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I should have loved biology

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Re: I should have loved biology

#61

Post by kosherhurricane »

khaledh wrote: post #42

When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling. I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design. https://youtu…

The coolest thing about biology is that it's not just in every cell of your body, but every cell on life on earth.

But the funny thing about that is that the genes for say the 'helicase' looks like it was made by a copy machine, churned out by the millions, for every life on earth. But if you look very carefully, it's not a copy made from a master copy, but copied from each other. There are small mistakes made by this 'copy machine', so that you can trace the different generations of the copy of the 'helicase' based on what mistakes have been accumulated. You dig further, and you can map out different generations and make a tree like diagram. The further away from each other the two helicases are, the more mistakes have been accumulated.

You keep doing that for every life on earth, and you get something like this [1].

And then you dig further and realize that there is no Hand of God there, and creationism is a primitive explanation for something people didn't understand, like how lightning was God being angry.

[1] https://www.sciencedirect.com/science/article/pii/S235234091...

Re: I should have loved biology

#62

Post by barry-cotter »

brnaftr361 wrote: post #49
barry-cotter wrote: post #35

Earlier quoted context omitted.

If you think US high school education is abysmal where do you think does it better? US Asians do very well compared to other Asians, US whites to other whites, etc. https://www.unz.com/isteve/the-new-2018-pisa-school-test-sco...

Is the purpose of education to make people take tests and get high scores that bureaucrats can wave around, routing their success? Or is it something a little more profound?

If they can’t do well on tests designed to measure skills the students have been failed. They have not learned skills. The US education system is quite good at teaching skills. A large majority of countries do worse. The skills that PISA tests are a prerequisite for almost any more rarefied learning that is often held up as the real purpose of education.

Being able to read for meaning, extract information, combine knowledge from two texts, distinguish between what is stated and what’s implied, even to figure out something is implied, all of those are the kinds of things we expect an educated person to be able to do. PISA tests them. Trying to make people care about academic subject matter is very difficult because most people do not care and do not find it useful. Thus they forget most of what they learn in school. Insofar as education is forcing the tastes of one class on everyone else it can burn. Most people don’t care, just like most academics don’t care about sports. Forcing sports on them would also be an injustice.

Re: I should have loved biology

#63

Post by AlecSchueler »

shpongled wrote: post #31
axg11 wrote: post #25

I think what is described here comes down to the fact that we don't have much (any?) _deep_ understanding of biology. The most concrete aspects of biology are observations. For example, anatomy is very well understood because it's essentially observations of structures within living organisms, as field it has been relatively stable for a long time, hence there are well-established methods for teaching anatomy. There'…

I would argue that depends on your definition of deep - we are certainly getting better at developing both genetic and chemical tools that allow us to probe specific pathways/sub-systems of biology, and read out the resulting perturbed phenotype(s). > There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). We don't have a good bottom-up system t…

> (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc)

I think I've seen all of those functionalities implemented in esoteric programming languages! Nice comparison.

Re: I should have loved biology

#64

Post by formerkrogemp »

brnaftr361 wrote: post #49
barry-cotter wrote: post #35

Earlier quoted context omitted.

If you think US high school education is abysmal where do you think does it better? US Asians do very well compared to other Asians, US whites to other whites, etc. https://www.unz.com/isteve/the-new-2018-pisa-school-test-sco...

Is the purpose of education to make people take tests and get high scores that bureaucrats can wave around, routing their success? Or is it something a little more profound?

Yes, yes. Education is multifaceted in its consequences. Merit depends upon objective testing. Common culture and high trust society depend in large amounts upon education and schooling. With the quality of schooling available, shortage of teachers and quality teaching personnel due to abuse and low salaries, political interference with teachers handling their own material, religious indoctrination in charter schools, and the amount of students requiring remedial classes in college. Of course, more data and parameters can be considered, but I don't think anyone can consider the broad state of secondary and primary education in the US as "healthy" or "improving."

Re: I should have loved biology

#65

Post by cercatrova »

al2o3cr wrote: post #52
khaledh wrote: post #42

When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling. I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design. https://youtu…

So you look at everything that we've been able to figure out, things we didn't know about even a few decades ago, and you conclude "WELL I CAN'T SEE THE REST OF THE PUZZLE RIGHT NOW SO I GUESS MY IMAGINARY FRIEND DID IT" So goddamn stupid that it's just sad.

