On BioScience and Life and Such

Posts Tagged ‘science’

A christmas revelation

In Uncategorized on December 21, 2016 at 10:17 am

Well, two revelations actually.

Yesterday I set out to watch Westworld.

HBO, for some reason, sort the episodes from bottom to top. Me, not always the master of clever, thought through decisions, pressed the top episode.

As I was watching the season finale, thinking it was the first episode, I thought to myself “Wow, this was an intricate and elaborate way of starting out, I hope at some point they explain the plot a bit more”. They didn’t. So I watched the whole season finale, and then I stopped watching Westworld.

From this I got two revelations:

  1. There’s a lot of time to be saved watching just the last episode.
  2. In the Michelangelo picture “The creation of Adam“, God sits within a human brain. We create God in our brains, not the other way around – this should be obvious to everyone and not really the revelation in itself. The revelation, rather, is that Michelangelo managed to communicate this right under the noses of the Christian authorities, in the centre of their power houses,  – and managed to get paid for it. What a great man Michelangelo was.



The shape around God, the angels and saints, may also be interpreted as a uterus. In this interpretation the green vail symbolizes an umbilical cord. Combining the two interpretations leads to the conclusion that not only is God a figment of our imagination, but the offspring we produce are god-like. Michelangelo comes full circle: We are the gods of our minds.

Merry christmas

Creación de Adán (Miguel Ángel).jpg

Tidbits from the www that makes you think

In Uncategorized on January 24, 2013 at 9:25 am

From a comment on a post on my friendfeed (I hope its ok that I quote this from you Kamilah Reed):

This makes me think of the mantis oothecae that I saw the mother lay on the edge of our deck. I saw her stand guard there until the cold killed her. The egg cases still out there, toughing it out through all this nasty cold weather. I can’t wait to see if we’ll actually have dozens of baby mantises next year. We’ve had them before, but I didn’t see where the case was last time.

I recently finished The Social Conquest of Earth (recommended), and found myself buying into Edward O. Wilsons arguments on social evolution vs. kin selection. We have become social beings based on traits like compassion of and empathy with, other individuals of our kind.

Based on th quote above though, you might want to expand the reach of those human traits to include other species as well. This quote encompasses empathy, compassion and sympathy towards a species far removed from our own. Importantly, a species I do not particularly care much about myself. Without the particular context of the story, I would gladly have gotten rid of those eggs, but since I find myself intrigued by the sacrifice of the mother-Mantis, I probably wouldn’t.

So, to all of you out there dooming the human race, despair not, – there may be hope. There are individuals out there that will share stories and facts that saves us – be thankful for diversity and keep listening.

Mantis religiosa trademark

Mantis religiosa trademark (Photo credit: macropoulos)

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Generalized Dontreallyknow Amount (GDA)

In Uncategorized on June 20, 2010 at 7:51 pm

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For no particular reason, it’s been a while since I have been to a McDonalds. We did go today though and I noticed that McDonalds like many other fast- or processed-food suppliers have started putting %GDA (Guideline Daily Amount) tables on their products. This is the Quarter Pounder one for women (!?):

So….according to the nutrinionists making these tables, eating two Quarter pounders with cheese a day will give you all the protein you need, all the fat you need and a bit more salt than you actually need. Throw in fries, a coke and a multi-vitamin pill. Result: a bit to much salt, but in general – healthy eating.

Anyone but me spotting a problem with these %GDA tables ?

A train (wreck) of (religious) thoughts

In Uncategorized on February 1, 2009 at 11:50 am

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Early science, particularly geometry and astro...
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I made this argument in the last post that being “natural” (or biologically unaltered, which is more accurate in this setting) means keeping our self-reliance. And, loosing that self-reliance may be one of the main reasons people fear biomedical technology.

Then it occurred to me, what about religion ? After all mankind at all times have used religion in one form or another to justify/explain our existence, – and usually there is one or more almighty deities that are in control. Pledging allegiance to a god must certainly be to give away self-reliance ?

I’d like to argue the opposite. Religion is our way of pretending we control things that are clearly outside of our control. Thus, with a deity on our side we are self reliant even though it’s quite obvious in our daily lives that we are not. The central underlying assumption is that this God is on our side, – on our team.

Technology on the other hand does not take sides. Statistics, mathematics, physics, chemistry and biology are (in theory) completely objective – sometimes cruelly so.

