How a bacteria from your mouth can promote cancer in your colon!

Cancer is a vastly complicated phenomenon. Cancerous tumours can arise from any tissue of the body and the causes of tumorigenesis are even more variable than the tumour types. Innumerable environmental factors have been linked to cancer; some evidently more relevant than others[1]. Tumour cells can be actively destroyed by the body through a type of white blood cell called natural killer (NK) cells [2] . Like all cells these have an array of cell surface receptors through which they can communicate with other cells and detect stimuli within the extracellular environment. All receptors require a particular molecule, or a range of select molecules, to adhere to their binding site for activation. These are referred to as ligands[3]. A fundamental innovation of the immune system is the capacity to produce a vast range of cell surface receptors. NK cells possess two particular subsets of receptors. Depending on which subset is predominantly activated, the NK cell will be triggered into killing target cells (becoming cytotoxic) or remain deactivated. These receptor subsets are aptly referred to as activator or inhibitory receptors[2]. NK cells are not explicitly used for killing tumour cells. Bacteria, parasites and viruses can all be destroyed by the cytotoxic activity of NK cells [2]. Any disruption to the signals received by NK cells can result in a suboptimal immune system, with harmful cytotoxic targets remaining intact.

A recent study by Gur et al uncovered a remarkable connection between a common oral dwelling bacterium, our immune system, and tumour survival. The bacterium in question, Fusobacterium nucleatum, is traditionally known for its contribution to the development of gum disease[4]. However over the last decade this seemingly harmless microbe has been found to play a key role in preterm births and to frequently inhabit colon cancers [5,6].  With additional knowledge that F.nucleatum can interfere with our immune system Gur, and his colleagues at the University of Jerusalem, decided to investigate this bacterium further [7,8]. They wanted to know whether this species of bacteria could provide a survival advantage to the tumours it so commonly resides in.

Gur et al began by showing that F.nucleatum could efficiently colonise several tumours of different origin; corroborating the previous literature. Next they turned their heads to assessing the effects of F.nucleatum on NK cell cytotoxicity. Various tumour types, including F.nucleatum’s seemingly favoured colon cancer, were incubated with activated NK cells for 5 hours. After incubation the percentage killing was calculated by comparing the starting number of tumour cells with the number of survivors post NK cell incubation. This was repeated with the same tumour types but this time the tumours were prexposed to F.nucleatum. In all of the prexposed tumours there was a striking decrease in NK cell killing compared to the non-exposed tumours of the same tumour type[4]. To ensure this was not a strain specific phenomenon they repeated the same experiment with another strain of F.nucleatum. Again the prexposed tumours exhibited significantly lower numbers of cells being killed[4]. To check the killing inhibition was not simply the consequence of bacterial residence, they repeated this experiment with a completely different species. In this final test with E.coli, there was no difference in the percentage killing between non-exposed and pre-exposed tumours[4]. The data strongly suggested that the bacterial species of F.nucleatum interferes with the potency of NK cytotoxicity. But how does it do it?

It was hypothesised that F.nucleatum activates an inhibitory receptor common to all NK cells. This would result in cytotoxic repression and could explain the observed survival advantage of F.nucleatum invaded tumours. To date only one inhibitory receptor is known to be expressed by all NK cells. This receptor is called TIGIT and it became the main focus of their investigation [9]. The TIGIT receptor spans the cell membrane from its external binding site, to its cytoplasmic tail. Once activated by a ligand the cytoplasmic tail conveys the external message to intracellular effectors. These quickly instigate a cease to the cell’s cytotoxic activity. A cleverly designed assay allowed Gur et al to show that F.nucleatum can activate TIGIT receptors[4]. Using genetic manipulation they fused the extracellular component of TIGIT to the cytoplasmic tail of a mouse immune receptor called CD3. This chimeric protein was then actively expressed in a cell line. The swapping of cytoplasmic tails was necessary because the CD3 tail gives a clearer, more easily measured response to receptor activation. A protein called IL-2 is released when the CD3 tail is activated. It is this protein that was used to quantify TIGIT activation[10,4]. When F.nucleatum was finally exposed to cells expressing the chimeric TIGIT receptor, IL-2 was detected[4]. This provided strong evidence that F.nucleatum can both interact and activate TIGIT.

Further experimentation was required to confirm that the F.nucleatum-TIGIT interaction is capable of neutralising NK cell cytoxicity. A particular line of mutated NK cells were used for this experimentation. The NK cell mutants are deficient of all inhibitory receptors and thus their cytotoxic activity cannot be neutralised. Unsurprisingly, the mutant NK cells (∆NK) showed no signs of cytotoxic impairment when incubated with F.nucleatum exposed tumours[4]. Next they took the inhibitory receptor deficient ∆NK cells and restored their TIGIT receptor. With a fully functional TIGIT gene the ∆NK cells were equipped with a solitary mechanism for killing inhibition. If the cytotoxicity of these new ∆NK cells (∆NKTIGIT) was lost in presence of F.nucleatum then it had to be via an interaction with TIGIT. This is exactly what they saw [4].

With this confirmation the search began for the bacterial protein responsible for activating TIGIT. An F.nucleatum mutant library was created using transposon mutagenesis technology. Transposons are naturally occurring stretches of DNA that can move around the genome. In the process of relocation transposons can disrupt genes. Utilising this trait allows thousands of mutant bacteria to be created at so that each colony randomly contains a different disruption[11]. A good library of mutants will have at least one disruption mutant for every gene. All of their F.nucleatum mutants were exposed to tumour cells separately. These prexposed tumour cells were then incubated with ∆NKTIGIT cells. Only two mutant strains were unable to inhibit the ∆NKTIGIT cells from killing tumour cells. This implies the disrupted genes in these mutants are required for F.nucleatum’s TIGIT interaction. Fortunately for simplicity both mutants had disruptions to the same gene; Fap2[4]. Thanks to these experiments it has been established that F.nucleatum’s outer membrane protein, Fap2, is capable of localised inhibition to the cytotoxic activity of NK cells (Figure 1).

fap

Figure 1: NK cell cytotoxicity when exposed to wild type and mutant strains of F.nucleatum[4].

Due to this newly found trait it is obvious that F.nucleatum can provide a profound survival advantage to developing tumours. F.nucleatum cannot cause a systemic shut down of NK cell killing. NK cells have to have come in physical contact with the bacterium if they are to lose their cytotoxic capabilities. For a tumour to benefit from this survival advantage the bacterium has to inhabit its tissues. Due to the anoxic conditions in which the bacterium evolved to thrive, it is likely that F.nucleatum is capable of surviving in many different tumour types. Why then has F.nucleatum only really been found with any consistency in colon cancers? The answer is probably a simple matter of exposure. The ease at which F.nucleatum could passage from its native oral environment, through the GI tract, to colonic tumours may explain its prevalence in such carcinomas[4]. The authors highlight that F.nucleatum is an important player in the development and survival of colon cancers, but its role in other cancers remain uncertain. More data is required to fully assess F.nucleatum’s significance to other solid tumours. An interesting question that I would like to see answered is whether the administering of antibiotics alongside the standard treatments for colon cancer can better patients’ prognosis? Obviously this would have to be rigorously tested before any new combination therapies are put in place, but an interesting line of investigation no doubt.

