Biology posts
- September 25, 2009
- 01:55 AM
- 1,057 views
Friday Weird Science: The Hyena Mating Game
by Evil Monkey in Neurotopia
Today's post comes to you courtesy of Laelaps. Sci's been wanting to cover sex in other species for a while now (I mean, it's so WEIRD!), and Laelaps has kindly provided a whole series of great articles!!! This is good, as Pubmed is not particularly informative on other species. The weird science is flowing today. Or maybe oozing. I imagine weird science likes to ooze.
So. Hyenas. Having sex. Which they don't really seem to do very often. And there's a good reason. The females don't have it very easy. What they have...is masculinized genitalia.
Warning: pics below the fold. Does it count as NSFW if it's a hyena pseudopenis?
Szykman et al "Courtship and mating in free-living spotted hyenas". Behavior, 2007
And these scientists are DEDICATED. I know it takes a long time for me to get through grad school, but these folks spent 11 YEARS making various trips to watch hyenas on the savannah. While it's a much better and more exciting location than my graduate work calls for, it still might get kind of old. Eternal vigilance with low hope of success must grind you down after a while. Their perseverance impresses me. Read the rest of this post... | Read the comments on this post...... Read more »
Szykman, M., Van Horn, R., Engh, A., Boydston, E., & Holekamp, K. (2007) Courtship and mating in free-living spotted hyenas. Behaviour, 144(7), 815-846. DOI: 10.1163/156853907781476418
- September 24, 2009
- 11:56 PM
- 692 views
Unwarranted pessimism on IL26B & HCV?
by Keith Robison in Omics! Omics!
I finally got around to reading the Nature News & Views article by Iadonato and Katze summarizing and opining on the recent quartet of papers linking genetic variation around IL26B and the response to standard therapy for Hepatitis C Virus. The N&V has at least one glaring flaw and also (IMHO) goes down the cliched route of concluding that the result will be clinically useless.The four GWAS studies found the same cluster of SNPs around IL28B, nicely cross-validating the studies. One curious statement in the N&V isAlthough all of the identified variants in the three studies lie in or near the IL28B gene, none of them has an obvious effect on the function of this gene, which encodes interferon-3, a growth factor with similarities to the interferon- preparations used as treatment.Two of the papers provide direct evidence as to at least one effect of these SNPs; one showed that the SNPs are linked to the expression of both IL28B and the nearby related gene IL28A; the other looked only at IL28B. Lower expression of these loci was correlated with the genotype with worse prognosis.The N&V goes on with some boilerplate pessimism about GWAS studies impact on medicineThe question remains, however, as to how readily these and other observations from GWAS can be translated into meaningful changes in patient care. The field of human genetics has described many associations between specific mutations and medically important outcomes, but rarely have these observations resulted in new therapies to treat disease or in major shifts in existing treatments. This failure is exemplified by the lack of clinical benefit that followed the cloning in 1989 of the gene responsible for cystic fibrosis11 — the first example of the use of molecular genetics to discover the cause of an otherwise poorly understood condition. Although some progress has been made in treating patients with cystic fibrosis, in the ensuing 20 years neither of the two newly approved drugs for this condition were developed using knowledge of the gene mutations that cause it. Apart from a few well-characterized beneficial mutations (for example, those resulting in resistance to HIV infection), genetics has been an inefficient tool for drug discovery.So although these findings raise the tantalizing prospect of a more personalized approach to treating HCV by tailoring treatment to patients who are most likely to benefit, the reality is more sobering. Diagnostic testing to identify likely responders to interferon may be a future possibility, but clinical decision-making will be clouded by the fact that the effect of the advantageous variant is not absolute — not all carriers of the variant clear the virus, nor do all patients lacking the variant fail to benefit from treatment. Furthermore, there is currently no alternative to interferon therapy for the HCV-infected population.. They also pile on with graphs showing the exponential growth of Genbank and dbSNP vs. the flat numbers for INDs (new drugs into trials) and NMEs (new approvals). Of course, I could respond with the boilerplate response (found in at least one of the