The real delusion then is not the one that Dawkins points out – that God is a delusion (and I have commented on this before,  his arguments really doesn’t make a difference because beliefs or faith can easily be called delusional, but still serve the same purpose). Rather the real delusion is that God is on our side, – that god makes our team self reliant.

And consequently that science does not. But the naked truth is that the concept of self reliance is what is delusional – making scientific development go in the direction we want is  the least delusional and by far the safest way to make sure our reliance will be upon something benign.

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BIOpinionated quote-fest 0109

In Uncategorized on January 14, 2009 at 3:17 pm

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The costume of the science fiction character D...
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1. From “Darth Vader’s “Management” Secrets“:

Darth Vader is a Dark Lord of the Sith and second-in-command in the Galactic Empire, where he is the pupil of Emperor Palpatine. He studied the Jedi arts under Obi-Wan Kenobi and serves a Sith apprenticeship with Darth Sidious. Darth’s brother, Chad, is the Day-Shift Manager at Empire Market.

2. From ERV in response to George Johnson critizing science blogging:

Do you realize what this means to people, George? How much a preventative HIV vaccine or cheaper/better/easier medications for HIV/AIDS means to people? How fucking scary HIV is to people? What these kinds of messages (WE CURE AIDZ NAU! LOL NOT REALLY!) do to the general public? What it does to their trust of scientific research in this country?

3. From an Effect Measure post on research into effects of the the virginity pledge:

82% of pledgers denied ever having taken the pledge

4. A comment on this YouTube video:

not so far in the future, humans are taken over by the elite using this so called helpful science.

5. From this friendfeed discussion:

In order to die someday, you have to be alive. Everything is dangerous, I suggest not leaving your home, not using any type of equipment, electricity, gas, etc inside, and not eating any food from unknown sources. Also filter the inbound air, water and any other fluid. And don’t read the interwebs, there are crazy people out there. – Paulo Nuin

6. From another friendfeed discussion:

There are many scary things about today’s world. But one that is truly thrilling is that the means of spreading both knowledge and inspiration have never been greater. Five years ago, an amazing teacher or professor with the ability to truly catalyze the lives of his or her students could realistically hope to impact maybe 100 people each year. Today that same teacher can have their words spread on video to millions of eager students. There are already numerous examples of powerful talks that have spread virally to massive Internet audiences. – Will Richardson

7. From this post on Eye On DNA:

But sometimes, what’s in your genes isn’t in your heart. I’d rather my children followed their heart.

8. A tweet from Neil Saunders:

“not sure how a ceasefire is “unworkable”; surely you just stop firing?”

9. A comment on this post on A Blog Around The Clock:

This plays right into the hand of the sick-fuck right-wing, as all they have to do is trot out some phony propaganda shill, and the dumbfuck “journalists” go all “while it has been asserted that X, some critics say that not X”, without doing even the slightest bit of investigation that would reveal to them that the OVERFUCKINGWHELMING CONSENSUS among people who know what the fuck they are talking about, and are not either deranged wackaloon fuckwits or intentional propagandists, is “not X”. – Comrade PhysioProf

10. A tweet from Walter Jessen:

“@Berci What would be the alternative to evidence-based medicine? Hearsay medicine? Best-guess medicine?”

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DTC-testing concluded for now

In Uncategorized on November 6, 2008 at 11:15 am

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{{es|The Doctor.

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A lot has been said about (and argued over) Direct To Consumer (DTC) testing. For extensive coverage of the pros and cons of regulation of such genetic testing please go see The Gene Sherpa and Genetic Future (also, check out a number of recent papers in Nature, – to find them, go read the relevant posts at The Genetic Genealogist or Genetic Future). I have voiced opinions on this too, but have decided to desist more arguing (for a while) after reading this editorial in Nature biotechnology:

1. We need to move from late to early diagnosis

It is virtually impossible to conceive of a sustainable form of healthcare that operates as the current systems in industrialized nations do. At present, healthcare is based on the late diagnosis of disease and the division of diseases into a few categories based on some overarching gross similarities. And it firmly places physicians as the central gatekeepers of information.

2. To do this we need find ways to utilize the potential unleashed by large scale analysis of genetic-material.

The healthcare of the future, on the other hand, if the technical potential to provide personalized medicine is ever to be realized, will probably require a greatly expanded emphasis on diagnosis and monitoring, early and subtle intervention, monitoring of the impact of intervention, and gradual adaptation of treatment with the evolving physiology, metabolism and lifestyle of the individual.