  1. SCOTTING, P. 2010. Cancer A Beginner’s Guide. Oneworld Publications
  2. KOCH, J., STEINLE, A., WATZL, C. & MANDELBOIM, O. 2013. Activating natural cytotoxicity receptors of natural killer cells in cancer and infection.Trends in Immunology, 34, 182-191
  3. COOPER, G,. M. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Signaling Molecules and Their Receptors.Available from: http://www.ncbi.nlm.nih.gov/books/NBK9924/
    (Accessed 20/03/15)
  4. GUR, C., IBRAHIM, Y., ISAACSON, B., YAMIN, R., ABED, J., GAMLIEL, M., ENK, J., BAR-ON, Y., STANIETSKY-KAYNAN, N., COPPENHAGEN-GLAZER, S., SHUSSMAN, N., ALMOGY, G., CUAPIO, A., HOFER, E., MEVORACH, D., TABIB, A., ORTENBERG, R., MARKEL, G., MIKLIC, K., JONJIC, S., BRENNAN, C. A., GARRETT, W. S., BACHRACH, G. & MANDELBOIM, O. 2015. Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack.Immunity, 42, 344-355.
  5. HAN, Y. P. W., REDLINE, R. W., LI, M., YIN, L. H., HILL, G. B. & MCCORMICK, T. S. 2004. Fusobacterium nucleatum induces premature and term stillbirths in pregnant mice: Implication of oral bacteria in preterm birth.Infection and Immunity, 72, 2272-2279.
  6. KOSTIC, A. D., GEVERS, D., PEDAMALLU, C. S., MICHAUD, M., DUKE, F., EARL, A. M., OJESINA, A. I., JUNG, J., BASS, A. J., TABERNERO, J., BASELGA, J., LIU, C., SHIVDASANI, R. A., OGINO, S., BIRREN, B. W., HUTTENHOWER, C., GARRETT, W. S. & MEYERSON, M. 2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.Genome Research,22, 292-298.
  7. LIU, H., REDLINE, R. W. & HAN, Y. W. 2007. Fusobacterium nucleatum induces fetal death in mice via stimulation of TLR4-mediated placental inflammatory response (vol 179, pg 2501, 2007).Journal of Immunology, 179, 5605-5605.
  8. CHAUSHU, S., WILENSKY, A., GUR, C., SHAPIRA, L., ELBOIM, M., HALFTEK, G., POLAK, D., ACHDOUT, H., BACHRACH, G. & MANDELBOIM, O. 2012. Direct Recognition of Fusobacterium nucleatum by the NK Cell Natural Cytotoxicity Receptor NKp46 Aggravates Periodontal Disease.Plos Pathogens,
  9. STANIETSKY, N., ROVIS, T. L., GLASNER, A., SEIDEL, E., TSUKERMAN, P., YAMIN, R., ENK, J., JONJIC, S. & MANDELBOIM, O. 2013. Mouse TIGIT inhibits NK-cell cytotoxicity upon interaction with PVR.European Journal of Immunology, 43, 2138-2150.
  10. STANIETSKY, N., SIMIC, H., ARAPOVIC, J., TOPORIK, A., LEVY, O., NOVIK, A., LEVINE, Z., BEIMAN, M., DASSA, L., ACHDOUT, H., STERN-GINOSSAR, N., TSUKERMAN, P., JONJIC, S. & MANDELBOIM, O. 2009. The interaction of TIGIT with PVR and PVRL2 inhibits human NK cell cytotoxicity.Proceedings of the National Academy of Sciences of the United States of America, 106,17858-17863.
  11. PRAY, L. 2008.Transposons: The jumping genes. Nature Education 1(1):204 http://www.nature.com/scitable/topicpage/transposons-the-jumping-genes-518
    (Accessed 23/03/15)

Featured image from: https://www.google.co.uk/search?q=F.nucleatum&rlz=1C1CHFX_en-GBGB450GB450&espv=2&biw=1366&bih=629&source=lnms&tbm=isch&sa=X&ei=PbQaVcajOqfW7Aay94C4Dw&ved=0CAYQ_AUoAQ#imgdii=_&imgrc=csAJVNzpSBfuaM%253A%3B1M221WMILKQstM%3Bhttp%253A%252F%252Fsrxa.files.wordpress.com%252F2013%252F08%252Ffusobacterium_ll_111017_wg.jpg%3Bhttp%253A%252F%252Fsrxawordonhealth.com%252Ftag%252Ffusobacterium-nucleatum%252F%3B640%3B360

Investigating CIC. A gene associated with the development of Brain Cancer.

The New Year has seen me undertake a small research project as part of my master’s degree. The topic in question, or rather the gene in question, is a transcription factor called CIC. This gene has been associated with the development of a particular brain cancer known as Oligodendroglioma. Patients with this cancer do not survive and those that are diagnosed die within 2-15years[1]. A noteworthy 77% of Oligodendrogliomas have been shown to harbour a CIC mutation[2,3,4]. Some mutations can result in the perturbation of a gene’s functionality. If the disruption of a gene has the potential to contribute to cancer, the gene will fall into one of two categories. Oncogenes are determined when mutation leads to a gain of function in the encoded protein, where the newly acquired function aids cancer development [5]. A good example would be the Myc gene where mutations can cause irreversible activation of the protein. Activated Myc results in increased cellular proliferation; a key step in tumourigenesis [6]. The other type is referred to as a tumour suppressor (TS). Knudson’s two hit hypothesis was established, through the study of retinoblastoma genetics, to help define a TS. If a mutation causes a loss of function and the cellular consequences promote cancer development. The gene is regarded as a TS.  In order to completely lose protein functionality, two genetic events (hits) are required to ensure both alleles are affected [7].

The first recurrent genetic aberration found in ODG was the codeletion of the short arm of chromosome 1 and long arm of chromosome 19 (1p19q codeletion). This is seen in nearly two thirds of Oligodendroglomas and is regarded as a defining feature for this brain cancer [1]. Interestingly the CIC gene is located on the same arm of chromosome 19 that is lost during the codeletion. As both 1p19q codeletions and CIC mutations are so common to Oligodendroglioma, it has been speculated that CIC might be a TS [8]. It is easy to see how CIC could meet the two hit hypothesis in such tumours. The loss of an entire CIC allele via the 1p19q codeletion would act as the first hit. If the mutation in CIC’s remaining allele is deleterious then this would suffice a second hit (Figure1). But does a loss of CIC function actually contribute to cancer development? This is a difficult question to answer because of a lack of understanding in CIC’s conventional cellular functions. Without a clear understanding of how something works normally, you cannot fully understand the ramifications of when it goes wrong.

2 hit hypothesis

Figure 1: Knudson’s two-hit hypothesis applied to the CIC gene in 1p19 codeleted ODGs. The purple and green chromosomes correspond to chromosomes 1 and 19 respectively. Chromosome arms p and q are indicated with white lettering. The yellow rectangles represent wild type CIC alleles. The first allele is lost (1st Hit) due to an imbalanced reciprocal translocation between chromosomes 1 and 19. The second allele is disrupted (2nd Hit) by a somatic mutation capable of inhibiting protein function. This mutation is indicated by a red cross. With no functional CIC alleles remaining the gene is effectively lost and tumourigenesis can begin (Figure by Luke Webster).

