Challenger Society 2016 Conference – Oceans and Climate

So next week I’m going to the Challenger society 2016 conference which is being held in Liverpool. I can’t wait, it should be really interesting to get back into an academic environment. I have looked over the talks and made a plan of the ones I will attend, I will try to get a blog out for all the talks and posters that particular grab my attention . Hopefully it will be a good networking opportunity which may lead to work or post grad study, and if not at least it will be interesting.



Evil Apples?

Why my mind has been obsessed with apples?  Well, I don’t know if it’s because I’m not suited to the office environment and my mind is just wondering about the most peculiar of topics. I first started thinking of apples a few weeks ago, when my girlfriend was upset and confused, as every time she ate an apple, her throat would itch. I remember thinking that’s weird, but not giving it too much thought. But then quite a few people in the offices had the same complaint. I thought maybe there may be a strange batch of apples from Tesco or Aldi, that had some type of dust or chemical allergen on them which was in turn causing a minor reaction. No big deal right a few people bought some apples havent been washed properly or have been on the shelf gathering dust for a few days longer than normal. However, yesterday I saw on Dr Rae’s blog ( that him and a friend of his had the same issue from the apples in their garden.  So there goes my idea that a farmer, or store had a harvest or stock of dodgy apples.

So because I’m relatively sad, and I am literally sat at a desk waiting for the phone to ring, which granted, when it does it can have its entertaining and humorous moments, I thought I’d see if there was any valid scientific reason for these itchy apples.


Alas, it wasn’t long before I stumble across a plethora of questionable health and nutrition sites which branded apples evil and dangerous. However wading through the hysteria of these health sites I did find some valid sources of information which didn’t advice abstinence from all things Malus.

I started off looking on the NHS website, which talked about oral allergy syndrome (OAS). Basically, the site said that OAS is an unusual immune reaction to proteins found on a specific food. I know it sounds scary when the words food and allergy are in the same sentence. But in the case of OAS, it is usually a mild immune response that causes a dry itch in the throat, and on rare occasion it may cause swelling in the lips and even tongue.

Apparently it’s not just apples that are said to be ‘evil’; peaches, kiwis almonds and hazelnuts are all common causes of OAS. Basically OAS is caused by allergy antibodies mistaking certain proteins in fresh fruits, nuts or vegetables for pollen which is why it can also be referred to as pollen food syndrome (PFS).

Its thought that the immunological reaction is caused by pollen. OAS is a common allergy for people who suffer from seasonal allergies, particularly people who suffer from reactions to birch pollen and grasses. It turns out, that the protein structure of the pollen from many trees, grasses and weeds is similar to that of the essential defence and growth proteins in many fruits, nuts, veg and even spices. The protein structure is in fact so similar, that they are recognised by our immune system as pollen, which in a hay fever sufferer, can trigger an immune response. Cool right?

So now on to the science part, pathogenesis related proteins (PR) are proteins that involved in plant defences. The gene sequences which code for these proteins are highly conserved in most species. PR proteins are produced in plant species when under pathogenic attack. These proteins are induced as part of a systematic acquired resistance, when a plant gets an infection the genes are activated and PR proteins are produced. Some of the PR proteins can have antimicrobial properties, they function by attacking cell surface membranes and vital cell organelles in bacterium or fungi.

Recent studies have shown that PR proteins are a rich source of allergens, additionally PR proteins are not regarded as superfamily of proteins. They are a collection of unrelated protein families which collaboratively function as the plants defence system. To date there PR proteins have been classified into 14 families. Interestingly, the plant food allergens associated with causing the unusual immune response are homologues to proteins that are members of the PR protein family.

I know it’s not strictly zoological, but I found it interesting, well more interesting that sitting waiting between very few clearing calls.



Clearing 2016

Caller: Hello is this LJMU Clearing?

Me: Yes it is, rob speaking how can I help you?

Caller: I’d like to apply for a course please

Me: okay, what course would you like to apply to?

Caller: oh, erm.. I don’t know… what one should I do?

