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SCIENCE!!! (Read 73055 times)

tomtom

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#350 Re: SCIENCE!!!
September 13, 2019, 08:53:24 am
Some interesting reads about urban planning in the guardians ‘unbuilt cities’ series.. can’t link it so you’ll have to search.

tomtom

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#351 Re: SCIENCE!!!
October 10, 2019, 10:27:47 pm
Quote
We show that LaTeX users were slower than Word users, wrote less text in the same amount of time, and produced more typesetting, orthographical, grammatical, and formatting errors. On most measures, expert LaTeX users performed even worse than novice Word users.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115069

😂

Stu Littlefair

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#352 Re: SCIENCE!!!
October 11, 2019, 06:04:05 pm
I notice how selectively you quoted the abstract, the very next sentence being

Quote
LaTeX users, however, more often report enjoying using their respective software

andy_e

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#353 Re: SCIENCE!!!
October 11, 2019, 06:06:02 pm
Meh, I just bang it all down into word. Never caused me any issues. To each their own.

tomtom

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#354 Re: SCIENCE!!!
October 11, 2019, 07:26:23 pm
I notice how selectively you quoted the abstract, the very next sentence being

Quote
LaTeX users, however, more often report enjoying using their respective software

😂😂 Was waiting for someone to bite...

Oldmanmatt

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Oldmanmatt

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#356 Re: SCIENCE!!!
October 22, 2019, 07:02:30 pm
Apparently, this is pretty big:

https://www.nature.com/articles/s41586-019-1711-4

“ Okay, Science time.

A paper just came out yesterday in the scientific journal, Nature, and the entire biotech world is completely freaking out with excitement about it. I stayed up way too late last night reading it myself and I can't stop thinking about it now. Let me tell you about it.

You might have heard of CRISPR-Cas9. Discovered in bacteria, where it functions as an antiviral immune system, Cas9 is a programmable DNA scissors which takes an RNA barcode, scans DNA, and cuts wherever it finds a perfect match. Biological science has long aspired to the ability to make virtually any targeted change in the genome of any living cell or organism, and with CRISPR, the ability to precisely cut any region of DNA we want has opened up so many possibilities, it's no stretch to say that it ignited a revolution and sparked a whole new era in biology today.

One limitation of CRISPR is that on its own, breaking DNA is all it does. If we want to disable something, it's great- cells have an internal mechanism for quickly patching DNA breaks back together, which often disables the particular gene there by introducing small mutations at the seam.

But if we don't want to just break things, if we want to edit or insert or delete a specific thing, we need to add a second component: a DNA donor template that mostly matches the target site but contains the modifications that we want. Then, when the cell repairs the break, we hope that instead of mashing the ends together willy nilly, it uses the other DNA repair mechanism it has, which grabs the ends, seeks out similar-looking DNA, and uses that as a template for repair. Not only is this mechanism rare and slow, we also need to be lucky enough that a copy of our donor template happens to be close by.

In the lab, this limitation isn't a problem: we can blast a million cells, sort through them individually cell by cell, pick out the rare ones that perfectly integrated our template, and just grow those. But breaking the DNA at 90% of the cells to get that rare 10% of cells to accept our specific mutation has obvious limitations, and the ratios are usually even worse than that.

Here's where this paper comes in. Anzalone et. al. from the Broad Institute (pronounced Brode) took CRISPR and modified it into something they call CRISPR PRIME.

Their paper is titled, "Search and Replace Genome Editing Without Double-Strand Breaks or Donor DNA".

They started with a modified CRISPR that cuts only one strand, creating single-strand nicks instead of double-strand breaks. They took the RNA barcode, which programs CRISPR to recognize specific DNA sequences for cutting, and they added an extra long RNA tail to it containing the desired mutation. Finally, they welded another protein, Reverse Transcriptase, to CRISPR, which reads RNA and creates DNA strands from it.

They envisioned a system where instead of introducing our donor separately and hoping the cell happens to use it after CRISPR breaks the site, CRISPR carries the donor with it, gently nicks the site and immediately writes the patch in itself.