papers) that patients with the "poor response" genotype. And indeed, new HCV therapies are in the pipeline, perhaps most prominently a compound under development by Vertex. Understanding if these variants affect response to the new compounds now becomes an important research question. But, it's also stunning that the N&V authors didn't suggest a rather obvious approach suggested by these papers. Not only do patients with the "high expression" genotype respond better to therapy, but this genotype also predicts spontaneous clearance of the virus. Furthermore, these loci encode secreted immune factors. So to me at least, this can be viewed as a classic protein replacement therapy candidate -- a subset of patients produce too little of a natural protein (or two natural proteins) and providing them with recombinant protein might provide therapeutic benefit. I suspect that whatever companies hold patent claims on IL28A & IL28B are contemplating just such a strategy. This is also in stark contrast to cystic fibrosis, where the affected protein is damaged rather than underexpressed and is a membrane protein not a secreted protein. By focusing on the general difficulty of converting genetic information to therapy rather than the specific circumstances of these papers, the N&V authors completely blew it.IL28A & IL28B loci produce proteins classified as interferons and it is another interferon (alpha) which is a key part of the standard therapy. A more extreme version (or a bit of the flip side) of the protein shortage theory would posit that the sum of the interferons is important for response -- and perhaps also for side effects. If this were the case, then increasing the dose of alpha interferon in the "low expression" genotype (or better yet, actually typing patients white cells for expression of these proteins) might be a reasonable clinical approach. Given that interferon alpha is already approved, this is the sort of clinical experimentation that goes on all the time.Yet another angle suggested by the "IL28A/B deficiency hypothesis" is that a viable therapeutic discovery approach is to find compounds which increase expression of IL28A and/or IL28B in leukocytes. This has been a successful strategy for generating new therapeutic hypotheses in oncology. Better yet, hints may already exist -- some enterprising student should search the Broad's Connection Map or other databases of expression data for cell lines treated with compounds to identify compounds which upregulate IL28A/B transcripts. A hit in such a search or a broader screen of already approved compounds could potentially rapidly lead to clinical experiments.The one time I had an opportunity to write a N&V (as a grad student) I got writer's block and missed the boat. It will always irk me. But, perhaps it's better to blow a chance silently rather than write such an awful, unimaginative one which stuck to stock genomics negativity rather than creatively exploring the topic at hand.Iadonato SP, & Katze MG (2009). Genomics: Hepatitis C virus gets personal. Nature, 461 (7262), 357-8 PMID: 19759611Ge, D., Fellay, J., Thompson, A., Simon, J., Shianna, K., Urban, T., Heinzen, E., Qiu, P., Bertelsen, A., Muir, A., Sulkowski, M., McHutchison, J., & Goldstein, D. (2009). Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance Nature, 461 (7262), 399-401 DOI: 10.1038/nature08309Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O'huigin C, Kidd J, Kidd K, Khakoo SI, Alexander G, Goedert JJ, Kirk GD, Donfield SM, Rosen HR, Tobler LH, Busch MP, McHutchison JG, Goldstein DB, & Carrington M (2009). Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature PMID: 19759533... Read more »
Iadonato SP, & Katze MG. (2009) Genomics: Hepatitis C virus gets personal. Nature, 461(7262), 357-8. PMID: 19759611
Ge, D., Fellay, J., Thompson, A., Simon, J., Shianna, K., Urban, T., Heinzen, E., Qiu, P., Bertelsen, A., Muir, A.... (2009) Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature, 461(7262), 399-401. DOI: 10.1038/nature08309
Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O'huigin C, Kidd J, Kidd K, Khakoo SI, Alexander G.... (2009) Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature. PMID: 19759533
the Hepatitis C Study, Suppiah V, Moldovan M, Ahlenstiel G, Berg T, Weltman M, Abate ML, Bassendine M, Spengler U, Dore GJ.... (2009) IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nature genetics. PMID: 19749758
Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K, Sakamoto N, Nakagawa M, Korenaga M, Hino K, Hige S.... (2009) Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nature genetics. PMID: 19749757
- September 24, 2009
- 08:39 PM
- 776 views
Heat Shock Proteins and Exercise in Humans
by Reason in Fight Aging!