3. But, the medical professionals and healthcare systems do not currently have the capacity to adequately respond.

Faced with this huge expansion of data on ‘my’ health, it will simply not be affordable to maintain our dependence on medical gatekeepers, whether they are physicians or genetic counselors, without individuals taking a much greater responsibility for their own wellbeing. Whether the medical establishment likes it or not, it will be too cumbersome and too expensive to conduct personalized medicine if all diagnostic-to-therapeutic decisions depend on doctors.

4. Therefore, In order to adapt to this new situation, we need to find the golden mean between no regulation and over-regulation.

For personal genomics not to be stillborn, the medical community and regulators thus need to reevaluate their role as gatekeepers. Clearly, they need to be involved in the medical actions that might follow as a consequence of genetic or other diagnostic testing. And for any gene test, regulators must ensure that companies make claims to consumers that are both truthful and accurate. But simply shutting down the whole direct-to-consumer gene testing enterprise because it departs from the traditional genetic testing paradigm of doctorordered test will both retard progress and stifle investment in more advanced whole-genome sequencing technologies—technologies that have the potential to ultimately deliver the promise of genomedirected medicine.

Regulation is obviously needed at some level. However, I reside in a country where regulation completely stifles any attempt to do personalized medicine, even at the most innocent (Cyp 450) level. I strongly advise against such an approach. Transferring all testing currently offered by DTC companies, to existing health-care programs will flood the system, and hence is not an option either.

In my opinion, there is an imminent need to define the subgroup of genetic tests that needs to be accompanied by counseling/medical advice. Group those out sensibly, grade them according to counseling importance, and you have a solution.

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Quote of the month November 08

In Uncategorized on November 4, 2008 at 9:58 pm

Deepak at business|bytes|genes|molecules, on open access publishing (my highlighting):

Everyone should have access to the same scientific information (what that information should be is the subject of another post). It’s not even about who pays for it. It is science, and as such belongs to everyone.

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Hammering nails in the “junk-DNA” coffin

In Uncategorized on October 28, 2008 at 2:12 pm

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A replica of the coffin used for Abraham Linco...

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Enough talk (see this previous post and links within), on to the peer-reviewed science. Below you will find a list of references that I hope will contribute to the fall of the term “junk-DNA“, – some of it may (currently) lack a known function, but it is not junk !!!

Disclaimer: This is a list of useful references when arguing against the common overestimation of the amount of “junk”-DNA. By listing these I am not claiming anything beyond what I have already posted on this blog or in a comment somewhere. Also and importantly, I have not myself  had the time to review these articles as thoroughly as I would have wanted to, – some have been read carefully, others lightly and yet others just skimmed through. Thus, you are more than welcome to comment on these references if you have opinions on any of them, or find them unsuited for this list.

The list will be continuously expanded, and if you have references you would like to add, please notify me with a comment to the post.

The references are unsorted. Feel free to copy, rearrange and use as desired…

Last updated 5/8-13:

  1. Alu elements as regulators of gene expression. Häsler J, Strub K, Nucleic Acids Res. 2006;34(19):5491-7. Epub 2006 Oct 4.
  2. RNA editing, DNA recoding and the evolution of human cognition
    Trends in Neurosciences, , Volume 31, Issue 5, May 2008, Pages 227-233
    John S. Mattick, Mark F. Mehler
  3. Evolution of the mammalian transcription factor binding repertoire via transposable elements, Bourque, Guillaume, Leong, Bernard, Vega, Vinsensius B., Chen, Xi, Lee, Yen Ling, Srinivasan, Kandhadayar G., Chew, Joon-Lin, Ruan, Yijun, Wei, Chia-Lin, Ng, Huck Hui, Liu, Edison T. Genome Res. 2008 0: gr.080663.108. DOI: 10.1101/gr.080663.108
  4. Lin L, Shen S, Tye A, Cai JJ, Jiang P, et al. 2008 Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues. PLoS Genetics 4(10): e1000225 doi:10.1371/journal.pgen.1000225
  5. Dispensability of mammalian DNA. McLean C, Bejerano G., Genome Res. 2008 Oct 2. [Epub ahead of print]
  6. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs. John L. Rinn et al., Cell 129, 1311–1323, June 29, 2007
  7. A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT. A. T. Willingham, A. P. Orth, S. Batalov, E. C. Peters, B. G. Wen, P. Aza-Blanc, J. B. Hogenesch, and P. G. Schultz (2 September 2005). Science 309 (5740), 1570. [DOI: 10.1126/science.1115901]
  8. Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation, Genome Res. doi: 10.1101/gr.078378.108
  9. Non-coding RNAs in the nervous system, Mark F. Mehler and John S. Mattick, J Physiol Volume 575, Number 2, 333-341, September 1, 2006 DOI: 10.1113/jphysiol.2006.113191
  10. Specific expression of long noncoding RNAs in the mouse brain, Tim R. Mercer* et al., PNAS  January 15, 2008   vol. 105  no. 2  716-721
  11. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Philipp Kapranov et al., Science 8 June 2007: Vol. 316. no. 5830, pp. 1484 – 1488 DOI: 10.1126/science.1138341
  12. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene, Joseph A. Martens, Lisa Laprade and Fred Winston, Nature 429, 571-574 (3 June 2004) | doi:10.1038/nature02538
  13. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae, Joseph A. Martens, Pei-Yun Jenny Wu and Fred Winston, GENES & DEVELOPMENT 19:2695-2704, 2005
  14. Neuronal Untranslated BC1 RNA: Targeted Gene Elimination in Mice, Boris V. Skryabin et al., Molecular and Cellular Biology, September 2003, p. 6435-6441, Vol. 23, No. 18 0270-7306/03/$08.00+0 DOI: 10.1128/MCB.23.18.6435-6441.2003
  15. Pellionisz, A. (2008) The Principle of Recursive Genome Function. The Cerebellum (Springer), DOI 10.1007/s12311-008-0035-y
  16. Evolution of the mammalian transcription factor binding repertoire via transposable elements, Guillaume Bourque, Bernard Leong, Vinsensius B. Vega, et al.
    Genome Res. published online August 5, 2008; doi:10.1101/gr.080663.108
  17. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Regina S. Baucom et al. Genome Res. Published in Advance November 24, 2008, doi: 10.1101/gr.083360.108
  18. Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, et al. (2009) Death and Resurrection of the Human IRGM Gene. PLoS Genet 5(3): e1000403. doi:10.1371/journal.pgen.1000403.
  19. Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome. Stephen C. J. Parker, Loren Hansen, Hatice Ozel Abaan, Thomas D. Tullius, Elliott H. Margulies. Published Online March 12, 2009. Science DOI: 10.1126/science.1169050.
  20. A Functional Role for Transposases in a Large Eukaryotic Genome.
    Mariusz Nowacki, Brian P. Higgins, Genevieve M. Maquilan, Estienne C. Swart, Thomas G. Doak, Laura F. Landweber. Science 15 May 2009: Vol. 324. no. 5929, pp. 935 – 938 DOI: 10.1126/science.1170023.
  21. Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability. Marcelo D. Vinces, Matthieu Legendre, Marina Caldara, Masaki Hagihara, Kevin J. Verstrepen. Science 29 May 2009: Vol. 324. no. 5931, pp. 1213 – 1216. DOI: 10.1126/science.1170097.
  22. The regulated retrotransposon transcriptome of mammalian cells. Geoffrey J Faulkner1, Yasumasa Kimura2, Carsten O Daub2, Shivangi Wani1, Charles Plessy2, Katharine M Irvine3, Kate Schroder3, Nicole Cloonan1, Anita L Steptoe1, Timo Lassmann2, Kazunori Waki2, Nadine Hornig4,5, Takahiro Arakawa2, Hazuki Takahashi2, Jun Kawai2, Alistair R R Forrest2,6, Harukazu Suzuki2, Yoshihide Hayashizaki2, David A Hume7, Valerio Orlando4,5, Sean M Grimmond1 & Piero Carninci2. Nature Genetics 41, 563 – 571 (2009)
  23. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Eory L, Halligan DL, Keightley PD. Mol Biol Evol.2009; 0: msp219v1-msp219
  24. Characterization of viral and human RNAs smaller than canonical microRNAs. Zhihua Li, Sang Woo Kim, Yuefeng Lin, Patrick S. Moore, Yuan Chang, and Bino John. J. Virol. doi:10.1128/JVI.01325-09.
  25. SVA retrotransposons: Evolution and genetic instability. Dustin C. Hancksa and Haig H. Kazazian Jr. Seminars in Cancer Biology, doi:10.1016/j.semcancer.2010.04.001
  26. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Adam D Ewing and Haig H Kazazian. Genome Res.  gr.106419.110; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
  27. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J. Haveman & Pier Paolo Pandolfi. Nature Volume:465, Pages: 1033–1038. Date published: (24 June 2010). doi:10.1038/nature09144
  28. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Justin J.-L. Wong1, William Ritchie, Olivia A. Ebner, Matthias Selbach, Jason W.H. Wong, Yizhou Huang, Dadi Gao, Natalia Pinello, Maria Gonzalez, Kinsha Baidya, Annora Thoeng, Teh-Liane Khoo, Charles G. Bailey, Jeff Holst, John E.J. Rasko. Cell, Volume 154, Issue 3, 1 August 2013, Pages 583–595
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After whole genome sequencing comes PCR