And IT WORKS.

From the paper: "We performed more than 175 edits in human cells including targeted insertions, deletions, and all 12 types of point mutations... We applied prime editing in human cells to correct efficiently and with few byproducts the primary genetic causes of sickle cell disease and Tay-Sachs disease, to install a protective transversion in PRNP, and to insert various tags and epitopes precisely into target loci... Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct about 89% of known pathogenic human variants".

They're releasing this system free to everyone for academic and research use and I need need NEED to try it out myself. I don't think it's a stretch to say that CRISPR prime will be a revolution in how biologists do gene editing, and the entire field agrees.

This is seriously amazing work.”

Dr Zi Teng Wang

tomtom

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#357 Re: SCIENCE!!!
October 23, 2019, 06:46:18 pm
Thats cool OMM...

This looked good too! Quantum computer did a task in 200 secs that would take 10000 hours on a 'typical' supercomputer....

https://www.nature.com/articles/s41586-019-1666-5

remus

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#358 Re: SCIENCE!!!
October 23, 2019, 07:17:28 pm
Thats cool OMM...

This looked good too! Quantum computer did a task in 200 secs that would take 10000 hours on a 'typical' supercomputer....

https://www.nature.com/articles/s41586-019-1666-5

Looks like IBM have some beef with the Google claims https://www.ibm.com/blogs/research/2019/10/on-quantum-supremacy/

It would be interesting if they (IBM) could actually implement and perform the classical calculation they describe, that'd be a pretty solid refutation of Google's quantum supremacy claims.

tomtom

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#359 Re: SCIENCE!!!
October 23, 2019, 08:53:43 pm
From what I remember There are some tasks/calcs that QC are far better structured to run... that may be the case here.
Anyway - progress

JamieG

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#360 Re: SCIENCE!!!
February 11, 2020, 10:38:40 pm
Hi UKB collective,

I'm involved in a project studying bird flight and animations and we are collecting some data via the medium of citizen science. So if any of you have a bit of spare time and fancy it would you mind having a look at the link below. (I think it only works of PCs and laptops)

The basic gist is you watch animations of a bird flying and rate how realistic you think it is. It shouldn't take too long I think there a around 200 animations per person (which seems like a lot but it really doesn't take that long per animation).

As a final note can you fill out the participant ID at the start of the test as jamie_ then whatever you like afterwards (as long as its clean - my colleague is going to look at this) :-)

Heres the link.

https://research.sc/participant/login/dynamic/2E841B51-D11C-4F80-A6C9-759D17DF42B3

Much appreciated. A wad point for everyone that lets me know they've completed as a way of filthy bribery. :-)

Jamie

JamieG

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#361 Re: SCIENCE!!!
July 07, 2020, 03:06:30 pm
Really interesting new pre-print out that examines the performance of top men and women rock climbers and shows that unlike the vast majority of other sports the gap between genders is very small. In particular they compare climbing to 100m sprint and the marathon, and show the gap is much smaller in climbing.

They argue that this supports a more arboreal origin of human evolution. An idea that has gained a lot of steam over the last 20 odd years. Indeed, our bipedal type gait might have originally evolved in the trees, similar to the way orang-utans move in the trees. Which is something a colleague of mine has been pushing for many years now.

https://www.biorxiv.org/content/10.1101/2020.05.26.116244v1


remus

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#362 Re: SCIENCE!!!
July 07, 2020, 03:44:13 pm
Really interesting new pre-print out that examines the performance of top men and women rock climbers and shows that unlike the vast majority of other sports the gap between genders is very small. In particular they compare climbing to 100m sprint and the marathon, and show the gap is much smaller in climbing.

They argue that this supports a more arboreal origin of human evolution. An idea that has gained a lot of steam over the last 20 odd years. Indeed, our bipedal type gait might have originally evolved in the trees, similar to the way orang-utans move in the trees. Which is something a colleague of mine has been pushing for many years now.

https://www.biorxiv.org/content/10.1101/2020.05.26.116244v1

It's an interesting idea (and there may well be some merit to it) but I think the methodology is pretty weak.