The majority of what we do know about CIC has been established through the extrapolation of previous work on the Drosophila orthologue; Capicua. The primary function of Capicua is to act as a transcriptional repressor, turning off target genes. This repressor activity is fundamental to the anteroposterior patterning and wing vein differentiation of Drosophila development [9]. For Capicua to function as a transcriptional repressor the presence of co-repressor Groucho is required. CIC has also been shown to possess a transcriptional repressor activity in humans with the ability to target a group of genes called PEA3 [10, 11]. Furthermore, interaction with other proteins can heighten and encourage CIC’s repressor activity, much like Drosophila and Groucho. There are two domains that are vital for Capicua’s functionality. The first is a common DNA binding domain called the HMG box. This allows Capicua to interact with its target genes. The HMG box is highly conserved in mammalian CIC and actually facilitated CIC’s discovery during a neuronal development study [12]. The other is a C-terminal domain associated with the transcriptional repressor activity of Capicua. Within this domain are two conserved motifs. The first (C1) is thought to be the interface between Capicua and Groucho [13]. The second motif (C2) allows the inhibition of Capicua’s repressor activity in response to signalling cascades that phosphorylate C2. Human CIC shares this trait with Capicua as its repressor activity is also blocked in response to cell signalling dependent phosphorylation [11].

So of what interest is all of this to us? After assessing all the known recorded CIC mutations found in Oligodendrogliomas there are two regions within which nearly all missense mutations reside [2, 3,4,8,14]. These correspond to the two known functional domains; the HMG box and the C-terminal protein interaction domain (CPID). Furthermore protein structure simulation software predicted that these mutations were “probably damaging” to protein function [8]. This is all very encouraging as the identified functional domains do appear key to CIC’s cellular roles, and these domains are being disrupted in Oligodendrogliomas. If CIC is a TS then the loss of function that promotes the development of cancer is likely to be sourced from these recurrently mutated domains.

Previous work from my lab has shown that mammalian CIC can also interact with Groucho and suggests that such an interaction induces a repressor activity in CIC. The thesis goes on to provide some evidence that the CIC/Groucho interaction is in the N-terminal region[15]. This is rather contrasting to the Capicua literature. I wanted to assess whether CIC’s CPID could facilitate a Groucho interaction as the homology with Capicua suggests. I also wanted to see whether the CPID mutations seen in Oligodendroglioma could prevent a CIC Groucho interaction. My running hypothesis is that CIC is a TS and mutations in the CPID prevent a CIC Groucho interaction. Unable to bind its co-repressor, CIC loses the ability to repress target genes. The resulting cellular consequences encourage the formation of Oligodendroglioma.

To test some of my ideas I designed a nuclear translocation assay. CIC contains a nuclear localisation site (NLS) and is therefore believed to favour a nuclear residence within the cell. This is coherent with the idea that CIC is a transcription factor. Most forms of Groucho also contain an NLS however Groucho5 does not. This implies Groucho5 has a cytoplasmic subcellular localisation. I took a GFP fused Groucho5 (Grg5-GFP) and transfected it into COS7 cells. Fluorescent microscopy allowed the visualisation Grg5-GFP within the COS7 cells. Groucho5 did indeed reside in the cytoplasm. Next I co-transfected the Grg5-GFP along with CIC. This time the green fluorescence was predominantly nuclear, implying that CIC interacted with Groucho and facilitated its translocation to the nucleus. My next steps are to use a mutagenesis kit to create CIC mutants that mimic those seen in oligodendroglioma. When these CPID mutations are synthesised I will co-transfect the mutant CIC genes into COS7 cells along with Grg5-GFP. If a mutation disrupts the CIC Groucho interaction then the cells will display a cytoplasmic localisation of Grg5-GFP. If a mutation does not disrupt the CIC/Grg5 interaction then the green fluorescence will be seen predominantly in the nucleus. With this experiment there is unfortunately no way to tell the difference between a CIC mutant that blocks the Grg5-GFP interaction, and a failed co-transfection where the CIC mutant has not been successfully incorporated into the COS7 cells.

A solution to this problem would be to immunostain for the CIC mutants so that the CIC proteins fluoresce a different colour to the GFP. Unfortunately after many attempts and different antibodies I could not get specific binding for CIC. To show whether CIC genes have been successfully incorporated I will extract the RNA from co-tranfected cells. If CIC is successfully incorporated there will be CIC RNA within the cell. Converting this to DNA allows me to use qPCR which can tell me how much, and if any, CIC protein is being synthesised in the co-transfected cells.

Due to the time constraints on lab availability I will not be able to accomplish much more than the experiments described here. I hope my results can make a contribution, however small, to our understanding of CIC. Only once we have established the normal workings of CIC, can we move forward to assess CIC’s status as a TS, and its role in the formation of Oligodendroglioma.

Glossary

1p19q codeletion: This deletion of chromosome arms 1p and 19q occurs via an an imbalanced reciprocal translocation event. Both chromosomal breakpoints occur near the centromeres and homologies between these regions probably facilitate the translocation.

Domain: conserved region of a protein that can evolve function.

GFP:green florescent protein is from a deep sea jellyfish and is commonly used in Biology to tag proteins.

Missense mutation: Where a single base change causes a change in the translated amino acid.

Orthologue: Genes in different species that eveolved from a common ancestral gene. They usually retain the same or similar functions across species.

Phosphorylation: The addition of a phosphate group to a molecule. This can often cause an activation or inactivation of a protein.

Retinoblastoma: A malignant intraocular cancer that often arises in children.

Signalling cascade: This often starts in response to extracellular signalling that is picked up by cell surface receptor. The receptor becomes activated which often causes the phosphorylation of an intracellular protein. This protein phohorylates another, which in turn phospohrylates another and so on until the message reaches effectors. These effectors are usually transcription factors

Transcription factor: These proteins bind DNA and influence the level of transcription of its targets. Transcription factors may work alone, in protein complexes and may activate, repress or either their target gene.