Me: oh okay, I can’t advise you on that, I can refer you to our clearing website and you can find out what courses interest you if you’d like

Caller: oh, no its okay I think I’ll just leave it. have a good day



Haldane, Biogeography and the ‘Incomplete’ Fossil Record


J.B.S Haldane once said that he would give up his belief in evolution if someone found fossil rabbits in the Precambrian. Although this witty comment will bring a smirk to the face of many biologists. Through my time working with many high schools, colleges and sixth forms, and even to an extent at university, I felt that the significance of this bold statement is seemingly undervalued by many pupils and even undergraduates.




The statement actually underlines and highlights the constraining predictions of the evolutionary view. There are requirements which make the theory of evolution so elegant and so un-falsafiable. One of which is the general emergence of organic complexity from simpler systems in a relatively predictable way.

For example the progression of evolution (in a very simplistic watered down way) is generally understood to be as follows:

Single celled organisms > multicellular organisms (cell differentiation)>(insert ~1.5 billion years here)> Aquatic invertebrates (no rabbits!!)> Aquatic vertebrates> lungfish like creatures(still no rabbits)> Primitive quadrupedal, semi-terrestrial vertebrates which over the next few hundreds of millions of years diversified into amphibians, reptiles and eventually mammals. (and some way down the line we finally we get rabbits). *

(*I know it’s a little more complex than how I have briefly put it but I’m just putting forward a watered down model to paint a simplified picture)

Haldane made the rabbit statement as he knew, as many of us know, that the layering of the fossils we find is non random, it’s no coincidence that we find specific fossils where we would expect to find them. There is a chronological order of fossils, implied by stratigraphic layering which is reconfirmed by radiometric carbon dating. The results of the carbon dating precisely matches the chronological order of the fossils.


The evolutionary process requires a continuous genetic flow throughout the ages. There can be no inexplicable disjunction. Additionally evolution requires the same continuous gene flow through space. It sound simple when you think about it. Gene flow must be continuous, the organism must pass on its DNA to continue its lineage. To do this reproduction must take place, which generally implies, with few exceptions, that two individuals must be within a relative proximity to each other at the same time.

Therefore we could say, in a similar way to Haldane, that we could abandon the idea of evolution if we found animals in a place were we wouldn’t naturally expect to find them. For example if we were to find elephant fossils in the canary islands, or koalas in France, Tasmanian tigers in Scotland… you get the point. Each of these occurrences would represent an unacceptable and explained spatial disjunction. A reality in which these occurrences are true would be just as problematic for evolution as the temporal disjunction presented by Haldane’s Precambrian rabbit.

The chronological order of fossils has logical constraints which allow us to make accurate predictions, as mentioned earlier. Furthermore, the continuous gene flow which validates the evolutionary theory constrains the possible location of plants and animals.

Show Me The Missing Link

People who deny the facts and therefore deny evolution like to smugly point out gaps in the fossil record. Insisting that there must be observable intermediates for the theory to be true. Proudly claiming that ‘there is no evidence for evolution without observable macro evolution’ or as its more commonly put ‘I’ve never seen a chimp give birth to a human’…

There are obviously so many problems to this argument, too many to cover today, maybe one day I shall blog about more of the problems with denying evolution in the future, but today I will attempt to keep focus.

One main issue that the evolution deniers have with the theory of evolution is, as stated the fossil record has ‘gaps’. However, I can see a flaw in this request to plug the gaps, every time an ‘intermediate’ is found it will of course require two more ‘intermediates’ for example:

Denier: The fossil record has too many gaps, too many missing links, find a fossil, until you do there is no proof…

Species A—*(‘Missing link’)*—Species B

We found a fossil!! we found your ‘proof’

Species A—*(Species I)* —Species B

Denier: Hey! where is the missing link for species A and I and the link between I and B. This proves nothing!

*repeat over and over until you headbutt the wall…*

What many of the evolution deniers fail to see or understand is fossil records are not a great example of evidence for evolution. That’s not to say we can not support evolution from this evidence from the fossil record as discussed before, Haldane, biogeography etc.

But seeing as many of these people are obsessed with seeing intermediates, many examples do spring to mind, the one I have chosen is the one of the most cited and possibly the best example of a ring species that has been documented.