They have taken a list of the 90 hardest sport climbers and found that 3 of those are women which is a greater proportion than they've identified in some track and field events (e.g. 100m sprint, marathon). The discussion about gender split in each sport is passing at best ("The ratio of rock climbers by gender, according to an estimate by professional climber Sasha DiGiulian, is 60% men to 40% women") and no discussion about the population size of climbing vs track and field.

Population size in particular is pretty important: imagine a normal distribution of climbers by grade and another of sprinters by 100m PB, it only makes sense to compare list of the top x climbers and the top y runners if we know that they both represent a roughly equal percentage of climbers and runners. In other words it makes sense to say "1/20 of the top 1% of climbers are female, whereas 1/200 of the top 1% 100m sprinters are female" but comparing lists of pretty much arbitrary length doesn't make sense because we don't know how much of the population we're looking at.

JamieG

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#363 Re: SCIENCE!!!
July 07, 2020, 04:31:31 pm
Yeah, that seems like a fair critique. But it is just a preprint and I guess still need peer reviewed. But for sure an understanding of the size population you are looking at seems important for their methods. I imagine that for marathon running, there is fairly decent number of people taking part. Probably quite a bit more than climbing. But I wonder if that is true for sprinting. That seems a bit more niche. I wouldn't be surprised if that population is actually smaller than climbing.

If we look at it another way. Not by number of top male/female climbers. But at the level the top men and women are operating, what do the numbers look like? What is the rough grade difference? Sport climbing it is something like 9c to 9b. And in bouldering it is 9A to 8C. Both within 2 half grades, which is pretty impressive. Especially since there is only 1 9c route and 2 9A boulders (one of which has been repeated and potentially 8C+). So I think the margin is pretty narrow really.

Compared to sprinting where the fastest female 100m is only just under 10.5s. And the fastest marathon is 2.14. These seem like bigger gaps, but i'm no runner so perhaps that is just my perspective.

Definitely an interesting topic.

tomtom

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#364 Re: SCIENCE!!!
July 07, 2020, 04:37:55 pm
Comparing speed climbing times would be a more representative comparison between male/female and sprinting rather than bouldering/sport grades (that are ulimately subjective and can be highly dependent on body shape/type - especially when there are only '2' 9A's...)?

Edit: I'll answer my own question. Big old difference in the record times there...

https://en.wikipedia.org/wiki/Speed_climbing#Speed_Climbing_World_Records_and_Champions

JamieG

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#365 Re: SCIENCE!!!
July 07, 2020, 04:46:03 pm
I would disagree about that one tomtom. I think speed climbing is kind of contrived at the best of times and has more akin to sprinting that actual climbing ability. Not that it isn't skilled, just it doesn't really show climbing ability to me, especially within the context of human evolution.

tomtom

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#366 Re: SCIENCE!!!
July 07, 2020, 04:50:24 pm
I would disagree about that one tomtom. I think speed climbing is kind of contrived at the best of times and has more akin to sprinting that actual climbing ability. Not that it isn't skilled, just it doesn't really show climbing ability to me, especially within the context of human evolution.

Yes - thats exactly what I meant - if you were comparing sprinting to climbing (that the preprint does) then speed climbing would seem to be a better comparison.

Unless the paper is trying to push a different message (arboreal origin of human evolution) ;D

JamieG

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#367 Re: SCIENCE!!!
July 07, 2020, 05:17:43 pm
Ah okay, I'm with you now.

I think they are trying to frame it in movements that might have been important for human evolution. Long distance running has been suggested as important for running down big prey items. Sprinting i'm not so sure, but presumably also prey capture and escaping danger. Climbing, again foraging for food. Also safety in the trees especially at night.

And possibly they are trying to push climbing as important for human evolution.  ;D

Certainly my colleague is very keen on the idea. Here is an article in independent on his theories and research, if you are interested.

https://www.independent.co.uk/news/science/ascent-of-man-human-evolution-apes-chimpanzees-lucy-australopithecus-robin-crompton-a7230371.html

 

 

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