Sources

  1. ALENTORN, A., SANSON, M. & IDBAIH, A. 2012. Oligodendrogliomas: new insights from the genetics and perspectives.Current Opinion in Oncology, 24, 687-693.
  2. BETTEGOWDA, C., AGRAWAL, N., JIAO, Y., SAUSEN, M., WOOD, L. D., HRUBAN, R. H., RODRIGUEZ, F. J., CAHILL, D. P., MCLENDON, R., RIGGINS, G., VELCULESCU, V. E., OBA-SHINJO, S. M., MARIE, S. K. N., VOGELSTEIN, B., BIGNER, D., YAN, H., PAPADOPOULOS, N. & KINZLER, K. W. 2011. Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma.Science, 333, 1453-1455.
  3. YIP, S., BUTTERFIELD, Y. S., MOROZOVA, O., CHITTARANJAN, S., BLOUGH, M. D., AN, J., BIROL, I., CHESNELONG, C., CHIU, R., CHUAH, E., CORBETT, R., DOCKING, R., FIRME, M., HIRST, M., JACKMAN, S., KARSAN, A., LI, H., LOUIS, D. N., MASLOVA, A., MOORE, R., MORADIAN, A., MUNGALL, K. L., PERIZZOLO, M., QIAN, J., ROLDAN, G., SMITH, E. E., TAMURA-WELLS, J., THIESSEN, N., VARHOL, R., WEISS, S., WU, W., YOUNG, S., ZHAO, Y., MUNGALL, A. J., JONES, S. J. M., MORIN, G. B., CHAN, J. A., CAIRNCROSS, J. G. & MARRA, M. A. 2012. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.Journal of Pathology, 226, 7-16.
  4. SAHM, F., KOELSCHE, C., MEYER, J., PUSCH, S., LINDENBERG, K., MUELLER, W., HEROLD-MENDE, C., VON DEIMLING, A. & HARTMANN, C. 2012. CIC and FUBP1 mutations in oligodendrogliomas, oligoastrocytomas and astrocytomas.Acta Neuropathologica, 123, 853-860.
  5. SCOTTING, P. 2010. Cancer A Beginner’s Guide. Oneworld Publications.
  6. HSIAO, H. H., NATH, A., LIN, C. Y., FOLTA-STOGNIEW, E. J., RHOADES, E. & BRADDOCK, D. T. 2010. Quantitative Characterization of the Interactions among c-myc Transcriptional Regulators FUSE, FBP, and FIR.Biochemistry, 49, 4620-4634.
  7. BERGER, A. H., KNUDSON, A. G. & PANDOLFI, P. P. 2011. A continuum model for tumour suppression.Nature, 476, 163-169.
  8. EISENREICH, S., ABOU-EL-ARDAT, K., SZAFRANSKI, K., VALENZUELA, J. A. C., RUMP, A., NIGRO, J. M., BJERKVIG, R., GERLACH, E.-M., HACKMANN, K., SCHROECK, E., KREX, D., KADERALI, L., SCHACKERT, G., PLATZER, M. & KLINK, B. 2013. Novel CIC Point Mutations and an Exon-Spanning, Homozygous Deletion Identified in Oligodendroglial Tumors by a Comprehensive Genomic Approach Including Transcriptome Sequencing.Plos One,
  9. JIMENEZ, G., SHVARTSMAN, S. Y. & PAROUSH, Z. 2012. The Capicua repressor – a general sensor of RTK signaling in development and disease.Journal of Cell Science, 125, 1383-1391.
  10. KAWAMURA-SAITO, M., YAMAZAKI, Y., KANEKO, K., KAWAGUCHI, N., KANDA, H., MUKAI, H., GOTOH, T., MOTOI, T., FUKAYAMA, M., ABURATANI, H., TAKIZAWA, T. & NAKAMURA, T. 2006. Fusion between CIC and DUX4 up-regulates PEA3 family genes in Ewing-like sarcomas with t(4 ; 19)(q35 ; q13) translocation.Human Molecular Genetics,15, 2125-2137
  11. DISSANAYAKE, K., TOTH, R., BLAKEY, J., OLSSON, O., CAMPBELL, D. G., PRESCOTT, A. R. & MACKINTOSH, C. 2011. ERK/p90(RSK)/14-3-3 signalling has an impact on expression of PEA3 Ets transcription factors via the transcriptional repressor capicua.Biochemical Journal, 433, 515-525.
  12. LEE, C. J., CHAN, W. I., CHEUNG, M., CHENG, Y. C., APPLEBY, V. J., ORME, A. T. & SCOTTING, P. J. 2002. CIC, a member of a novel subfamily of the HMG-box superfamily, is transiently expressed in developing granule neurons.Molecular Brain Research, 106, 151-156.
  13. AJURIA, L., NIEVA, C., WINKLER, C., KUO, D., SAMPER, N., ANDREU, M. J., HELMAN, A., GONZALEZ-CRESPO, S., PAROUSH, Z., COUREY, A. J. & JIMENEZ, G. 2011. Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila.Development, 138, 915-924.
  14. JIAO, Y. C., KILLELA, P. J., REITMAN, Z. J., RASHEED, B. A., HEAPHY, C. M., DE WILDE, R. F., RODRIGUEZ, F. J., ROSEMBERG, S., OBA-SHINJO, S. M., MARIE, S. K. N., BETTEGOWDA, C., AGRAWAL, N., LIPP, E., PIROZZI, C. J., LOPEZ, G. Y., HE, Y. P., FRIEDMAN, H. S., FRIEDMAN, A. H., RIGGINS, G. J., HOLDHOFF, M., BURGER, P., MCLENDON, R. E., BIGNER, D. D., VOGELSTEIN, B., MEEKER, A. K., KINZLER, K. W., PAPADOPOULOS, N., DIAZ, L. A. & YAN, H. 2012. Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas.Oncotarget, 3, 709-722.
  15. WAI, I.-C. 2004. Characterisation of CIC – A Novel Sox-like Factor. PhD Thesis. University of Nottingham: United Kingdom.

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The Origin of Eukarya; Evidence behind an old debate.

From multicellular giants to microscopic protists, the eukaryotes contain the most complex forms of life that Earth has to offer. It is a fascinating prospect that the diverse eukaryotic kingdoms were all derived from a common ancestor. Explaining the origins of this ancestor has been problematic and inspiring of countless hypotheses. Many textbooks will speak of three primary domains in the tree of life; Archaeabacteria, Eubacteria and the Eukarya. These are usually depicted so that Eukarya are more closely related to the Archaeabacteria (Archaea) than Eubacteria (Bacteria)[1](Figure1A). In this tree arrangement all three domains are deemed monophyletic lineages that arose about the same time. The three domains hypothesis is one of many hypotheses that suggest an autogeneous origin for the eukaryotes. An autogeneous origin would mean that Eukaryotes emerged and developed all of their complexities, through stepwise mutation, without any external genetic material[2].This is certainly perplexing when you consider it has been widely accepted that mitochondria, the organelle responsible for the production of cellular energy, has a bacterial origin[3,4] . Those in favour of an autogeneous origin of eukaryotes do not discard the fact that an endosymbiosis of the mitochondrial ancestor occurred, nor do they discard that this was a landmark event in biological history.  They just believe the eukaryotic cell was well established before this event occurred[2] (Figure1B). There is a strong opposing argument to the various autogeneous models and these differ in two vital aspects. The first is that there were only two primary domains; Bacteria and Archaea (Figure1C). Eukarya emerged much later as the result of an endosymbiosis event between an Archaeon and an alphaproteobacterium; the mitochondrial ancestor[2,5] (Figure1D) The mutual exclusivity of these two arguments has led to much debate over the past decades. In this blog I shall look at the current evidence to see which argument has the most backing.

1: The Two Arguments. A) The three domains tree. B) An autogeneous view on the endosymbiosis event. C) A tree depicting only two primary lineages with Eukarya emerging late. D) The endosymbiosis view on the origin of Eukarya.