In Uncategorized on October 23, 2008 at 8:56 am

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I attended an Applied Biosystems SOLiD seminar the other day. Let me tell you this: the SOLiD system packs some serious sequencing power (as does it’s competitors like Illumina, -and possibly others). Only imagination sets limits to the potential uses for such whole genome (and whole transcriptome !) sequencing. Thus, I found myself continuously drifting off, dream-designing new projects we could set up. But, at the same time I couldn’t keep from thinking that in terms of diagnostics, this a massive overkill. Too much information is not always a good thing when it comes to disease and disease predisposition. If one particular genetic variation is relevant to the symptoms presented, then there’s hardly necessary to return the whole genome or transcriptome. You would end up giving the patient information on a whole range of diseases, – the patient may not want/need to know this. Especially since we know that (currently) there is considerable uncertainty surrounding the future disease-risk associated with most genetic markers. Besides, once you know the relevant genetic regions it would probably be sufficient to run a couple of million markers to determine any predisposition.

Early model of a Polymerase Chain Reaction mac...

Good (?, and really) old PCR.

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Thus, all of these projects ended with good old PCR, which is kind of strange since sequencing one would think, is the superior of the two technologies. Here’s how I figured my (would be) whole genome sequencing projects would go:

  1. Pick species/subspecies/individual trait or disease group
  2. Sequence everything you can get your hands on
  3. Characterize genetic differences be it SNPs, indels, repeats, CNV or any other
  4. And then, …..design PCR/real-time PCR assays for diagnostics/further research and such.

Because, obviously, once everything is sequenced, there’s no need to keep sequencing. My prediction is that at that point (real-time) PCR (and quite possibly Sanger sequencing capillary electrophoresis) will regain it’s lost status as preferred tools for molecular biologists.

So, as a comfort to all those who are unable to jump on the whole genome sequencing train: Not to worry ! We’re just going through a phase. This too shall pass.

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Here’s why I get fat when I exercise

In Uncategorized on October 20, 2008 at 9:03 pm

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In an attempt to probe deeper into my ongoing exercise/obesity confusion, I have read three papers (1,2,3)  that illuminated the issue to some extent. And the answer is, not surprisingly: I’m not exercising enough.

It turns out that you need something like 225 to 275 minutes of weekly exercise to loose 5-10 % of your body weight over 16-24 months. Which means exercising a minimum of 45 minutes a day 5 days a week over a long period of time to achieve……in my case, – not that much. Which again translates into: not bloody likely to happen. Or as stated more elegantly in Donnelly JE et al.:

Application of the results from the present study to the general population will require considerable help from behavioral scientists to encourage adoption and adherence to a long-term exercise program that becomes part of an individual’s lifestyle and can be maintained indefinitely.

The intensity of the training does not seem to matter too much. Any hint of comfort in that however, is swept away by the fact that the rather unimpressive 5 % weight loss from 45 minute exercise pr. day was achieved by young people, ….- I’m not that young anymore and that’s a big chunk of the problem at hand…..

Relentlessly, I will keep exercising of course. There are after all so many other benefits to it. Plus, the exercise I do is fun and inspiring. The conclusion therefore still is: exercise helps, – even if it does so mostly as in “exercise restraint” (when it comes to food intake).

That’s it, it took me 4 blog posts to reach the conclusions I started out with in the first place:

1) Less food = desired weight loss

2) Exercise not essential to loose weight.

And then one would think I am all done on this subject.

But alas no, there’s more to it, – plenty more. Have a look at this “Obesity System Influence Diagram” (Thank you Laura for pointing me here through friendfeed):

Sometimes knowledge it seems, is just confusing. The only reasonable conclusion from this diagram is that the interplay between factors contributing to obesity is extremely complex.

It’s tempting to leave it at that, – it’s all just very complex, let’s move on. But, instead I’ll try and take this as a challenge: Plenty more posts to come…..perhaps on aging and obesity, – seems like a natural next step.

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