Heat shock proteins (HSPs) are increasingly seen as important players in the response of our biochemistry to stresses and damage. HSPs are fundamentally chaperones and monitors: they look for damaged proteins that can compromise cellular functions and help to ensure that those proteins are rapidly recycled. When events - such as exposure to heat, hence the name - cause damage in our cells, HSP activity increases for a while to compensate. This is one basis for the phenomenon of hormesis, wherein a little damage applied regularly results in a better, longer lasting biological system: the HSPs are overcompensating. Since aging is an accumulation of biochemical damage - or, looked at another way, all forms of unrepaired damage lead to loss of function and degeneration - we would expect that greater HSP activity translates into longer lives and a more more robust, resiliant biochemistry. This seems to be the case in laboratory animals: Heat-shock proteins (Hsps) are increasingly being implicated in aging phenotypes and control of life span across species. They are targets of the conserved heat-shock factor and insulin/IGF1-like signaling pathways that affect life span and aging phenotypes. Hsps are expressed in tissue-specific and disease-specific patterns during aging, and their...... Read more »
Morton JP, Kayani AC, McArdle A, & Drust B. (2009) The exercise-induced stress response of skeletal muscle, with specific emphasis on humans. Sports medicine (Auckland, N.Z.), 39(8), 643-62. PMID: 19769414
- September 24, 2009
- 02:10 PM
- 944 views
Boundary Issues
by Journal Watch Online in Journal Watch Online
Scientists propose nine thresholds for a safe planet
... Read more »
Rockström, J., Steffen, W., Noone, K., Persson, �., Chapin, F., Lambin, E., Lenton, T., Scheffer, M., Folke, C., Schellnhuber, H.... (2009) A safe operating space for humanity. Nature, 461(7263), 472-475. DOI: 10.1038/461472a
- September 24, 2009
- 12:08 PM
- 685 views
No T-cell left behind, an explanation to why we sleep and more in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated into Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that ... Read more »
van Heijst, J., Gerlach, C., Swart, E., Sie, D., Nunes-Alves, C., Kerkhoven, R., Arens, R., Correia-Neves, M., Schepers, K., & Schumacher, T. (2009) Recruitment of Antigen-Specific CD8 T Cells in Response to Infection Is Markedly Efficient. Science, 325(5945), 1265-1269. DOI: 10.1126/science.1175455
Ascher, M., Sheppard, H., Jr, W., & Vittinghoff, E. (1993) Does drug use cause AIDS?. Nature, 362(6416), 103-104. DOI: 10.1038/362103a0
Nattrass, N. (2008) AIDS and the Scientific Governance of Medicine in Post-Apartheid South Africa. African Affairs, 107(427), 157-176. DOI: 10.1093/afraf/adm087
Siegel, J. (2009) Sleep viewed as a state of adaptive inactivity. Nature Reviews Neuroscience, 10(10), 747-753. DOI: 10.1038/nrn2697
- September 24, 2009
- 12:00 PM
- 1,046 views
Capture and Illumina Sequencing of Human Exomes
by Daniel Koboldt in Massgenomics
This month in Nature, a group from Jay Shendure’s lab reported perhaps the most ambitious targeted resequencing study to date - the whole exome sequences of 12 individuals.
Using an array-based hybridization capture method (2 microarrays, 10 g of input DNA), Ng et al selectively targeted CCDS regions totaling 26.6 Mb of sequence (~0.83% of the [...]... Read more »
Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE.... (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461(7261), 272-6. PMID: 19684571
- September 24, 2009
- 11:37 AM
- 730 views
Paint the Town Green
by Journal Watch Online in Journal Watch Online
Planted rooftops can sequester significant amounts of carbon
... Read more »
Getter, K., Rowe, D., Robertson, G., Cregg, B., & Andresen, J. (2009) Carbon Sequestration Potential of Extensive Green Roofs. Environmental Science , 2147483647. DOI: 10.1021/es901539x
- September 24, 2009
- 09:15 AM
- 1,064 views
The Next Steps in Synthetic Biology
by Tim Sampson in The Times Microbial
The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."... Read more »
Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759
- September 24, 2009
- 09:15 AM
- 1,078 views