The autogeneous model initially appears to be supported by many phylogenetic studies. When looking at particular genes that are known to be highly conserved, such as ribosomal genes, the trees form to resemble that of the three domains hypothesis[2]. Phylogenetics has however become more sophisticated in recent years, with broader analysis over entire genomes now possible. The new trees indicate 2 primary lineages with the eukaryotes arising later from the archaeal lineage[2]. Thus modern phylogenetic evidence actually backs the endosymbiosis argument. But what about the hard evidence in the fossil records?

Earth is thought to be 4.5 billion years old and the earliest evidence for life are inclusions of minerals found in the rocks of Greenland. These inclusions are dated back to 3.85 billion years ago [6]. The oldest remnants of cells to be found are 3.4 billion years old, and these are undistinguishable in terms of domain. What is certain is that these ancient cells showed no signs of any characteristic features of eukaryotes. The oldest confirmed eukaryotic fossils are approximately 1.6-1.8 billion years old which is coherent with the predicted emergence of extant eukaryotes from molecular clock studies [7,8]. Until a eukaryotic fossil that predates 3.4billion years is identified, the fossil records will remain in agreement with a later emergence of eukaryotes.

A seemingly glaring fault in the endosymbiosis argument is that prokaryotic cells cannot undergo cell fusion. Without the ability to take up the mitochondrial ancestor how could this event define the origin of eukaryotes? Many Eukaryotic cells have the ability to engulf others through phagocytosis. Actin proteins form structures called lamellipodia or filopodia which allow this engulfment and fusion [2]. For an alphaproteobacterium to be taken up, the host must have been an established eukaryote with actin proteins. This seemed the case until it was discovered that some Archaea contain actin like proteins that can also facilitate cell fusions[9]. It is plausible that primitive versions of these actin resembling proteins enabled the uptake of the mitochondrial ancestor[9].

Another key line of evidence that has been assessed is bioenergetics. For a cell to be as complex as a eukaryote, relatively large amounts of energy are required. One study has highlighted that without a sophisticated method of energy production, a cell is not capable of reaching the levels of complexity exhibited by the  eukaryotes. They go on to explore the best ways of producing such an energy source in such a confined space; only to end up describing what is ultimately a mitochondria. Without the mitochondria it would be energetically impossible for the eukaryotes to exist as they do [10]. Furthermore in order for the mitochondria to become established it’s ancestor would have needed to lose most of its genes as to prevent overeplication within in the host cell. This provided a selection advantage for those cells where endosymbiosis gene transfer (EGT) took place. Genetic analysis has unveiled a chimeric nature to the eukaryotic genome that supports such extensive EGT and horizontal gene transfer from other  sources[11]. It has been shown that the majority of housekeeping genes appear to be of archaeal decent whereas the genes involved in metabolism are more closely related to those from bacteria[12]. It is paradoxical for an organism to autogenously materialise with a chimeric genome. This becomes even more confusing when you consider the proposed genetic donors for this chimera, and the chimera itself, are all supposed to have emerged separately and in parallel of each other.

It appears the majority of evidence across a wide variety fields supports an endosymbiosis origin over an autogenous origin for Eukarya. This has significant consequences to how we perceive and depict the tree of life. We should have the two prokaryotic domains as the primary lineages of the tree. Eukaryotes should be regarded as a secondary lineage arising much later as the consequence of an endosymbiosis between the other domains[2]. It is hard to ignore the weight of evidence and so I too support the endosymbiosis argument. The hypothesis that best describes what it think occurred is the Phagocytosing Archaeon and I shall summarise below (Figure2).

2: Phagocytosing Archaeon Theory. 1) Archaeon with first actin like proteins (blue). 2) Loss of cell wall allows evolution of basic cytoskeleton with cellular protrusions. 3) Primitive phagocytic machinery established and uptake of foreign DNA (red, green, yellow, pink, purple) is now possible. 4) Invagination results in a protective boundary around the DNA. 5) Endosymbiosis of the mitochondrial ancestor and EGT leads to increased energy supply, development of cellular complexities and the formation of an early eukaryotic cell [5].

Here an Archaeon containing the first actin-like proteins slowly develops a primitive cytoskeleton. In the process it loses the prokaryotic cell wall. Without a cell wall the actin like proteins could form cellular protrusions resembling phagocytotic machinery. The engulfing of passing prokaryotes would have exposed the cell to large amounts of foreign DNA. Frequent horizontal gene transfer could explain some of the mosaic nature in the eukaryotic genome. A by product of all this random recombination is genetic instability. This in turn may have sped up evolution in these organisms. Which could explain why similarities between eukaryotic and archaeal genes are usually minimal compared to the more extensive conservation seen in Alphaproteobacteria and mitochondria. Next is the compartmentalisation of the genome through invaginations of the cell membrane. This would protect the genome from engulfed genetic material and restabilise its rate of evolution. An alphaproteobacterium is phagocytosed but not degraded and develops a symbiosis. They even speculate that a symbiosis may have been present before phagocytosis. As said the additional energy production could permit all the eukaryotic complexities to arise and develop to how we see them today[5]. The mitochondrial ancestor undergoes reductive evolution to eventually become the organelle we recognise today.

Many other endosymbiosis theories are equally justified as we have no evidence of the intermediary stages eukaryotic evolution to prove otherwise. Although this hypothesis is the one I personally feel is the most intellectually pleasing, I would happily have it proven wrong if any contradictory evidence should arise.

Sources

  1. WOESE, C. R., KANDLER, O. & WHEELIS, M. L. 1990. TOWARDS A NATURAL SYSTEM OF ORGANISMS – PROPOSAL FOR THE DOMAINS ARCHAEA, BACTERIA, AND EUCARYA.Proceedings of the National Academy of Sciences of the United States of America, 87, 4576-4579.
  2. MCINERNEY, J. O., O’CONNELL, M. J. & PISANI, D. 2014. The hybrid nature of the Eukaryota and a consilient view of life on Earth.Nature Reviews Microbiology, 12, 449-455.
  3. GRAY, M. W., BURGER, G. & LANG, B. F. 1999. Mitochondrial evolution.Science,283, 1476-1481.
  4. GRAY, M. W., BURGER, G. & LANG, B. F. 2001. The origin and early evolution of mitochondria.Genome Biology,
  5. MARTIJN, J. & ETTEMA, T. J. G. 2013. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.Biochemical Society Transactions, 41, 451-457.
  6. MOJZSIS, S. J., ARRHENIUS, G., MCKEEGAN, K. D., HARRISON, T. M., NUTMAN, A. P. & FRIEND, C. R. L. 1996. Evidence for life on Earth before 3,800 million years ago.Nature, 384, 55-59.
  7. KNOLL, A. H., JAVAUX, E. J., HEWITT, D. & COHEN, P. 2006. Eukaryotic organisms in Proterozoic oceans.Philosophical Transactions of the Royal Society B-Biological Sciences, 361, 1023-1038.
  8. PARFREY, L. W., LAHR, D. J. G., KNOLL, A. H. & KATZ, L. A. 2011. Estimating the timing of early eukaryotic diversification with multigene molecular clocks.Proceedings of the National Academy of Sciences of the United States of America,108, 13624-13629.
  9. YUTIN, N., WOLF, M. Y., WOLF, Y. I. & KOONIN, E. V. 2009. The origins of phagocytosis and eukaryogenesis.Biology Direct,
  10. LANE, N. & MARTIN, W. 2010. The energetics of genome complexity.Nature, 467,929-934.
  11. TIMMIS, J. N., AYLIFFE, M. A., HUANG, C. Y. & MARTIN, W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes.Nature Reviews Genetics, 5, 123-U16.
  12. RIVERA, M. C., JAIN, R., MOORE, J. E. & LAKE, J. A. 1998. Genomic evidence for two functionally distinct gene classes. Proceedings of the National Academy of Sciences of the United States of America, 95, 6239-6244.