 Ensatina eschscholtzii the living intermediates!

On the Western coast of America, the rich coastal forests of California to the Western reaches of Nevada there is a rich habitat for amphibian life. It is here that we find one of the most compelling evidence of evolution happening before our eyes in the ensatina salamander (Ensatina eschscholtzii ).We can see observable aesthetic change as we progress from north to south.


To put it simply, as the population of salamander moved south, it was met by a geographical barrier which divided to populations. These two populations were split and are referred to being in reproductive isolation. Two populations of the same organism divided by the central valley. Both groups were exposed to different selection pressures created from the slightly differed environments. As the populations travelled further south, over time these different selection pressures have altered the phenotypes of these animals (How they look). Although these changes do alter how these animals look, the genome is not altered beyond the point where postzygotic barriers arise. Each population can breed freely with the neighbouring populations producing hybrids, this is true except for one pair. These pairs inhabit the region located south of the geographic barrier. The yellow blotted ensatina salamander and the Monterey salamander are sub species of Ensatina eschscholtzii. Therefore the reproductive isolation of the eastern valley salamanders has resulted in the diversification of one species, into two subspecies through a process called allopatric speciation.  

I guess in summary the point I am trying to make is evolution is a wonderful, beautifully constructed and most importantly true idea. It’s thought-provoking and inspiring, one of natures great puzzles. Although we know natural selection is true, there is still a lot to learn. Progress is being made, universities and research institutes continue to make new discoveries and more religious groups are excepting the theory of evolution as fact. The phrase ‘well its only a theory!’ is becoming more of a rarity in today’s society. Science is making more of a strive, new generations of intrigued pupils enter the educational system every year. There are more younger people getting involved in science, getting excited about science. I’ve shared these ideas here as this was the type of biology which inspired me to pursue a degree and hopefully a career in zoology.

Shark Conservation Posters For Liverpool Light Night 2016

I just thought I’d post these two posters I made for Liverpool light night 2016. The environmental team the outreach team at Liverpool john moores university had stalls which focused on the marine sciences with topics such as ocean acidification to shark conservation. Even though the event was back in may I thought I would just put up these posters as they are easy to read and they look nice.

shark conservation light night  deep sea sharks light night

You’re How Old?

I recently found a very interesting news article regarding the longevity of the Greenland shark (Somniosus microcephalus). At first I didn’t quiet believe it, so I had a little dig to find the academic paper and my mind hasn’t stopped racing, pondering what it is that allows this mysterious animal to have such a long life.

The Greenland shark is an iconic a mysterious,deep-sea species of the Arctic Seas. it has a slow growth rate and can reach >500 centimetres (cm) in total length. the paper suggests a life span well beyond those of other vertebrates just shy of 400 years!!

The study radiocarbon dated the eye lens nuclei from 28 female sharks. Additionally from the research it was estimated that these fish reach sexual maturity at around 156 ± 22 years of age. This slow growth rate, and maturity age raises many concerns about the conservation of this species. Additionally it could have ramifications about the conservation of many other species of shark. Research into the age of sharks in limited, therefore there could be other species that have a longer longevity the current estimates.

Here’s a link to the paper

What about the Genetics?

The study gives us this information but it has left me wanting to know much more. One thing that has particularly sparked my interest is what genetic mechanisms allow such a long life? Are there a set of mutations which have caused this longevity? if so do we see the same mutations in other long-lived species?

Many studies, usually involving the genetic model organism Caenorhabditis elegans have found some genes that have been shown to promote longevity across taxa. However, how these genes do so still remains poorly understood. Various isoforms (any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are encoded by different genes) of the FoxO transcription factors, such as DAF-2 and DAF-16 have been shown to massively increase longevity in mutant C.elegans. Furthermore, a variant of FOXO3 has been shown to be associated with longevity in humans. It is commonly found the genome of most centenarians and a variety of ethnic groups around the globe.

I think it would be very interesting as a follow-up study with the Greenland shark to do a genome-wide functional genomic screen for longevity genes. I would imagine that a study like this is applying for funding or even in the early stages of study. Either way I do look forwards to see the results to such a study in the near future.