The Next Steps in Synthetic Biology
by Tim Sampson in The Times Microbial
The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."More than 20 years later, this description is being realized. With the great minds and funds of the Venter Institute, we have seen the development of a completely synthetic genome and whole genome transplantation. The genome of Mycoplasma genitalium (at ~580Kbp) was synthesized primarily in vitro before being pieced together in Saccharomyces cereviseae. The whole genome of M. mycoides was transplanted into M. genitalium, changing the metabolism, physiology, structure, and subsequently the species of the recipient.Now, this group has taken this technology one step further. The synthetic genome they pieced together in yeast, must be isolated and transplanted into a donor cell; thus completing the construction of a synthetic, replicating organism.In a soon-to-be published article in Science, the group describes a method for modifying the complete bacterial genome while in yeast, and then transferring the modified genome back into the original cell. This process allows bacterial genomes to be modified using the well-described genetic systems in yeast, before being introduced. Thus, new possibilities are open for bacteria that once had little to no genetic tools available.The authors emphasize this development as it directly relates to Mycoplasma biology. They focus on the fact that Mycoplasma and related species now have an entire repertoire of manipulations available to them, however, the ramifications of this experiment certainly do not escape them and should not escape us.This is the first example of a bacterial cell being created and engineered completely outside the cell itself. Although the recipient cell began with all the necessary physical components for life, this group synthetically created a new organism to control and change those components. This is the closest we have come to synthesizing an organism from scratch.Some may say this is playing God; however, it will certainly have a positive impact on the development of biofuels, environmental remediation, and chemical synthesis on an industrial scale.Citation:Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N., Alperovich, N., Thomas, D., Merryman, C., Hutchison, C., Smith, H., Venter, J., & Glass, J. (2009). Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast Science DOI: 10.1126/science.1173759Other Articles of Interest:Phage + Metal = Battery?Free Hydrogen -- Algal Biofuel Prodution
... Read more »
Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759
- September 24, 2009
- 07:43 AM
- 665 views
Science News: Week of September 20, 2009
by Susan Steinhardt in BioData Blogs
Our weekly compilation of science news for the week of September 20, 2009.... Read more »
Duris, J., Haack, S., & Fogarty, L. (2009) Gene and Antigen Markers of Shiga-toxin Producing E. coli from Michigan and Indiana River Water: Occurrence and Relation to Recreational Water Quality Criteria. Journal of Environmental Quality, 38(5), 1878-1886. DOI: 10.2134/jeq2008.0225
Behan, J., Yun, J., Proektor, M., Ehsanipour, E., Arutyunyan, A., Moses, A., Avramis, V., Louie, S., Butturini, A., Heisterkamp, N.... (2009) Adipocytes Impair Leukemia Treatment in Mice. Cancer Research. DOI: 10.1158/0008-5472.CAN-09-0800
Cenna, J., Hunter, M., Tan, G., Papaneri, A., Ribka, E., Schnell, M., Marx, P., & McGettigan, J. (2009) Replication‐Deficient Rabies Virus–Based Vaccines Are Safe and Immunogenic in Mice and Nonhuman Primates. The Journal of Infectious Diseases, 200(8), 1251-1260. DOI: 10.1086/605949
- September 24, 2009
- 04:00 AM
- 689 views
Rehabilitating logged rainforests...
by Rob Goldstein in Conservation Maven
A new study explores the practice of forest rehabilitation and measures the impacts that this carbon sequestration strategy can have on habitat for birds...read more... Read more »
EDWARDS, D., ANSELL, F., AHMAD, A., NILUS, R., & HAMER, K. (2009) The Value of Rehabilitating Logged Rainforest for Birds. Conservation Biology. DOI: 10.1111/j.1523-1739.2009.01330.x
- September 23, 2009
- 08:39 PM
- 696 views
Accelerated Immune System Aging That Illustrates Normal Immune System Aging
by Reason in Fight Aging!