Featured image: https://www.google.co.uk/search?q=the+eukaryotic+cell&rlz=1C1CHFX_en-GBGB450GB450&espv=2&biw=1366&bih=681&source=lnms&tbm=isch&sa=X&ei=eKUaVZywAYzX7QaMt4CYBQ&ved=0CAYQ_AUoAQ#tbm=isch&q=the+eukaryotic+cell+3D&imgdii=_&imgrc=-bgaMgb2j6Vr2M%253A%3BguH4zXFRwULLPM%3Bhttps%253A%252F%252Fc2.staticflickr.com%252F4%252F3020%252F5839627161_46c1610918.jpg%3Bhttps%253A%252F%252Fwww.flickr.com%252Fphotos%252F61048931%2540N08%252F5839627161%252F%3B500%3B500

Why scientific practice can fall short of the ethical ideal.

Introduction

Science is one of the greatest achievements of mankind. The discoveries, innovations and healthcare improvements yielded since the beginning of curiosity are astonishing. Science relies on its unique method and its established codes of conduct to ensure the data it provides is of the highest quality, and our best representation of the world around us. Honesty is imperative for science and the integrity of its claims. Important extensions of this honesty are the abstention from plagiarism and respecting fellow researchers by acknowledging their contributions at every opportunity. Openness is another important aspect which entails publishing your findings, subject to peer review, and retaining raw data for anyone that is inclined to look deeper[1]. Despite these ideals being adhered to by the majority, like nature itself, there are cheats that try to leapfrog the competition. I shall discuss two examples of where the scientific ideals have been abused for personal gain.

Jan Hendrik Schön

Jan Hendrik Schön was thought of as one of the brightest young physicists to emerge in the new millennium. Between 2000 and 2002 he published 20 articles, 13 of which were published in prestigious journals Science and Nature. This is truly a remarkable achievement but his dazzling statistics didn’t end there. He was averaging 4-5 papers a month and his best effort saw him publish 7 in November 2001. His astonishing turnover of scientific literature did not affect the quality as brilliant discoveries were churned out one after the other[2]. To put this in perspective a great scientist may publish in the top end journals a dozen times in their life. Even theoretical scientists, with no data production constraints, rarely publish 7 papers in a year. Schön’s field of research was “molecular electronics” and the goal of this field is to reduce the size of computer chips down to that of single molecules. His discoveries included the manufacturing of nanoscale transistors and organic plastics for use as superconductors. Science described one of his papers as the “breakthrough of the year” in 2001[2]. His success brought him international admiration, he was a modern genius; it was almost too good to be true.                                                                                                              

jan-hendrik-schon-photo-3

Jan Hendrik Shön

 

Suspicions over the integrity of Schön’s work first arose when a fellow expert pointed out some glaring obscurities. His data appeared unrealistic because it mimicked the theoretical outcome. For example some of his data was predicted to follow a bell shaped curve and it did, but to comical accuracy[2]. There were no outliers or signs of experimental noise. If anyone asked to see his raw data he told them he deleted it to save space on his computer. Fascinated peers asked him to show them a demonstration of his discoveries, to which he would decline because his equipment resided in his old German laboratory[2].

Further investigation in 2002 revealed that Schön was nothing but a sophisticated and elaborate fraud. Malcolm Beasley, a professor from Stanford University, lead the investigations and found that Schön had breached the scientific codes of conduct and was guilty of substituting data, producing data of unrealistic precision and results that contradicted known physics[2]. He extensively fabricated data, reusing graphs and changing the labelled axis to appear as though many different materials had achieved similar results. His heavily manipulated data was poorly disguised by the absence of raw data. These blatant examples of scientific misconduct were exhibited in 16 of his 24 papers. The remaining 6 were deemed troubling if not intentionally fraudulent[2]. So how did these papers ever get published, let alone in the top journals in which they did?

It is believed that the peer review process actually helped Schön’s forgery. The criticisms his papers received provided the information he required to produce a perfect piece of work. By fabricating the missing components he won over many skeptics[2]. It appears that the timing of Schön’s rise also aided him no end. Science and Nature were looking to expand their horizons and publish more papers regarding fields outside of medical research. Materials science certainly filled this void. Schön’s articles were even fast-tracked through the peer review process being published 25% faster than the average. In one case his paper was seen by a single referee[2]. This careless approach by these top journals is eye-opening and highlights the necessity for vigilant peer reviewing with an appropriate number of referees.

In addition to the lowered guard at the top journals, Schön’s employers were under extreme pressure at the time. Bell Labs was in a troubling financial state and had laid off 50% of their staff between 1997 and 2001[2]. Middle management with little lab experience were brought in to tackle these corporate troubles. In light of the financial unrest it is conceivable to see how Schön’s wrongdoings could be overlooked by the desperate company. Schön was churning out gold for very little input costs[2]. The miracle papers appeared to be just that to the heads at Bell Labs. Fortunately the out of hand facade came to an end and Schön’s fraudulent papers were retracted.

The social implications of the Schön scandal did not really stretch further than the academic community. This is not always the case and scientific scandals can have a huge external effect with long term consequences.

Annie Dookhan

Annie Dookhan was a forensic chemist who worked for the Department of Public Health in Massachusetts. She worked at the Hinton state laboratory in Jamaica plain, for nine years from 2003. Her biggest responsibility was to weigh and test drugs found as evidence. Due to the dependence of sentence length on the quantity and category of drugs found, Dookhan’s results would directly affect the courts and the guilty. Mistakes could easily lead to illegitimate incarceration of the prosecuted[3,4].

In 2011 it was noted that 90 drug samples given as evidence were incorrectly recorded. This sparked investigation into the Hinton laboratory and led to its closure in 2012. Dookhan had her evidence handling duties revoked yet she continued to testify in court.  Two weeks before the police ordered the closure of her laboratory Dookhan resigned[3].  The 36 year old was taken to court and pleaded guilty to “27 counts of misleading investigators, filing false reports, and tampering with evidence.” She went on to confess her fabrication of test results, mixing of samples and lying under oath[4]. Ironically her motif for these crimes was the desire to boost her professional profile and reputation. Her actions not only cost her freedom for 3-5 years but also her marriage.