This is known as the God of the gaps argument [0]

[0] https://en.wikipedia.org/wiki/God_of_the_gaps

Re: I should have loved biology

#66

Post by rjtobin »

codeflo wrote: post #58

I have to wonder where this person’s school circumstances. For example, why was the triangle area formula only memorized and not demonstrated to them? I thought this should be standard everywhere in the world? Maybe they just don’t remember, it happens early (age 11-12 for me IIRC). Similarly, and this is from two decades ago at this point, some basics of gene expression and cell differentiation were covered in my la…

I interpret the article quite differently. The triangle example (which as the author writes is actually an example from “Lockhart’s Lament” on American math education) isn’t about whether triangle-area-formula was ever justified to students. It’s that students aren’t given the chance to really ask the question themselves - a chance to approach math, or biology, in the way that a mathematician or biologist does in reality: trying to work it out for themselves, and being invited to wonder at just how improbable textbook biological facts are etc.

I agree with your point that some students will be more inquisitive, and will need less prompting to do the above thinking themselves. But many (most?) students are not like this, and it’s a shame that many of these students could enjoy a subject that they instead come to loathe.

Re: I should have loved biology

#67

Post by gilleain »

ip26 wrote: post #57
bognition wrote: post #8

There is a large gap between the mechanisms of chemistry and the magic of biology that most people do not see closed until late in their education. It's a real shame that this gap cannot be closed sooner. In undergrad I took a bunch of biology and chemistry classes. It wasn't until I took Biochemistry (a senior level class) that everything came together. The biochemistry class I took was a re-telling of all the stori…

I went through biochem, but didn’t fully understand just how gigantic & complicated proteins are until I started learning about computational protein folding. There’s several levels of abstraction just between rna/ribosomes and functional proteins… that’s one of the most shocking complexities to me, most pieces of life are rather elegant when you come to understand them but it’s hard to imagine how complex proteins e…

I worked for a professor (James Milner-White) who was interested in early protein evolution and I remember a conversation we had about the possibility that proteins could have evolved from large to small.

Not sure if it was from a published paper, but the idea was that early proteins might have been large - say several hundred residues - but mostly disordered.

The smaller, more ordered 'domains' would then have evolved within these larger chains. Recombination and deletion would then have pruned down the disordered parts to leave more efficient smaller proteins.

No idea if that idea makes sense or has any research behind it, but it's quite a neat theory.

Re: I should have loved biology

#68

Post by cercatrova »

Not sure where the author went to school, but when I was in school, this is in fact how we learned biology, as well as mathematics and chemistry. Maybe our teachers were good, but we derived facts like the area of a triangle through geometric as well as algebraic means, and same for biology.

Re: I should have loved biology

#69

Post by eesmith »

khaledh wrote: post #42

When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling. I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design. https://youtu…

Your references are all computer animations, smoothed and simplified. I'll quote liberally from https://freethoughtblogs.com/pharyngula/2008/02/03/buffeted-... on an animation of "Inner Life of a Cell" by Harvard Biovisions:

> Here’s the central problem: molecules don’t behave that way. What is portrayed is wonderfully precise movement; it looks like the molecules are all directed, purposeful, and smooth. Take for instance the behavior of kinesin, that stalk-like molecule seen marching in a stately way down a tubule, with two “feet” in alternating step, towing a large vesicle. That’s not how it moves! We have experiments in which kinesin is tagged — it’s towing a fluorescent sphere — and far from a steady march, what it does is take one step forward, two steps forward, one step back, two steps forward, one back, one forward … it jitters. On average it progresses in one direction, but moment by moment it’s a shivery little dance. Similarly, the movie shows the monomers of tubulin zooming in to assemble a microtubule. No! What it should show is a wobbly cloud of monomers bouncing about, and when one bumps into an appropriate place in the polymer, then it locks down. I made this same criticism in my review of Mark Haw’s excellent book, Middle World, which does get it right. For purposes of drama and minimizing complexity and confusion, though, the animators of that video have stripped out one of the most essential properties of systems at that scale: noise, variability, and the stochastic nature of chemical interactions.

> That’s particularly unfortunate, because it is the seeming purposefulness of the activity of the cell that has made that clip so popular with creationists. It fits with their naive notions of directed activity at every level of the cell, and of their denial of the central role of chance in chemistry and biology.

Re: I should have loved biology

#70

Post by czbond »

civilized wrote: post #21

Pet theory: for most of human history, biology has been an increasingly complex detective story, a notepad of mysteries laying on a table next to an unfathomably massive evidence room stuffed with barely organized facts. This appeals to certain people and not to others. Only recently has it become possible to approach it from more of an engineering perspective, which appeals to a different set of people.

can you expand this thought? I'm on your path but not to your destination yet.

Can I summarize it as: Earlier, biology was "hunt and peck" or "observe" ... and now we're moving to a more "rigor of process & ability to create as seen in the past few decades of computer science now applying to biology" type of world?

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