The study of forms of accelerated aging often provides insight into the biochemical processes of normal (and equally undesirable) degenerative aging. Here, we'll look at the aging of the immune system, a comparatively structured form of degeneration that might be viewed as the natural consequence of evolutionary selection: Evolution is a harsh but efficient mistress; you can consider yourself surprisingly well optimised as a piece of machinery, but your warranty only goes so far as the number of years in which your recent ancestors contributed to the success of their offspring. After that, you're on your own - biochemical processes unwind and break down free from any past selective pressure to do better. Take the immune system, for example, one of many absolutely vital components in the very complex system that supports your life. It is remarkably well optimized for reliable and effective use of resources in early and mid-life, but the rules that govern that optimization lead to a system that breaks down badly after extended usage. For a low cost in biological resources you get a good immune system at the very start of your life - but that system's prowess is all front-loaded. It is not set...... Read more »
Sauce, D., Larsen, M., Fastenackels, S., Duperrier, A., Keller, M., Grubeck-Loebenstein, B., Ferrand, C., Debré, P., Sidi, D., & Appay, V. (2009) Evidence of premature immune aging in patients thymectomized during early childhood. Journal of Clinical Investigation. DOI: 10.1172/JCI39269
- September 23, 2009
- 01:06 PM
- 1,050 views
Fisheries in Peril: The Evolution of Exploitation
by Johnny in Ecographica
What happens when the commercial fishing industry and recreational fishers target certain species for size? Do these practices of selective harvest equate to active artificial selection for smaller fish? Do these practices reverberate in the fish DNA in such a way that humans can be said to be manipulating the evolutionary trajectory of marine life? Thanks to the journal of Evolutionary Applications, here’s your chance to find out!... Read more »
McClenachan, L. (2009) Historical declines of goliath grouper populations in South Florida, USA. Endangered Species Research, 175-181. DOI: 10.3354/esr00167
- September 23, 2009
- 12:34 PM
- 556 views
Indications of failure
by Jeremy in Agricultural Biodiversity Weblog
A group of over 20 biodiversity experts from a slew of international conservation agencies have a paper out in Science bemoaning the state of the biodiversity indicators agreed in 2006. These indicators are important because they are supposed to be used to track progress towards fulfillment of the promise made by Parties under the Convention [...]... Read more »
Walpole, M., Almond, R., Besancon, C., Butchart, S., Campbell-Lendrum, D., Carr, G., Collen, B., Collette, L., Davidson, N., Dulloo, E.... (2009) Tracking Progress Toward the 2010 Biodiversity Target and Beyond. Science, 325(5947), 1503-1504. DOI: 10.1126/science.1175466
- September 23, 2009
- 10:58 AM
- 668 views
Gender Gap
by Journal Watch Online in Journal Watch Online
Female monarch butterflies are dwindling in parts of North America
... Read more »
Davis, A.K., & Rendón-Salinas, E. (2009) Are female monarch butterflies declining in eastern North America? Evidence of a 30-year change in sex ratios at Mexican overwintering sites. Biology Letters. info:/10.1098/rsbl.2009.0632
- September 23, 2009
- 08:45 AM
- 1,907 views
Tip of the week: JBrowse, a game changer?
In most of software and database development the changes that are coming along all the time seem to be tweaks and polishes on the existing strategies. Every so often, though, there’s a big shift in the strategy or mechanism. This week the JBrowse paper I read made me realize that is now firmly underway. Today’s tip of the week will introduce JBrowse, and here I’ll describe some of the reasons this is a game changer.... Read more »
Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009) JBrowse: A next-generation genome browser. Genome Research, 19(9), 1630-1638. DOI: 10.1101/gr.094607.109
- September 23, 2009
- 08:07 AM
- 1,219 views
Hedgehog signalling and new cancer therapies
by Sally Church in Pharma Strategy Blog
Having written about hedgehog signalling in cancer a few times on this blog (see here, here and here for examples), including it's potential role in CML, it came as no surprise to see some very exciting new data presented in...... Read more »
Von Hoff, D., LoRusso, P., Rudin, C., Reddy, J., Yauch, R., Tibes, R., Weiss, G., Borad, M., Hann, C., Brahmer, J.... (2009) Inhibition of the Hedgehog Pathway in Advanced Basal-Cell Carcinoma. New England Journal of Medicine, 361(12), 1164-1172. DOI: 10.1056/NEJMoa0905360
Rudin, C., Hann, C., Laterra, J., Yauch, R., Callahan, C., Fu, L., Holcomb, T., Stinson, J., Gould, S., Coleman, B.... (2009) Treatment of Medulloblastoma with Hedgehog Pathway Inhibitor GDC-0449. New England Journal of Medicine, 361(12), 1173-1178. DOI: 10.1056/NEJMoa0902903
Dlugosz, A., & Talpaz, M. (2009) Following the Hedgehog to New Cancer Therapies. New England Journal of Medicine, 361(12), 1202-1205. DOI: 10.1056/NEJMe0906092
- September 23, 2009
- 03:20 AM
- 537 views
Istanbul on the Rhine
by Jeremy in Agricultural Biodiversity Weblog
Good news for sun-loving Germans. By 2071-2080 parts of their country are going to have the climate that parts of Greece have now. That’s according to a paper in Plant Ecology which ran a bunch of climate change models for Europe. Have a look at the money map.
