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As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. (See also comments below this answer.) These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all... In fact, even if we just consider the probability of constructing one of Shakespeare's sonnets in terms of a trigram language model build on words, instead of letters, a reasonable guestimate might be 10^-240. These kind of numbers, where "information" is just considered as some kind of "given" don't mean much. We have to ask: how did that "given" develop.)

As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. (See also comments below this answer.) These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all... In fact, even if we just consider the probability of constructing one of Shakespeare's sonnets in terms of a trigram language model build on words, instead of letters, a reasonable guestimate might be 10^-240. These kind of numbers, where "information" is just considered as some kind of "given" don't mean much. We have to ask: how did that "given" develop.)

As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. (See also comments below this answer.) These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all...)

As to (2) this implicitly appeals to laypeople's intuitions about what might be "probable". However, those intuitions don't have a good sense of the time-scale on which evolution occurs and don't have any sense of the speed at which evolution can occur ("can" in the sense of "provably can" and "empirically has"). One way to get a better intuition for this is to consider evolutionary algorithms. (Another way is to look at the speed of viral evolution, where the time-scale does make intuitive sense to us. The mechanisms there are essentially the same as those general evolution. Isn't it kind of suspicious that no one speaks of "design" working itself out on that level?)

As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. (See also comments below this answer.) These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all... In fact, even if we just consider the probability of constructing one of Shakespeare's sonnets in terms of a trigram language model build on words, instead of letters, a reasonable guestimate might be 10^-240. These kind of numbers, where "information" is just considered as some kind of "given" don't mean much. We have to ask: how did that "given" develop.)

As to (2) this implicitly appeals to laypeople's intuitions about what might be "probable". However, those intuitions don't have a good sense of the time-scale on which evolution occurs and don't have any sense of the speed at which evolution can occur ("can" in the sense of "provably can" and "empirically has"). One way to get a better intuition for this is to consider evolutionary algorithms. (Another way is to look at the speed of viral evolution, where the time-scale does make intuitive sense to us. The mechanisms there are essentially the same as in general evolution. Isn't it kind of suspicious that no one speaks of "design" working itself out on that level?)

As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all...)

As to (1), the OPs first article actually does mention several probability measures "to construct" a functioning protein. (See also comments below this answer.) These estimates seem to me rather like back-of-the-envelope guestimates. Moreover, they also completely ignore the recursive evolutionary process in which those proteins might have developed. (If we simply calculate the "probability" of "constructing" Shakespeare's collected plays by considering the space of all random alphabetic sequences (in a given length range), then that probability would also be "vanishingly" small, much smaller than 1 in 10⁶⁵. It's a miracle they could ever be created at all...)