muscle result in different binding properties. In turn, the variability in these properties underlie the amazing diversity of lifestyles found in nature, from humans to birds to giant whales capable of holding their breath for up to an hour.

Image That brings us back to the electron transport chain and Oxygen’s electronegativity, where Ois used as a ‘magnet’ for the electron traveling down the pathway from one molecule to the next. As it goes it loses some of its energy, which is converted into a new form that the cell can use. Once the electron, now at a lower energy state, gets to O2, the Oxygen splits  and takes up a Hydrogen ion to form water.

So, electronegativity and binding affinity are the forces that both transport Oxygen through the body and pulls electrons from one molecule to another. Together, the movement of electrons, like that of water through a mill, powers processes that lead to the synthesis of ATP, the energy currency of the cell (see below).



Note the electron traveling down the chain (in pink)

Given what we’ve discussed here, how do you think a baby ever gets to pull the Oxygen away from its mother’s blood / hemoglobin?


Posted by on June 26, 2013 in Uncategorized


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An autotrophic animal

ImageHere’s the article that I stumbled upon today. It describes an animal (a sea slug) that ‘steals’ chloroplasts from the algae it eats and retains them in a functional way such that they can provide nourishment to the animal for many months.

This is not a true photosynthesizing animal – meaning that it can only temporarily harbor chloroplasts from its food, but it is still an amazing oddity.


Posted by on September 25, 2012 in Uncategorized


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