On the left are today’s Germany-like climates in [...]... Read more »
Bergmann, J., Pompe, S., Ohlemüller, R., Freiberg, M., Klotz, S., & Kühn, I. (2009) The Iberian Peninsula as a potential source for the plant species pool in Germany under projected climate change. Plant Ecology. DOI: 10.1007/s11258-009-9664-6
- September 23, 2009
- 03:00 AM
- 689 views
Comparing natural, restored, and created wetlands...
by Rob Goldstein in Conservation Maven
How do natural, restored, and created wetlands match up when it comes to vegetation and soil properties? A new study looks at wetlands in Hawaii...read more... Read more »
Bantilan-Smith, M., Bruland, G., MacKenzie, R., Henry, A., & Ryder, C. (2009) A Comparison of the Vegetation and Soils of Natural, Restored, and Created Coastal Lowland Wetlands in Hawai‘i. Wetlands, 29(3), 1023-1035. DOI: 10.1672/08-127.1
- September 22, 2009
- 10:36 PM
- 1,056 views
Bioinformatics: A recipe-based approach is biggest curse
by Abhishek Tiwari in Fisheye Perspective
Some time back Deepak Singh wrote an interesting post The curse of BLAST describing how BLAST has become synonymous to the bioinformatics. Although his article highlights a general perception about bioinformatics especially within bench scientists it does not account for the reason which lead us to generalize bioinformatics with BLAST or any other protocol. I was reading an article by Pavel A. Pevzner, Educating Biologists in the 21st Century: Bioinformatics Scientists vs. Bioinformatics Technicians, where Pevzner takes a shot over the current recipe-based approach in bioinformatics training programs. Further he explains how a Bioinformatics 101 based approach is preparing bioinformatics technicians rather than bioinformatics scientists.Many recent bioinformatics books cater to a protocol-centric pragmatic approach to bioinformatics. They focus on parameter settings, application-specific features, and other details without revealing the computational ideas behind the algorithms. This trend often follows the tradition of biology books to present material as a collection of facts and discoveries. In contrast, introductory books in algorithms and mathematics usually focus on ideas rather than on the details of computational recipes. In principle, one can imagine a calculus book teaching physicists and engineers how to take integrals without any attempt to explain what is integral. Although such a book is not that difficult to write, physicists and engineers somehow escaped this curse, probably because they understand that the recipe-based approach to science is doomed to fail. Biologists are less lucky and many biology departments now offer recipe-based bioinformatics courses without sending their students first to Algorithms 101 and Statistics 101. Some of students who take these classes get excited about bioinformatics and try to pursue a research career in bioinformatics. Many of them do not understand that, with a few exceptions, such courses prepare bioinformatics technicians rather than bioinformatics scientists.Bioinformatics is often defined as "applications of computers in biology". In recent decades biology has raised fascinating mathematical problems and reducing bioinformatics to "applications of computers in biology" diminishes the rich intellectual content of bioinformatics. Bioinformatics has become a part of modern biology and often dictates new fashions, enables new approaches, and drives further biological developments. Simply using bioinformatics as a toolkit without understanding of the main computational ideas is not very different than using a PCR kit without knowing how PCR works.So much true. Simply using bioinformatics tools or protocols as part of a collection of cookbook style recipes without understanding how they work does not make anyone bioinformatics scientist. As Pevzner writes Users that do not know how BLAST works might misapply the algorithm or misinterpret the results it returns . Biologists sometimes use bioinformatics tools simply as computational protocols in quite the same way that an uninformed mathematician might use experimental protocols without any background in biochemistry or molecular biology. In either case, important observations might be missed or incorrect conclusions drawn. Besides, intellectually interesting work can quickly become mere drudgery if one does not really understand it.I could not agree more, Bioinformatics is perfect example how intellectually interesting work can quickly become mere drudgery if one does not really understand it.Reference: Pevzner, P. (2004). Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians Bioinformatics, 20 (14), 2159-2161 DOI: 10.1093/bioinformatics/bth217
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Pevzner, P. (2004) Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics, 20(14), 2159-2161. DOI: 10.1093/bioinformatics/bth217
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