Annie Dookhan, a former chemist at the Hinton State Laboratory Institute, listens to the judge during her arraignment at Brockton Superior Court in Brockton, Massachusetts

Annie Dookhan

 

It is believed Dookhan was involved in more than 40,000 cases during her time at the Hinton laboratory[4]. The repercussions of her irresponsibility are ongoing for the Massachusetts legal system. A huge number of defendants are demanding release and retrial. By November 2013 the courts have spent $8.5 million on the reviewing of cases and a further $8.6 million has been set aside for the same function. Of the 600 released prisoners approximately 13% have recommitted. The worst of these was a drug-related murder[4]. It is predicted that further release of prisoners will lead to a crime wave but the courts’ hands are tied by their need to fulfill fair justice requirements[4]. As of July 2014 only 8900 of the 40,000 cases had been assessed by lawyers[5]. Dookhan has left the Massachusetts legal system in turmoil.Thousands of people could be unfairly suffering and paying for crimes they didn’t commit, furthermore many legitimate criminals may take advantage of the situation and instigate their release. Dookhan’s actions are a vivid example of how disregard for the ethical ideals of science can have lasting effects on the wider society and even safety of the public. Abuses like this lead to public unrest and mistrust of scientific professionals.

Conclusion

Mistrust of science is growing within society and this is partly down to frauds like Dookhan and Schön. This growing unrest is stimulated by the fact that scientific misconduct is more alluring to journalists than plain scientific discovery. Scandals are always an interesting read but they portray science in an unfair light. This does not mean that the offenders should be ignored, but their minority should be reiterated. As we have seen from the Schön scandal, quite shockingly, that even the top journals can be guilty of relaxed protocols. The scientific community, funding bodies, institutions and journals need to be more vigilant.

The reason for the forgery seen in these cases was the potential personal gain acquired from their success. The temptation of recognition clearly outweighed the moral justification for these two. For me the Dookhan case is the most alarming. Her complete disregard for the knock on effects of her forgery is beyond me. The lives she has effected is incalculable. One light of optimism that can be taken from these cases and many others is that the frauds are often ousted. Sooner or later they get caught.

 

Sources

  1. , (2013). BBSRC Statement on Safeguarding Good Scientific Practice. http://www.bbsrc.ac.uk/organisation/policies/position/policy/good-scientific-practice.aspx
    (Accessed 27/11/14).
  2. D. (2009). Physics and Pixie Dust. American Scientist.
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  3. M. J. (2012). State says chemist at drug lab imperilled evidence. The Boston Globe.
    http://www.bostonglobe.com/metro/2012/08/30/problems-uncovered-with-state-drug-lab-jamaica-plain-state-police-plan-news-conference/zHsjfZxigQVCxwRHM3Gd2I/story.html
    (Accessed 5/12/14).
  4. M. J., Ellement. J. R. (2013). Annie Dookhan pleads guilty in drug lab scandal. The Boston Globe. http://www.bostonglobe.com/metro/2013/11/22/annie-dookhan-former-state-chemist-who-mishandled-drug-evidence-agrees-plead-guilty/7UU3hfZUof4DFJGoNUfXGO/story.html
    (Accessed 6/12/14).
  5. L. (2014). Thousands in Annie Dookhan cases still not identified. The Boston Globe.
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    (Accessed 6/12/14).
  6. Picture; Jan Hendrik Schön.
    Active Science via Google images.
    https://activescience.files.wordpress.com/2012/12/jan-hendrik-schon-photo-3.jpg
    (Accessed 7/12/14)
  7. Picture; Annie Dookhan. Reuters Media via Google images. http://s1.reutersmedia.net/resources/r/?m=02&d=20130204&t=2&i=700775387&w=580&fh=&fw=&ll=&pl=&r=CBRE9131GON00
    (Accessed 7/12/14)

What is Science?

Science is one of the greatest achievements of mankind. It is our most logical and impartial way of explaining the world around us. The unique scientific method is based on evidence and there are several requirements to meet in order for information to be deemed scientific. These requirements largely remain the same but not all scientific knowledge will perfectly match these imperfect guidelines. Science is difficult to define and it is the ambiguity of this elusive definition that has had many pondering the question; what is Science?

Science is divided into three major categories; biology, chemistry and physics. Biology attempts to answer questions relating to living entities. Chemistry tackles the behaviour, structure and properties of matter, while physics investigates the motion, forces and energy that confines matter to the natural world. There are large overlaps between these fields and their definitions are nearly as indeterminate as Science itself. Collaboration between these areas can allow a much broader understanding of the world around us. Questions pertaining the meaning of life, the human soul and the existence of God can never be answered through Science. A common misconception is that Science can contradict the existence of God and therefore discredit religion. All three factions of Science exclusively relate to the natural (physical) world. This strictly prohibits the involvement of Science in supernatural arguments[1].

The aim of Science is to better our understanding of the natural world. Well-accepted ideas within the scientific community are open to adjustments or even complete discard. The manner of this system is alarming to some and may construe Science as unreliable; a common misunderstanding. Well-supported scientific ideas are exactly that, because of the large body of evidence that supports it. Lesser accepted ideas are usually the ideas with minimal or conflicting evidence. Science is constantly striving for new evidence which can inevitably lead to old ideas being cast aside. For example in 1938 an ancient fish (coelacanth), ubiquitously accepted to be extinct, was discovered living off the coast of South Africa[2]. Even the greatest theories have flaws. If there is no better explanation than a marginally or majorly flawed theory, then this is the best we have. Regardless of confounding factors the majority of accepted scientific knowledge is extremely useful. Our understanding of thrust and lift, among other knowledge, enabled the engineering of aeroplanes and space shuttles. All around us Science is being applied to great success with some of the most astonishing achievements being seen in medicine. Nothing is set in stone and the forward striving motion of Science is behind its impressive success[2].

Portrayed imagery of a great, all powerful machine that relentlessly ploughs forward, churning out brilliant discovery after brilliant discovery, is not necessarily an accurate one. Science achieves what it does through the accumulation of tiny forward steps that combat many knockbacks to give a net forward motion. There are two ways in which Science can be researched; applied and pure. Applied is where an ultimate goal is set and the research is focussed on attaining that goal. The more successful of the two is the “blue skies” or pure Science which is driven by curiosity[2]. Both can lead to unpredictable discoveries and many of the greatest discoveries were “unintentional.” Applied science is more abundant in the modern era due to the extremely high costs of scientific research. Commercialism in science feels it needs to justify spending and aim to produce either an agreed goal or a marketable product. The best example of this is the pharmaceutical industry where huge investments in research are made and a final product is demanded. On many occasions this product remains elusive. Governments are another protagonistic funder of science. As governments are largely run by professionals without a scientific background there are often misunderstandings of what a “good” scientific result is. Politicians want to justify their spending by having a sense of security that what is discovered can be applied to the wider society and will be a beneficial contribution for the nation. It is difficult to disagree with this notion but these are promises that can rarely be guaranteed.

