Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

I should have loved biology

jsomers.net

Post reply on HN
Print view View original

121–130 of 282 posts

Re: I should have loved biology

#121

Post by MereInterest »

gilleain wrote: post #73
bsedlm wrote: post #56

Earlier quoted context omitted.

I like to think that in life the code is also the runtime, unlike in computer technology where the hardware is the runtime.

I must be running on slower code, as I can't quite unpack that. So the code in life is the DNA which is also the 'runtime'?

Proteins are the runtime on which DNA is executed, because they are the mechanism that "reads" DNA. But proteins are the compiled output of DNA, because they are the result of "reading" DNA. So the DNA defines the runtime environment that is necessary for DNA to run.

Re: I should have loved biology

#122

Post by eesmith »

khaledh wrote: post #75
cercatrova wrote: post #65

Earlier quoted context omitted.

This is known as the God of the gaps argument [0] [0] https://en.wikipedia.org/wiki/God_of_the_gaps

Ok let's stay scientific. What are the odds of forming a single enzyme (necessary for life) composed of a chain of roughly 200 amino acids, each is drawn from a pool of 20 possible amino acids? 20^200, right? The estimated number of atoms in the entire universe is 10^80 atoms. Can you explain what process would consistently keep winning the protein lottery with those kind of odds?

That's not how evolution works. You've omitted natural selection. Quoting from "The Failures of Mathematical Anti-Evolutionism" by Jason Rosenhouse at https://skepticalinquirer.org/2022/05/the-failures-of-mathem...

> However, this argument is premised on the notion that genes and proteins evolve through a process analogous to tossing a coin multiple times. This is untrue because there is nothing analogous to natural selection when you are tossing coins. Natural selection is a non-random process, and this fundamentally affects the probability of evolving a particular gene.

> ... Modern proponents of intelligent design (ID) are usually too sophisticated to make such an error. Instead, they present a superficially more sophisticated probability-based argument. Their idea is best illustrated by example. ... ID proponents argue that it is the combination of improbability and matching a pattern that makes them suspect that something other than chance or purely natural processes are at work. They use the phrase “complex, specified information” to capture this idea. In this context, “complex” just means “improbable,” and “specified” means “matches a pattern.” ...

> The argument likewise founders on the question of complexity. According to ID proponents, establishing complexity requires carrying out a probability calculation, but we have no means for carrying out such a computation in this context. The evolutionary process is affected by so many variables that there is no hope of quantifying them for the purposes of evaluating such a probability.

Back in the 1990s, the newsgroup talk.origins put together a long index of creationist claims. Your example is http://www.talkorigins.org/indexcc/CB/CB010.html

> The calculation of odds assumes that the protein molecule formed by chance. However, biochemistry is not chance, making the calculated odds meaningless. Biochemistry produces complex products, and the products themselves interact in complex ways.

> The calculation of odds assumes that the protein molecule must take one certain form. However, there are innumerable possible proteins that promote biological activity. Any calculation of odds must take into account all possible molecules (not just proteins) that might function to promote life.

> The calculation of odds assumes the creation of life in its present form. The first life would have been very much simpler.

> The calculation of odds ignores the fact that innumerable trials would have been occurring simultaneously.

It links to further discussion at http://www.talkorigins.org/faqs/abioprob/abioprob.html ("Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations")

Richard Dawkin's book "Climbing Mount Improbable" "is about probability and how it applies to the theory of evolution. It is designed to debunk claims by creationists about the probability of naturalistic mechanisms like natural selection." (quoting https://en.wikipedia.org/wiki/Climbing_Mount_Improbable ).

Five copies of the book are available to borrow right now for free (with an account) from archive.org, at https://archive.org/search.php?query=%22Climbing+Mount+Impro... .

All of these explain why your probability calculation is not meaningful.

Re: I should have loved biology

#123

Post by dizzant »

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…

While retaining the typical high school separation between math, biology, chemistry, and physics, but given control over the curricula taught in those courses, do you think it is possible to teach a single very high-level concept such as the Krebs cycle in full complexity at a high school level (i.e. starting from algebra and very limited science education, completed in four full-time years)? This seems like a foothold for a potentially interesting restructuring of how we educate children, oriented toward depth in a few things to enlighten future breadth. I ask specifically about feasibility, since that seems like a necessary prerequisite to a discussion of beneficial value.

Re: I should have loved biology

#124

Post by User23 »

This is part of why I’m grateful for my Christian faith. I view the scientific endeavor with endless wonder, because it’s incredibly satisfying to better understand creation. I don’t need to be convinced the cell is a glorious marvel.

It’s certainly not the only way to have that intellectual posture, but it’s a powerful one.

Re: I should have loved biology

#125

Post by randcraw »

gilleain wrote: post #67
ip26 wrote: post #57

Earlier quoted context omitted.

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 evolv…

Knowledge Distillation is a related concept in deep NNs, as are the concepts behind the compression of data in signal processing.

Re: I should have loved biology

#126

Post by randcraw »

MereInterest wrote: post #118
gilleain wrote: post #67

Earlier quoted context omitted.

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 evolv…

There was a paper a few years ago about a similar effect in artificial neural networks [0]. The gist was that a large network can contain many subnetworks, and the number of subnetworks grows much faster than the size of the network they are contained in. They were able to find a subnetwork in a randomly weighted network with equivalent performance to a trained network of a much smaller size. [0] https://arxiv.org/ab…

Nice. Sounds like these self-assembling subnets could be the basis for a viable model explaining the mechanisms behind early evolution.

Re: I should have loved biology

#127

Post by randcraw »

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…

Yeah, I think programmers would better appreciate the complexity and subtlety of biology much better if they had to evolve their programs rather than code them up explicitly. (I say this as someone with degrees in both subjects.)

Re: I should have loved biology

#128

Post by mkr-hn »

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…

The more I understand about biology, the more bizarre it is that people try to beat it down to simple, obvious, narrow, and globally consistent binaries to serve their ideological purposes.

Re: I should have loved biology

#130

Post by huachimingo »

telesilla wrote: post #16

"Everywhere you look—the compiler, the shell, the CPU, the DOM—is an abstraction hiding lifetimes of work. Biology is like this, just much, much worse, because living systems aren’t intentionally designed. It’s all a big slop of global mutable state". Brings me to wonder, could we ever create anything so marvellous as what biology does so effortlessly.

Conway's Game of Life
Post reply on HN