Only testable ideas contribute to science. An idea needs to provoke the conjuring of logical predictions that can be tested. Experiments are designed to test specific ideas. If expected observations are seen in an experiment then this can infer the idea is correct. Observations that infer an idea is incorrect are equally important. It can be difficult to devise an appropriate experiment to test a particular idea. Sometimes the development new technologies and techniques are required[3]. Many experiments are imperfect and have to integrate a number of assumptions, thus limitations need to be considered when interpreting data. Ideas that can equally explain mutually exclusive outcomes are not testable. This reiterates the point that science cannot test the supernatural. For example science cannot test the extent of God’s control over everything. Every possible scenario or outcome of a test can stem from the unworldly being’s higher agenda[3].

Scientific ideas must actually be tested. Highly regarded ideas are ones that are backed by multiple lines of evidence that have been repeatedly tested. The same or very similar results should occur time and time again even if tested by many different scientists. Ideas that do not have supporting evidence are not accepted as science[4]. The involvement of the scientific community is an imperative aspect of science. This community contains all the researching institutions, scientists, journals, funding bodies and conference participants. Without this community science could not exist in its well established format. Feedback and contributions within the community are vital for improving our knowledge whether it be cross-field involvement, refereeing of articles or awareness exercises[5].

Science is ongoing. Solving old questions only stimulates an array of new ones, some of which can be picked up by researchers half way round the globe[6]. Although we cannot specifically define Science there are some key elements that are mostly integral to this phenomenon. Without Science the world would be an unrecognisable and arguably inauspicious place.

Sources

  1. University of California Museum of Paleontology. A Science Checklist. Understanding Science how science really works. http://undsci.berkeley.edu/article/0_0_0/whatisscience_03
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  6. University of California Museum of Paleontology. Scientific ideas lead to ongoing research. Understanding Science how science really works. http://undsci.berkeley.edu/article/0_0_0/whatisscience_08
    (Accessed 6/12/14)

Reanimation of Mammoth Proportions

Spielberg’s 1993 rendition of the novel Jurassic Park captured the world’s attention and exposed our imagination to the idea of de-extinction. Innovations in genetic technology and a huge leap in our understanding has brought this science fiction closer to reality[1]. Pleistocene Park (Figure1) in the north east of Siberia is trying to revert the existing desolate ecosystem back to the organism rich landscape it once was.  The Park has grown in size since their establishment in 1996 and they have already successfully introduced reindeer, bison and oxen  but they are missing the key protagonist for their Mammoth Steppe restoration[1,2,3]..  It is hoped that Mammoths could be cloned from DNA found in ancient remains and then released back into the wild.

mam2

Figure1: Global location of Plastocene Park with magnification to see the park boundaries. The red line shows its original size before the more recent expansion shown in blue.

The idea is to clone a mammoth in the same way that dolly the sheep was cloned in 1997; via somatic cell nuclear transfer(SCNT)[1,6]. This is where scientists take DNA from a normal cell and place it into an empty female egg (Figure2). Proteins in the egg then reprogram the DNA from its normal restricted format to a more accessible format. Like opening a closed book this reveals information and unlocks the instructions needed to form an embryo. The egg with its newly unlocked DNA is implanted into a surrogate mother who can then carry the embryo through to birth. Unfortunately this reprogramming is not very efficient and leads to many complications and few successful clones[7]. These problems have been reiterated in the attempted revival of the bucardo; an extinct goat. After hundreds of tries only one goat was successfully delivered via caesarean section. Despite being a perfect clone the bucardo’s return to earth lasted merely a few minutes before its lungs failed[8].

mammoth

Figure2: Diagrammatic method of Somatic Cell Nuclear Transfer using Mammoth DNA.

For SCNT to work an intact genome is required. This means that we need to find a mammoth cell containing the entire library of DNA with no damage. This is an extremely challenging task as DNA breaks down and loses its integrity with time[1,4]. Due to the permafrost melting more mammoth remains are being found and one of the most recent finds was extremely well preserved with muscle, hair and even blood (Figure3)[4,5]. Despite this promising specimen the genome remains elusive but some believe there is an alternative solution. It has been proposed that filling in the gaps of the mammoth genome with DNA from its closest modern day relative, the Asian elephant, you could produce an enhanced hybrid[9]. It sounds like simple patchwork but is extremely complex and debatable as to whether a viable organism could be produced[1,10].

Woolly mammoth

Figure3: Photograph of the wooly mammoth remains with preserved hair.

Resurrecting Mammoths or other extinct animals may be possible in the future but is this endeavour wise? Many with religious backgrounds would argue against de-extinction believing it is “playing God” and perverting nature. They believe environmental solutions to conservation are the ideal response and this biological manipulation is morally wrong and against a higher power’s intentions [11]. Yet many do not see such biological interference as categorically immoral and the “playing God” argument may not have strength with those of different cultural backgrounds. Some believe that it is not how life is created that should be morally questioned but its ability to fit in[12].

When ‘alien’ species are introduced to new habitats they can have a detrimental effect on the ecosystem as seen with escaped boa-constrictors in the everglades, USA[13]. These worries can be translated to introducing an extinct species to the wild. Food webs are often disrupted in nature by migration, alien invasion and extinctions yet they always seem to endure[11]. Natures ‘balance’ is dynamic, it adapts and moves forward. Mammoths would certainly be at home with little ecological collateral in Pleistocene Park as the same plants still dominate this habitat.

One of the biggest concerns with any de-extinction is the welfare of the organism in question. Inefficient SCNT results in deaths to surrogates as well as newborns and this fact alone is enough for some to deem the science not worth it[14]. Mammoths may be susceptible to modern diseases even harbour unknown pathogens[10].  In order to fully understand the mammoths’ requirements they would be studied before being released into the wild and this may cause unfair distress[11].       Mammoths are social creatures and solitary production for entertainment would be widely regarded as unacceptable. Many that oppose zoos for their exploits of animals as attractions will not consent to such uses of mammoths. However the underling curiosity and wonderment of seeing a real life mammoth remains a strong motif for their production[10].

Man played a significant role in the extinction of the Mammoth and if we had the technology to bring it back would this not mean we had a moral obligation to do so? Allocating resources for de-extinction instead of species protection is controversial but the technology could enable development of more powerful conservation tools[9].

Sources

  1. ROAST, A. 2013. De-extinction: Mammoth prospect, or just wooly?. BBC NEWS Science & Environment. http://www.bbc.co.uk/news/science-environment-23602142 (Accessed 21/2/14)
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Figures

Figure1: Adaptation by LUKE WEBSTER using two images:
LEWIS, M. 2012. Pleistocene Park: The Regeneration of the Mammoth Steppe? GeoCurrents. http://www.geocurrents.info/place/russia-ukraine-and-caucasus/siberia/pleistocene-park-the-regeneration-of-the-mammoth-steppe (Accessed 23/2/14)
KRONBERG, D. 2012. Pleistocene Park Photo Gallery. NESS & Pleistocene Park.http://www.pleistocenepark.ru/en/photo/1/ (Accessed 23/2/14)

Figure2: Created and illustrated by LUKE WEBSTER

Figure3: NOGI, K.2013. Frozen remains of woolly mammoth present cloning possibilities. Examiner.com http://www.examiner.com/article/frozen-remains-of-woolly-mammoth-present-cloning-possibilities (Accessed 23/2/14)